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
TARDBP	23435	broad.mit.edu	37	1	11076918	11076918	+	Missense_Mutation	SNP	G	T	T			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11076918G>T	uc001art.2	+	3	390	c.256G>T	c.(256-258)GAT>TAT	p.D86Y	TARDBP_uc010oap.1_Intron	NM_007375	NP_031401	Q13148	TADBP_HUMAN	TAR DNA binding protein	86					3'-UTR-mediated mRNA stabilization|cell death|mRNA processing|negative regulation by host of viral transcription|RNA splicing|transcription from RNA polymerase II promoter	nucleus	double-stranded DNA binding|mRNA 3'-UTR binding|nucleotide binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2	Ovarian(185;0.249)	Lung NSC(185;1.04e-05)|all_lung(284;1.31e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00262)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0578)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.37e-07)|COAD - Colon adenocarcinoma(227;7.38e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000299)|Kidney(185;0.000754)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|READ - Rectum adenocarcinoma(331;0.0487)		AAGAAAAATGGATGAGACAGA	0.368													5	189	---	---	---	---	PASS
UQCRHL	440567	broad.mit.edu	37	1	16133911	16133911	+	Silent	SNP	C	T	T			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16133911C>T	uc009vol.1	-	1	284	c.234G>A	c.(232-234)AAG>AAA	p.K78K		NM_001089591	NP_001083060			ubiquinol-cytochrome c reductase hinge												0						CGCAATGGTCCTTTGCATGCA	0.463													4	114	---	---	---	---	PASS
FAM131C	348487	broad.mit.edu	37	1	16361875	16361875	+	Missense_Mutation	SNP	A	G	G	rs11807054		TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16361875A>G	uc010obz.1	-	7	831	c.641T>C	c.(640-642)CTC>CCC	p.L214P	CLCNKB_uc001axw.3_Intron	NM_182623	NP_872429	Q96AQ9	F131C_HUMAN	hypothetical protein LOC348487	214	Pro-rich.										0		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.32e-08)|COAD - Colon adenocarcinoma(227;5.56e-06)|BRCA - Breast invasive adenocarcinoma(304;9.12e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00656)|READ - Rectum adenocarcinoma(331;0.0649)		GGAGGGGCTGAGCGAGGAGAA	0.662													5	11	---	---	---	---	PASS
VWA5B1	127731	broad.mit.edu	37	1	20657460	20657460	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20657460A>G	uc009vps.2	+	11	1752	c.1556A>G	c.(1555-1557)GAG>GGG	p.E519G	VWA5B1_uc001bdd.2_Missense_Mutation_p.E226G|VWA5B1_uc010odc.1_Missense_Mutation_p.E414G|VWA5B1_uc001bde.3_5'Flank|VWA5B1_uc009vpt.2_5'Flank	NM_001039500	NP_001034589	Q5TIE3	VW5B1_HUMAN	von Willebrand factor A domain containing 5B1	519	VWFA.					extracellular region					0						ATGGAGGGGGAGCGGCTGCAA	0.512													4	33	---	---	---	---	PASS
CDC42	998	broad.mit.edu	37	1	22417987	22417987	+	Missense_Mutation	SNP	A	T	T			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22417987A>T	uc001bfq.2	+	7	845	c.553A>T	c.(553-555)AGC>TGC	p.S185C	CDC42_uc001bfr.2_Missense_Mutation_p.S185C|CDC42_uc010odr.1_Missense_Mutation_p.S230C|CDC42_uc010ods.1_Missense_Mutation_p.S227C|CDC42_uc009vqh.2_Missense_Mutation_p.S144C	NM_001039802	NP_001034891	P60953	CDC42_HUMAN	cell division cycle 42 isoform 1	185					actin cytoskeleton organization|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|establishment or maintenance of cell polarity|macrophage differentiation|muscle cell differentiation|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of protein complex assembly|positive regulation of muscle cell differentiation|positive regulation of pseudopodium assembly|regulation of filopodium assembly|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction|T cell costimulation	cytosol|filopodium|plasma membrane	GTP binding|GTPase activity|protein binding|thioesterase binding			haematopoietic_and_lymphoid_tissue(1)	1		Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;6.55e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)|Prostate(1639;0.0792)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0452)|OV - Ovarian serous cystadenocarcinoma(117;7.32e-26)|Colorectal(126;1.35e-07)|COAD - Colon adenocarcinoma(152;7.73e-06)|GBM - Glioblastoma multiforme(114;8.62e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000649)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00767)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.207)		ACCGAAGAAGAGCCGCAGGTG	0.453													18	71	---	---	---	---	PASS
KDM4A	9682	broad.mit.edu	37	1	44128741	44128741	+	Silent	SNP	T	C	C			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44128741T>C	uc001cjx.2	+	5	772	c.606T>C	c.(604-606)TTT>TTC	p.F202F	KDM4A_uc010oki.1_Silent_p.F202F	NM_014663	NP_055478	O75164	KDM4A_HUMAN	jumonji domain containing 2A	202	JmjC.				interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	centrosome|nucleolus	histone demethylase activity (H3-K36 specific)|nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|zinc ion binding			skin(1)	1						ACCTGCACTTTGGAGAACCAA	0.453													28	76	---	---	---	---	PASS
TMEM69	51249	broad.mit.edu	37	1	46156752	46156752	+	Silent	SNP	C	T	T			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46156752C>T	uc001cor.1	+	2	208	c.12C>T	c.(10-12)TTC>TTT	p.F4F		NM_016486	NP_057570	Q5SWH9	TMM69_HUMAN	transmembrane protein 69	4						integral to membrane				ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)					TGCTTCGCTTCATCCAGAAGT	0.308													73	168	---	---	---	---	PASS
CYP4Z2P	163720	broad.mit.edu	37	1	47325354	47325354	+	RNA	SNP	G	A	A	rs4660360	by1000genomes	TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47325354G>A	uc001cqo.1	-	9		c.1214C>T				NR_002788				Homo sapiens cDNA FLJ40054 fis, clone TBAES2000315, weakly similar to CYTOCHROME P450 4A1 (EC 1.14.15.3).												0						CATCTGGAAAGGTAATGGGTT	0.438													4	39	---	---	---	---	PASS
ZCCHC11	23318	broad.mit.edu	37	1	52991350	52991350	+	Silent	SNP	T	C	C			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52991350T>C	uc001ctx.2	-	2	837	c.603A>G	c.(601-603)GGA>GGG	p.G201G	ZCCHC11_uc001cty.2_Silent_p.G201G|ZCCHC11_uc001ctz.2_Silent_p.G201G|ZCCHC11_uc009vze.1_Silent_p.G201G|ZCCHC11_uc009vzf.1_Intron|ZCCHC11_uc001cub.2_Silent_p.G201G|ZCCHC11_uc001cuc.2_RNA|ZCCHC11_uc001cud.2_Silent_p.G201G	NM_015269	NP_056084	Q5TAX3	TUT4_HUMAN	zinc finger, CCHC domain containing 11 isoform	201					miRNA catabolic process|pre-miRNA processing|RNA 3'-end processing|stem cell maintenance	cytoplasm|nucleolus	nucleic acid binding|protein binding|protein binding|RNA uridylyltransferase activity|zinc ion binding			ovary(2)|skin(1)	3						CACATTTTTCTCCCCCTACAG	0.393													7	333	---	---	---	---	PASS
MIER1	57708	broad.mit.edu	37	1	67437388	67437388	+	Silent	SNP	A	G	G			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67437388A>G	uc001dde.2	+	10	1109	c.975A>G	c.(973-975)AGA>AGG	p.R325R	MIER1_uc010opf.1_Silent_p.R289R|MIER1_uc009way.2_Silent_p.R289R|MIER1_uc001ddc.2_Silent_p.R325R|MIER1_uc001ddh.2_Silent_p.R209R|MIER1_uc001ddf.2_Silent_p.R289R|MIER1_uc001ddg.2_Silent_p.R245R|MIER1_uc010opg.1_Silent_p.R289R|MIER1_uc001ddj.1_Silent_p.R272R|MIER1_uc001ddi.2_Silent_p.R272R	NM_001077700	NP_001071168	Q8N108	MIER1_HUMAN	mesoderm induction early response 1 isoform b	296	ELM2.|Interaction with HDAC1.				positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity			ovary(1)	1						AAGCATTGAGAAGATTAAGAT	0.274													8	687	---	---	---	---	PASS
LRRC7	57554	broad.mit.edu	37	1	70502282	70502282	+	Missense_Mutation	SNP	G	C	C			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70502282G>C	uc001dep.2	+	18	2179	c.2149G>C	c.(2149-2151)GTA>CTA	p.V717L	LRRC7_uc009wbg.2_Intron|LRRC7_uc001deq.2_5'UTR	NM_020794	NP_065845	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	717						centrosome|focal adhesion|nucleolus	protein binding			ovary(9)|breast(2)|central_nervous_system(2)|liver(1)	14						TAAAGATGCAGTACATAATTC	0.423													15	459	---	---	---	---	PASS
ST6GALNAC3	256435	broad.mit.edu	37	1	77042635	77042635	+	Intron	SNP	C	G	G	rs41291518	byFrequency	TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:77042635C>G	uc001dhh.2	+						ST6GALNAC3_uc001dhg.3_3'UTR|ST6GALNAC3_uc010orh.1_Intron	NM_152996	NP_694541	Q8NDV1	SIA7C_HUMAN	sialyltransferase 7C isoform 1						protein glycosylation	integral to Golgi membrane	sialyltransferase activity			ovary(3)|skin(2)	5						aagaaagaaacaaacaaacaa	0.338													10	147	---	---	---	---	PASS
LOC400759	400759	broad.mit.edu	37	1	89890132	89890132	+	RNA	SNP	G	A	A			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89890132G>A	uc009wcy.1	+	5		c.873G>A				NR_003133				Homo sapiens cDNA, FLJ17004.												0						TTGCTTACTTGTACTTTTCAA	0.453													5	9	---	---	---	---	PASS
COL11A1	1301	broad.mit.edu	37	1	103385868	103385868	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:103385868T>C	uc001dul.2	-	49	4079	c.3761A>G	c.(3760-3762)AAG>AGG	p.K1254R	COL11A1_uc001duk.2_Missense_Mutation_p.K450R|COL11A1_uc001dum.2_Missense_Mutation_p.K1266R|COL11A1_uc001dun.2_Missense_Mutation_p.K1215R|COL11A1_uc009weh.2_Missense_Mutation_p.K1138R	NM_001854	NP_001845	P12107	COBA1_HUMAN	alpha 1 type XI collagen isoform A	1254	Triple-helical region.				collagen fibril organization|detection of mechanical stimulus involved in sensory perception of sound|visual perception	collagen type XI	extracellular matrix binding|extracellular matrix structural constituent|protein binding, bridging			ovary(6)|breast(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	12		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		CATATTTACCTTTTCTCCAAC	0.363													6	316	---	---	---	---	PASS
WDR77	79084	broad.mit.edu	37	1	111985985	111985985	+	Silent	SNP	C	A	A			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111985985C>A	uc001ebb.2	-	7	690	c.651G>T	c.(649-651)TCG>TCT	p.S217S	WDR77_uc010owd.1_RNA|WDR77_uc010owe.1_Silent_p.S153S	NM_024102	NP_077007	Q9BQA1	MEP50_HUMAN	WD repeat domain 77	217	WD 4.				ncRNA metabolic process|spliceosomal snRNP assembly	cytosol|nucleus	ligand-dependent nuclear receptor transcription coactivator activity|protein binding				0		all_cancers(81;0.000902)|all_epithelial(167;0.00056)|all_lung(203;0.00277)|Lung NSC(277;0.0043)		Lung(183;0.0238)|Colorectal(144;0.0296)|all cancers(265;0.0488)|Epithelial(280;0.0732)|COAD - Colon adenocarcinoma(174;0.114)|LUSC - Lung squamous cell carcinoma(189;0.135)		GCCAAGCCAGCGAGGTAGGAA	0.493													4	53	---	---	---	---	PASS
SLC16A1	6566	broad.mit.edu	37	1	113456751	113456751	+	Missense_Mutation	SNP	G	T	T			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113456751G>T	uc001ecx.2	-	5	2097	c.1265C>A	c.(1264-1266)ACA>AAA	p.T422K	SLC16A1_uc001ecy.2_Missense_Mutation_p.T422K	NM_003051	NP_003042	P53985	MOT1_HUMAN	solute carrier family 16, member 1	422	Extracellular (Potential).				blood coagulation|leukocyte migration|organic anion transport|pyruvate metabolic process	integral to membrane|membrane fraction|plasma membrane	mevalonate transmembrane transporter activity|protein binding|secondary active monocarboxylate transmembrane transporter activity|symporter activity			central_nervous_system(1)	1	Lung SC(450;0.246)	all_cancers(81;7.6e-08)|all_epithelial(167;3.82e-07)|all_lung(203;3.07e-05)|Lung NSC(69;5.51e-05)|Prostate(1639;0.00232)		Epithelial(280;7.31e-13)|all cancers(265;5.1e-10)|Kidney(133;5.29e-07)|KIRC - Kidney renal clear cell carcinoma(1967;8.63e-06)|OV - Ovarian serous cystadenocarcinoma(397;1.48e-05)|BRCA - Breast invasive adenocarcinoma(282;0.003)|LUSC - Lung squamous cell carcinoma(189;0.008)|Lung(183;0.00948)|Colorectal(144;0.0325)|COAD - Colon adenocarcinoma(174;0.0643)	Pyruvic acid(DB00119)	TGCCCAGTATGTGTATTTGTA	0.383													6	127	---	---	---	---	PASS
CSDE1	7812	broad.mit.edu	37	1	115272930	115272930	+	Silent	SNP	T	C	C			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115272930T>C	uc001efk.2	-	12	1771	c.1305A>G	c.(1303-1305)GAA>GAG	p.E435E	CSDE1_uc001efi.2_Silent_p.E481E|CSDE1_uc001efj.2_RNA|CSDE1_uc001efl.2_Silent_p.E404E|CSDE1_uc001efm.2_Silent_p.E450E|CSDE1_uc009wgv.2_Silent_p.E435E|CSDE1_uc001efn.2_Silent_p.E404E	NM_001007553	NP_001007554	O75534	CSDE1_HUMAN	upstream of NRAS isoform 1	435					male gonad development|regulation of transcription, DNA-dependent	cytoplasm	DNA binding|protein binding|RNA binding			ovary(1)	1	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;2.21e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		AAAAAGTGGCTTCTTTTTCTA	0.378													8	378	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	142813129	142813129	+	Intron	SNP	G	A	A			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142813129G>A	uc001eiw.1	+						uc001ejb.2_Intron|uc001ejd.1_Intron|uc001ejc.2_RNA					Homo sapiens PNAS-130 mRNA, complete cds.																		CTTCCTTGAAGGTAATTAATT	0.338													4	83	---	---	---	---	PASS
LASS2	29956	broad.mit.edu	37	1	150939585	150939585	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150939585T>C	uc001evy.2	-	8	1093	c.706A>G	c.(706-708)ATG>GTG	p.M236V	LASS2_uc001evz.2_Missense_Mutation_p.M236V|LASS2_uc009wmh.2_Missense_Mutation_p.M86V	NM_181746	NP_859530	Q96G23	CERS2_HUMAN	LAG1 longevity assurance 2	236	Lumenal (Potential).|TLC.					endoplasmic reticulum membrane|integral to membrane|nuclear membrane	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sphingosine N-acyltransferase activity				0	all_lung(15;8.07e-35)|Lung NSC(24;7.93e-31)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			TGCAGAGCCATGATTAGAGTC	0.488													48	78	---	---	---	---	PASS
C1orf112	55732	broad.mit.edu	37	1	169822077	169822077	+	Silent	SNP	G	A	A			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169822077G>A	uc001ggp.2	+	25	2821	c.2511G>A	c.(2509-2511)GCG>GCA	p.A837A	C1orf112_uc001ggj.2_RNA|C1orf112_uc001ggq.2_Silent_p.A837A|C1orf112_uc009wvt.2_Silent_p.A514A|C1orf112_uc001ggr.2_Silent_p.A702A|C1orf112_uc010plv.1_Silent_p.A779A|SCYL3_uc010plw.1_3'UTR|SCYL3_uc001ggs.2_3'UTR|SCYL3_uc001ggt.2_3'UTR|SCYL3_uc001ggu.2_RNA	NM_018186	NP_060656	Q9NSG2	CA112_HUMAN	hypothetical protein LOC55732	837											0	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					AAATGGAGGCGCTCCAAGAAA	0.458													4	102	---	---	---	---	PASS
CDC73	79577	broad.mit.edu	37	1	193119494	193119494	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193119494A>G	uc001gtb.2	+	9	1132	c.889A>G	c.(889-891)AGA>GGA	p.R297G		NM_024529	NP_078805	Q6P1J9	CDC73_HUMAN	parafibromin	297					cell cycle|histone H2B ubiquitination|histone monoubiquitination|transcription, DNA-dependent	Cdc73/Paf1 complex	protein binding			parathyroid(46)|ovary(1)|breast(1)|pancreas(1)	49						CGATCAGGAAAGATTCAAAGG	0.383									Hyperparathyroidism_Familial_Isolated|Hyperparathyroidism-Jaw_Tumor_Syndrome				6	284	---	---	---	---	PASS
TAF1A	9015	broad.mit.edu	37	1	222753155	222753155	+	Silent	SNP	A	G	G			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222753155A>G	uc009xdz.1	-	4	540	c.351T>C	c.(349-351)AGT>AGC	p.S117S	TAF1A_uc001hni.1_Silent_p.S3S|TAF1A_uc001hnj.2_Silent_p.S117S|TAF1A_uc001hnk.2_Silent_p.S3S|TAF1A_uc010pur.1_Silent_p.S117S	NM_139352	NP_647603	Q15573	TAF1A_HUMAN	TBP-associated factor 1A isoform 2	117					regulation of transcription, DNA-dependent|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter	RNA polymerase I transcription factor complex	DNA binding				0				GBM - Glioblastoma multiforme(131;0.0186)		AAGTATTGAAACTCTCCATGT	0.323													8	380	---	---	---	---	PASS
RYR2	6262	broad.mit.edu	37	1	237895427	237895427	+	Silent	SNP	C	A	A			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237895427C>A	uc001hyl.1	+	78	11137	c.11017C>A	c.(11017-11019)CGG>AGG	p.R3673R	RYR2_uc010pya.1_Silent_p.R69R	NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	3673					cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			TCTGTTTAGTCGGACAGCTTT	0.443													72	122	---	---	---	---	PASS
ZNF238	10472	broad.mit.edu	37	1	244218338	244218338	+	Missense_Mutation	SNP	G	T	T			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244218338G>T	uc001iae.2	+	1	1757	c.1235G>T	c.(1234-1236)TGC>TTC	p.C412F	ZNF238_uc001iad.3_Missense_Mutation_p.C421F|ZNF238_uc001iaf.1_3'UTR	NM_006352	NP_006343	Q99592	ZN238_HUMAN	zinc finger protein 238 isoform 2	412	C2H2-type 2.|Interaction with DNMT3A.				negative regulation of transcription from RNA polymerase II promoter|skeletal muscle tissue development	nuclear chromosome	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)|pancreas(2)	5	all_cancers(71;6.42e-05)|all_epithelial(71;7e-05)|Breast(184;0.0333)|Ovarian(71;0.0619)|all_lung(81;0.089)|all_neural(11;0.101)|Lung NSC(105;0.123)		all cancers(7;1.35e-08)|GBM - Glioblastoma multiforme(7;1e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00223)			GTGCCCACGTGCTCGCTGTGT	0.632													7	14	---	---	---	---	PASS
MYT1L	23040	broad.mit.edu	37	2	1926721	1926721	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1926721C>T	uc002qxe.2	-	10	1647	c.820G>A	c.(820-822)GTT>ATT	p.V274I	MYT1L_uc002qxd.2_Missense_Mutation_p.V274I|MYT1L_uc010ewl.1_RNA	NM_015025	NP_055840	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	274					cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|central_nervous_system(1)	6	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)		GAGAGCACAACACCGTGTCCT	0.428													51	95	---	---	---	---	PASS
GTF2A1L	11036	broad.mit.edu	37	2	48960052	48960052	+	Silent	SNP	G	A	A			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48960052G>A	uc002rwt.2	+	9	1416	c.1350G>A	c.(1348-1350)TCG>TCA	p.S450S	LHCGR_uc002rwu.3_Intron|LHCGR_uc002rwv.2_Intron	NM_172196	NP_751946	Q9UNN4	TF2AY_HUMAN	general transcription factor IIA, 1-like isoform	Error:Variant_position_missing_in_Q9UNN4_after_alignment					regulation of transcription, DNA-dependent|transcription initiation from RNA polymerase II promoter	transcription factor TFIIA complex	DNA binding|transcription coactivator activity				0		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			GAAGGACATCGTTTAACACCT	0.244													77	145	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	96568655	96568655	+	Intron	SNP	A	T	T			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96568655A>T	uc002sva.1	-						uc002suz.1_5'UTR|uc002svb.1_Intron					Homo sapiens cDNA FLJ41632 fis, clone FCBBF1000297, highly  similar to Human protein immuno-reactive with anti-PTH polyclonal antibodies mRNA.																		TTTTCTCCATACTTTTTTCCT	0.279													4	73	---	---	---	---	PASS
POLR1B	84172	broad.mit.edu	37	2	113332691	113332691	+	Missense_Mutation	SNP	G	T	T			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113332691G>T	uc002thw.2	+	15	3373	c.2793G>T	c.(2791-2793)GAG>GAT	p.E931D	POLR1B_uc010fkn.2_Missense_Mutation_p.E875D|POLR1B_uc002thx.2_Missense_Mutation_p.E792D|POLR1B_uc010fko.2_Missense_Mutation_p.E748D|POLR1B_uc010fkp.2_Missense_Mutation_p.E370D|POLR1B_uc010yxn.1_Missense_Mutation_p.E969D|POLR1B_uc002thy.2_Missense_Mutation_p.E792D|POLR1B_uc010yxo.1_Missense_Mutation_p.E708D	NM_019014	NP_061887	Q9H9Y6	RPA2_HUMAN	RNA polymerase I polypeptide B isoform 1	931					termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|protein binding|ribonucleoside binding			ovary(1)	1						TGTTAATTGAGAGTATGGCCG	0.498													5	124	---	---	---	---	PASS
PABPC1P2	728773	broad.mit.edu	37	2	147345348	147345348	+	5'UTR	SNP	G	A	A			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:147345348G>A	uc002twf.3	+	1						NR_026904				RecName: Full=Putative protein PABPC1-like; AltName: Full=Polyadenylate-binding protein pseudogene 2;												0						GCGATCTATCGCTGCGCAAAA	0.493													6	1	---	---	---	---	PASS
PABPC1P2	728773	broad.mit.edu	37	2	147346046	147346046	+	Missense_Mutation	SNP	C	A	A			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:147346046C>A	uc002twf.3	+	1	1422	c.506C>A	c.(505-507)GCA>GAA	p.A169E		NR_026904				RecName: Full=Putative protein PABPC1-like; AltName: Full=Polyadenylate-binding protein pseudogene 2;												0						GTAGCTAAAGCAGTTACAGCA	0.438													3	23	---	---	---	---	PASS
FASTKD1	79675	broad.mit.edu	37	2	170428428	170428428	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170428428G>A	uc002uev.3	-	2	500	c.112C>T	c.(112-114)CCA>TCA	p.P38S	FASTKD1_uc002uew.3_RNA|FASTKD1_uc002uex.3_Missense_Mutation_p.P24S|FASTKD1_uc002uey.2_Missense_Mutation_p.P24S	NM_024622	NP_078898	Q53R41	FAKD1_HUMAN	FAST kinase domains 1	38					apoptosis|cellular respiration	mitochondrion	ATP binding|protein kinase activity			ovary(4)	4						ATAATTAGTGGTTCACAACTG	0.378													5	174	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179436399	179436399	+	Missense_Mutation	SNP	T	A	A			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179436399T>A	uc010zfg.1	-	275	66980	c.66756A>T	c.(66754-66756)GAA>GAT	p.E22252D	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.E15947D|TTN_uc010zfi.1_Missense_Mutation_p.E15880D|TTN_uc010zfj.1_Missense_Mutation_p.E15755D	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	23179							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CAGCTGTCACTTCATCCATTT	0.423													4	118	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179444407	179444407	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179444407A>G	uc010zfg.1	-	268	60037	c.59813T>C	c.(59812-59814)CTA>CCA	p.L19938P	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.L13633P|TTN_uc010zfi.1_Missense_Mutation_p.L13566P|TTN_uc010zfj.1_Missense_Mutation_p.L13441P|uc002umv.1_3'UTR	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	20865							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AGAGTACTGTAGGCTTAAGGA	0.403													5	290	---	---	---	---	PASS
DNAH7	56171	broad.mit.edu	37	2	196723250	196723250	+	Missense_Mutation	SNP	G	T	T			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196723250G>T	uc002utj.3	-	43	8116	c.8015C>A	c.(8014-8016)GCC>GAC	p.A2672D		NM_018897	NP_061720	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	2672	Stalk (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			skin(10)|ovary(2)	12						TATTGGCAAGGCACCTGCCAG	0.453													18	125	---	---	---	---	PASS
CFLAR	8837	broad.mit.edu	37	2	201994484	201994484	+	5'UTR	SNP	T	C	C			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201994484T>C	uc002uxb.3	+	2					CFLAR_uc002uwy.2_5'UTR|CFLAR_uc002uwz.2_5'UTR|CFLAR_uc002uxa.3_5'UTR|CFLAR_uc010zhk.1_Intron|CFLAR_uc002uxc.3_5'UTR|CFLAR_uc010zhl.1_Intron|CFLAR_uc010fsw.1_RNA|CFLAR_uc002uxd.3_5'UTR|CFLAR_uc002uxe.2_5'UTR|CFLAR_uc002uxf.2_5'UTR|CFLAR_uc010fsy.2_RNA|CFLAR_uc010fsx.2_5'UTR	NM_003879	NP_003870	O15519	CFLAR_HUMAN	CASP8 and FADD-like apoptosis regulator isoform						anti-apoptosis|apoptosis|induction of apoptosis by extracellular signals|interspecies interaction between organisms|positive regulation of I-kappaB kinase/NF-kappaB cascade|proteolysis		cysteine-type endopeptidase activity|protein binding				0						CTGAAAGAAATGAAGTCAGCC	0.443													12	24	---	---	---	---	PASS
LOC200726	200726	broad.mit.edu	37	2	207509193	207509193	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207509193A>G	uc010fuh.1	+	2	408	c.233A>G	c.(232-234)TAC>TGC	p.Y78C		NM_001102659	NP_001096129			hypothetical protein LOC200726												0				LUSC - Lung squamous cell carcinoma(261;0.0703)|Epithelial(149;0.115)|Lung(261;0.133)		TTTATGATCTACCTGAAGTCA	0.488													4	118	---	---	---	---	PASS
SPHKAP	80309	broad.mit.edu	37	2	228860275	228860275	+	Missense_Mutation	SNP	G	T	T			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228860275G>T	uc002vpq.2	-	8	4631	c.4584C>A	c.(4582-4584)GAC>GAA	p.D1528E	SPHKAP_uc002vpp.2_Missense_Mutation_p.D1528E|SPHKAP_uc010zlx.1_Intron	NM_001142644	NP_001136116	Q2M3C7	SPKAP_HUMAN	sphingosine kinase type 1-interacting protein	1528						cytoplasm	protein binding			skin(5)|ovary(4)|lung(1)	10		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		CATCTGGGTTGTCTTCCTCAT	0.557													6	129	---	---	---	---	PASS
SLC4A7	9497	broad.mit.edu	37	3	27451006	27451006	+	Silent	SNP	C	T	T			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27451006C>T	uc003cdv.2	-	13	1826	c.1755G>A	c.(1753-1755)TTG>TTA	p.L585L	SLC4A7_uc011awu.1_Intron|SLC4A7_uc011awv.1_Intron|SLC4A7_uc003cdu.3_Silent_p.L466L|SLC4A7_uc011aww.1_Silent_p.L594L|SLC4A7_uc011awx.1_Silent_p.L581L|SLC4A7_uc011awy.1_Silent_p.L577L|SLC4A7_uc011awz.1_Intron|SLC4A7_uc011axa.1_Silent_p.L466L|SLC4A7_uc011axb.1_Silent_p.L581L|SLC4A7_uc010hfl.2_Silent_p.L135L|SLC4A7_uc003cdw.2_Silent_p.L461L	NM_003615	NP_003606	Q9Y6M7	S4A7_HUMAN	solute carrier family 4, sodium bicarbonate	585	Extracellular (Potential).					apical plasma membrane|basolateral plasma membrane|integral to membrane|stereocilium	inorganic anion exchanger activity|protein binding|sodium:bicarbonate symporter activity			ovary(3)|central_nervous_system(1)|skin(1)	5						TGTCAAGTATCAAACCACCAA	0.408													7	40	---	---	---	---	PASS
SEMA3F	6405	broad.mit.edu	37	3	50225421	50225421	+	Missense_Mutation	SNP	A	T	T			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50225421A>T	uc003cyj.2	+	19	2429	c.2231A>T	c.(2230-2232)CAG>CTG	p.Q744L	SEMA3F_uc003cyk.2_Missense_Mutation_p.Q713L	NM_004186	NP_004177	Q13275	SEM3F_HUMAN	semaphorin 3F precursor	744					axon guidance	extracellular space|membrane	chemorepellent activity|receptor activity			lung(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.00013)|KIRC - Kidney renal clear cell carcinoma(197;0.00599)|Kidney(197;0.00688)		CTCATCCACCAGTACTGCCAG	0.692													2	0	---	---	---	---	PASS
C3orf45	132228	broad.mit.edu	37	3	50324620	50324620	+	Missense_Mutation	SNP	A	T	T			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50324620A>T	uc003cyz.2	+	4	509	c.482A>T	c.(481-483)CAA>CTA	p.Q161L		NM_153215	NP_694947	Q8N112	CC045_HUMAN	hypothetical protein LOC132228	161						integral to membrane				ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		AGTGAGGCCCAAGCACCCAGC	0.612													11	11	---	---	---	---	PASS
ZDHHC23	254887	broad.mit.edu	37	3	113675206	113675206	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113675206A>G	uc003eau.2	+	4	1192	c.893A>G	c.(892-894)GAA>GGA	p.E298G	ZDHHC23_uc003eav.2_Missense_Mutation_p.E292G|ZDHHC23_uc003eaw.1_5'Flank	NM_173570	NP_775841	Q8IYP9	ZDH23_HUMAN	zinc finger, DHHC domain containing 23	298	DHHC-type.					integral to membrane	acyltransferase activity|zinc ion binding			ovary(2)	2						TGCGTTGGAGAATCAAATCAT	0.358													8	603	---	---	---	---	PASS
ATP2C1	27032	broad.mit.edu	37	3	130716502	130716502	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130716502T>C	uc003enl.2	+	25	2518	c.2296T>C	c.(2296-2298)TGG>CGG	p.W766R	ATP2C1_uc011blg.1_Missense_Mutation_p.W800R|ATP2C1_uc011blh.1_Missense_Mutation_p.W761R|ATP2C1_uc011bli.1_Missense_Mutation_p.W800R|ATP2C1_uc003enk.2_Missense_Mutation_p.W750R|ATP2C1_uc003enm.2_Missense_Mutation_p.W766R|ATP2C1_uc003enn.2_Missense_Mutation_p.W750R|ATP2C1_uc003eno.2_Missense_Mutation_p.W766R|ATP2C1_uc003enp.2_Missense_Mutation_p.W766R|ATP2C1_uc003enq.2_Missense_Mutation_p.W766R|ATP2C1_uc003enr.2_Missense_Mutation_p.W766R|ATP2C1_uc003ens.2_Missense_Mutation_p.W766R|ATP2C1_uc003ent.2_Missense_Mutation_p.W766R|ATP2C1_uc003enu.2_Missense_Mutation_p.W444R	NM_014382	NP_055197	P98194	AT2C1_HUMAN	calcium-transporting ATPase 2C1 isoform 1a	766	Cytoplasmic (By similarity).				actin cytoskeleton reorganization|ATP biosynthetic process|calcium-dependent cell-cell adhesion|cellular calcium ion homeostasis|cellular manganese ion homeostasis|epidermis development|Golgi calcium ion homeostasis|Golgi calcium ion transport|positive regulation of I-kappaB kinase/NF-kappaB cascade	Golgi apparatus|Golgi membrane|integral to membrane|trans-Golgi network	ATP binding|ATP binding|calcium ion binding|calcium-transporting ATPase activity|manganese ion binding|manganese-transporting ATPase activity|metal ion binding|signal transducer activity			skin(1)	1					Arsenic trioxide(DB01169)|Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Miconazole(DB01110)|Sevoflurane(DB01236)	TCCTCGCAACTGGAAAGACAG	0.343									Hailey-Hailey_disease				8	495	---	---	---	---	PASS
ACTL6A	86	broad.mit.edu	37	3	179292225	179292225	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179292225T>C	uc003fjw.2	+	5	619	c.446T>C	c.(445-447)TTC>TCC	p.F149S	ACTL6A_uc003fjx.2_Missense_Mutation_p.F107S|ACTL6A_uc003fjy.2_Missense_Mutation_p.F107S	NM_004301	NP_004292	O96019	ACL6A_HUMAN	actin-like 6A isoform 1	149					chromatin remodeling|DNA recombination|DNA repair|histone H2A acetylation|histone H4 acetylation|nervous system development|regulation of growth|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	Ino80 complex|npBAF complex|NuA4 histone acetyltransferase complex|plasma membrane|SWI/SNF complex	ATP binding|chromatin binding			ovary(1)	1	all_cancers(143;3.94e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.98e-26)|GBM - Glioblastoma multiforme(14;0.0169)			ATCCCTGCCTTCTTCCTTTGC	0.378													6	295	---	---	---	---	PASS
ALG3	10195	broad.mit.edu	37	3	183961713	183961713	+	Silent	SNP	G	T	T			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183961713G>T	uc003fne.2	-	6	829	c.798C>A	c.(796-798)CGC>CGA	p.R266R	ALG3_uc011brc.1_Silent_p.R231R|ALG3_uc011brd.1_Silent_p.R210R|ALG3_uc011bre.1_Silent_p.R218R|ALG3_uc003fnf.1_Silent_p.R226R	NM_005787	NP_005778	Q92685	ALG3_HUMAN	alpha-1,3-mannosyltransferase ALG3 isoform a	266					dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|integral to membrane	alpha-1,3-mannosyltransferase activity				0	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			ACAGAAACTGGCGGCCAAGGT	0.622													3	8	---	---	---	---	PASS
SLC30A9	10463	broad.mit.edu	37	4	42088238	42088238	+	3'UTR	SNP	G	C	C			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42088238G>C	uc003gwl.2	+	18					SLC30A9_uc011byx.1_3'UTR	NM_006345	NP_006336	Q6PML9	ZNT9_HUMAN	solute carrier family 30 (zinc transporter),						nucleotide-excision repair|zinc ion transport	cytoskeleton|integral to membrane|nucleus	cation transmembrane transporter activity|nucleotide binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|ovary(1)	3						GAAAGACTCAGTGCCATGCAG	0.413													6	205	---	---	---	---	PASS
TMPRSS11F	389208	broad.mit.edu	37	4	68930600	68930600	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68930600T>C	uc003hdt.1	-	8	867	c.818A>G	c.(817-819)AAA>AGA	p.K273R	LOC550112_uc003hdl.3_Intron|uc011cak.1_Intron|SYT14L_uc010ihn.2_5'Flank	NM_207407	NP_997290	Q6ZWK6	TM11F_HUMAN	transmembrane protease, serine 11F	273	Peptidase S1.|Extracellular (Potential).				proteolysis	extracellular region|integral to plasma membrane	serine-type endopeptidase activity			ovary(1)	1						CACATTTCGTTTCACTGCGGG	0.353													6	294	---	---	---	---	PASS
RUFY3	22902	broad.mit.edu	37	4	71648807	71648807	+	Splice_Site	SNP	G	T	T			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71648807G>T	uc003hfq.2	+	9	1490	c.895_splice	c.e9-1	p.L299_splice	RUFY3_uc003hfp.3_Splice_Site_p.L359_splice|RUFY3_uc011cax.1_Splice_Site_p.L317_splice|RUFY3_uc003hfr.2_Splice_Site_p.L299_splice|RUFY3_uc011cay.1_Splice_Site_p.L235_splice	NM_014961	NP_055776	Q7L099	RUFY3_HUMAN	RUN and FYVE domain containing 3 isoform 2						negative regulation of axonogenesis	filopodium|growth cone					0		all_hematologic(202;0.248)	Lung(101;0.235)			tttatCCACAGCTTGCAGTTG	0.308													103	196	---	---	---	---	PASS
CCNG2	901	broad.mit.edu	37	4	78080579	78080579	+	Silent	SNP	A	G	G			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:78080579A>G	uc003hkq.3	+	3	501	c.198A>G	c.(196-198)TTA>TTG	p.L66L	CCNG2_uc003hkn.3_Silent_p.L66L|CCNG2_uc011ccc.1_Silent_p.L66L|CCNG2_uc003hkp.3_Silent_p.L66L	NM_004354	NP_004345	Q16589	CCNG2_HUMAN	cyclin G2	66					cell cycle checkpoint|cell division|mitosis	cytoplasm				ovary(2)|lung(1)	3						TAAGGAGTTTAGCCAACTTTT	0.338													7	627	---	---	---	---	PASS
PTPN13	5783	broad.mit.edu	37	4	87696460	87696460	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87696460C>T	uc003hpz.2	+	34	6125	c.5645C>T	c.(5644-5646)CCG>CTG	p.P1882L	PTPN13_uc003hpy.2_Missense_Mutation_p.P1887L|PTPN13_uc003hqa.2_Missense_Mutation_p.P1863L|PTPN13_uc003hqb.2_Missense_Mutation_p.P1691L|PTPN13_uc003hqc.1_Missense_Mutation_p.P248L	NM_080683	NP_542414	Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type	1882	PDZ 5.					cytoplasm|cytoskeleton|plasma membrane	protein binding|protein binding|protein tyrosine phosphatase activity			ovary(4)|breast(1)|kidney(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		CATTTGCTACCGGACATAACA	0.383													60	122	---	---	---	---	PASS
MAD2L1	4085	broad.mit.edu	37	4	120981284	120981284	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:120981284C>T	uc003idl.2	-	5	731	c.607G>A	c.(607-609)GTC>ATC	p.V203I	MAD2L1_uc003idm.2_3'UTR	NM_002358	NP_002349	Q13257	MD2L1_HUMAN	MAD2-like 1	203	Required for assuming the closed conformation and for interaction with CDC20.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|negative regulation of apoptosis|negative regulation of mitotic anaphase-promoting complex activity|positive regulation of mitotic cell cycle spindle assembly checkpoint	condensed chromosome kinetochore|cytosol|nucleus|perinuclear region of cytoplasm	protein homodimerization activity				0						CAGTCATTGACAGGAATTTTG	0.353													98	203	---	---	---	---	PASS
TMEM184C	55751	broad.mit.edu	37	4	148545115	148545115	+	Missense_Mutation	SNP	G	C	C			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:148545115G>C	uc003ila.3	+	2	823	c.254G>C	c.(253-255)AGG>ACG	p.R85T		NM_018241	NP_060711	Q9NVA4	T184C_HUMAN	transmembrane protein 184C	85						integral to membrane					0						CCAATAATAAGGTATGTCTTA	0.308													129	441	---	---	---	---	PASS
ADAM29	11086	broad.mit.edu	37	4	175898846	175898846	+	Nonsense_Mutation	SNP	C	T	T			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:175898846C>T	uc003iuc.2	+	5	2840	c.2170C>T	c.(2170-2172)CGA>TGA	p.R724*	ADAM29_uc003iud.2_Nonsense_Mutation_p.R724*|ADAM29_uc010irr.2_Nonsense_Mutation_p.R724*|ADAM29_uc011cki.1_Nonsense_Mutation_p.R724*	NM_014269	NP_055084	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29 preproprotein	724	Cytoplasmic (Potential).				proteolysis|spermatogenesis	integral to plasma membrane	metalloendopeptidase activity|zinc ion binding			skin(5)|central_nervous_system(3)|ovary(3)|large_intestine(2)|lung(2)|pancreas(1)	16		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		AATTCAGCGTCGACCTCATGA	0.438													22	51	---	---	---	---	PASS
DCTD	1635	broad.mit.edu	37	4	183812459	183812459	+	3'UTR	SNP	G	A	A			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183812459G>A	uc003ivf.2	-	6					DCTD_uc003ivg.2_3'UTR|DCTD_uc010irw.2_3'UTR|DCTD_uc003ivh.2_3'UTR	NM_001921	NP_001912	P32321	DCTD_HUMAN	dCMP deaminase isoform b						nucleotide biosynthetic process|pyrimidine base metabolic process|pyrimidine nucleoside biosynthetic process|pyrimidine nucleotide metabolic process	cytosol	dCMP deaminase activity|zinc ion binding				0		all_lung(41;5.16e-14)|Lung NSC(41;1.33e-13)|Colorectal(36;0.00666)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.202)		all cancers(43;1.65e-24)|Epithelial(43;3.44e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.39e-10)|Colorectal(24;4.69e-07)|COAD - Colon adenocarcinoma(29;7.07e-05)|STAD - Stomach adenocarcinoma(60;0.000118)|GBM - Glioblastoma multiforme(59;0.000472)|LUSC - Lung squamous cell carcinoma(40;0.00984)|READ - Rectum adenocarcinoma(43;0.0419)		ATACTGGCTAGTAAGAAGTTA	0.368													7	78	---	---	---	---	PASS
CDH18	1016	broad.mit.edu	37	5	19520813	19520813	+	Missense_Mutation	SNP	C	A	A			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19520813C>A	uc003jgc.2	-	9	1842	c.1465G>T	c.(1465-1467)GCC>TCC	p.A489S	CDH18_uc003jgd.2_Missense_Mutation_p.A489S|CDH18_uc011cnm.1_Missense_Mutation_p.A489S	NM_004934	NP_004925	Q13634	CAD18_HUMAN	cadherin 18, type 2 preproprotein	489	Extracellular (Potential).|Cadherin 5.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|large_intestine(1)|skin(1)	7	Lung NSC(1;0.00734)|all_lung(1;0.0197)					TATTCCCTGGCAAGTTCGGGT	0.393													167	302	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	5	23980775	23980775	+	RNA	SNP	G	A	A			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:23980775G>A	uc003jgq.1	+	4		c.1382G>A								Homo sapiens cDNA FLJ34836 fis, clone NT2NE2010400.																		AGGAGATAGAGGTGGCACCCC	0.512													11	24	---	---	---	---	PASS
C5orf22	55322	broad.mit.edu	37	5	31551468	31551468	+	Silent	SNP	A	T	T			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31551468A>T	uc003jhj.3	+	8	1255	c.1128A>T	c.(1126-1128)ATA>ATT	p.I376I	C5orf22_uc011cnw.1_RNA|C5orf22_uc003jhk.3_Silent_p.I111I|C5orf22_uc010iuj.2_Silent_p.I111I	NM_018356	NP_060826	Q49AR2	CE022_HUMAN	hypothetical protein LOC55322	376										ovary(2)	2						AACAAGAAATAGAGTGTCTTA	0.308													23	328	---	---	---	---	PASS
FNIP1	96459	broad.mit.edu	37	5	131008580	131008580	+	Missense_Mutation	SNP	T	G	G			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131008580T>G	uc003kvs.1	-	14	1699	c.1557A>C	c.(1555-1557)TTA>TTC	p.L519F	RAPGEF6_uc003kvp.1_Intron|FNIP1_uc003kvt.1_Missense_Mutation_p.L491F|FNIP1_uc010jdm.1_Missense_Mutation_p.L474F	NM_133372	NP_588613	Q8TF40	FNIP1_HUMAN	folliculin interacting protein 1 isoform 1	519					regulation of protein phosphorylation	cytoplasm	protein binding			pancreas(1)|skin(1)	2		all_cancers(142;0.00347)|Lung NSC(810;0.106)|all_lung(232;0.123)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0665)		CAGTCCTTGCTAACCGTACGG	0.403													16	81	---	---	---	---	PASS
TGFBI	7045	broad.mit.edu	37	5	135379760	135379760	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135379760G>A	uc003lbf.3	+	3	408	c.247G>A	c.(247-249)GAG>AAG	p.E83K	TGFBI_uc003lbg.3_5'UTR|TGFBI_uc003lbh.3_5'UTR|TGFBI_uc011cyb.1_5'Flank	NM_000358	NP_000349	Q15582	BGH3_HUMAN	transforming growth factor, beta-induced, 68kDa	83	EMI.				angiogenesis|cell adhesion|cell proliferation|negative regulation of cell adhesion|response to stimulus|visual perception	extracellular space|proteinaceous extracellular matrix	integrin binding			breast(3)|ovary(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CATCAGCTACGAGTGCTGTCC	0.537													56	178	---	---	---	---	PASS
PCDHB6	56130	broad.mit.edu	37	5	140532190	140532190	+	Silent	SNP	C	A	A	rs146937630		TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140532190C>A	uc003lir.2	+	1	2352	c.2352C>A	c.(2350-2352)ACC>ACA	p.T784T	PCDHB6_uc011dah.1_Silent_p.T648T	NM_018939	NP_061762	Q9Y5E3	PCDB6_HUMAN	protocadherin beta 6 precursor	784	Cytoplasmic (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to plasma membrane	calcium ion binding	p.T784T(1)		skin(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TGGAAGAAACCCCCACCTCTC	0.433													25	104	---	---	---	---	PASS
HMGXB3	22993	broad.mit.edu	37	5	149403938	149403938	+	Silent	SNP	T	C	C			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149403938T>C	uc003lrk.3	+	7	1731	c.1155T>C	c.(1153-1155)AAT>AAC	p.N385N		NM_014983	NP_055798	Q12766	HMGX3_HUMAN	HMG box domain containing 3	631						nucleus	DNA binding|kinase activity			kidney(1)|central_nervous_system(1)	2						CTAAGGAAAATGCCTCCAAAC	0.483													52	58	---	---	---	---	PASS
SLC36A3	285641	broad.mit.edu	37	5	150666892	150666892	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150666892T>C	uc003ltw.2	-	6	1042	c.623A>G	c.(622-624)AAC>AGC	p.N208S	GM2A_uc011dcs.1_Intron|SLC36A3_uc003ltv.2_Missense_Mutation_p.N193S|SLC36A3_uc003ltx.2_Missense_Mutation_p.N249S	NM_181774	NP_861439	Q495N2	S36A3_HUMAN	solute carrier family 36, member 3 isoform 2	208	Cytoplasmic (Potential).					integral to membrane				ovary(2)|skin(1)	3		Medulloblastoma(196;0.109)|all_hematologic(541;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CACCTTGAGGTTCTGGATAAA	0.522													6	261	---	---	---	---	PASS
NSD1	64324	broad.mit.edu	37	5	176665505	176665505	+	Missense_Mutation	SNP	C	G	G			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176665505C>G	uc003mfr.3	+	7	4327	c.4189C>G	c.(4189-4191)CCA>GCA	p.P1397A	NSD1_uc003mft.3_Missense_Mutation_p.P1128A|NSD1_uc003mfs.1_Missense_Mutation_p.P1294A|NSD1_uc011dfx.1_Missense_Mutation_p.P1045A	NM_022455	NP_071900	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	1397				P -> Q (in Ref. 3; AAK92049).	negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	androgen receptor binding|chromatin binding|estrogen receptor binding|histone methyltransferase activity (H3-K36 specific)|histone methyltransferase activity (H4-K20 specific)|ligand-dependent nuclear receptor binding|retinoid X receptor binding|thyroid hormone receptor binding|transcription corepressor activity|zinc ion binding			ovary(2)|kidney(1)	3	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)		AGTTAAAACGCCAGGTAAGGT	0.478			T	NUP98	AML		Sotos Syndrome		Beckwith-Wiedemann_syndrome|Sotos_syndrome|Weaver_syndrome	HNSCC(47;0.14)			19	27	---	---	---	---	PASS
DNAH8	1769	broad.mit.edu	37	6	38891890	38891890	+	Silent	SNP	T	C	C			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38891890T>C	uc003ooe.1	+	71	10863	c.10263T>C	c.(10261-10263)CCT>CCC	p.P3421P	uc003oof.1_Intron	NM_001371	NP_001362			dynein, axonemal, heavy polypeptide 8											skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	21						GGAAAATTCCTTTCACAGAAA	0.358													7	366	---	---	---	---	PASS
HMGN3	9324	broad.mit.edu	37	6	79944257	79944257	+	Intron	SNP	A	C	C			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:79944257A>C	uc003pit.2	-						HMGN3_uc003pis.2_Intron|HMGN3_uc003piu.1_Intron|uc003piv.1_RNA	NM_004242	NP_004233	Q15651	HMGN3_HUMAN	high mobility group nucleosomal binding domain 3						chromatin modification	chromatin|cytoplasm|nucleus	DNA binding|thyroid hormone receptor binding				0		all_cancers(76;0.000116)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.0393)		BRCA - Breast invasive adenocarcinoma(397;0.125)		TTTTGGTAAGACTTACCTTTC	0.498													45	94	---	---	---	---	PASS
MAP3K7	6885	broad.mit.edu	37	6	91254351	91254351	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:91254351G>A	uc003pnz.1	-	12	1373	c.1211C>T	c.(1210-1212)GCC>GTC	p.A404V	MAP3K7_uc003poa.1_Missense_Mutation_p.A404V|MAP3K7_uc003pob.1_Intron|MAP3K7_uc003poc.1_Intron	NM_145331	NP_663304	O43318	M3K7_HUMAN	mitogen-activated protein kinase kinase kinase 7	404					activation of MAPK activity|activation of NF-kappaB-inducing kinase activity|histone H3 acetylation|I-kappaB phosphorylation|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-2 production|positive regulation of JUN kinase activity|positive regulation of NF-kappaB transcription factor activity|positive regulation of T cell cytokine production|stress-activated MAPK cascade|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|transforming growth factor beta receptor signaling pathway	Ada2/Gcn5/Ada3 transcription activator complex|cytosol|endosome membrane	ATP binding|magnesium ion binding|MAP kinase kinase kinase activity|protein binding|protein binding			ovary(2)|lung(2)|upper_aerodigestive_tract(1)|stomach(1)	6		all_cancers(76;6.4e-08)|Acute lymphoblastic leukemia(125;1.43e-09)|Prostate(29;9.32e-09)|all_hematologic(105;3.69e-06)|all_epithelial(107;0.000187)|Ovarian(999;0.0164)		OV - Ovarian serous cystadenocarcinoma(136;2.05e-11)|all cancers(137;3.25e-11)|GBM - Glioblastoma multiforme(226;0.0416)|BRCA - Breast invasive adenocarcinoma(108;0.0429)		CTTGGAATAGGCTGCAAAAAC	0.388													5	131	---	---	---	---	PASS
ZUFSP	221302	broad.mit.edu	37	6	116977892	116977892	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116977892C>T	uc003pxf.1	-	5	1162	c.916G>A	c.(916-918)GAA>AAA	p.E306K	ZUFSP_uc010kef.1_Missense_Mutation_p.E110K	NM_145062	NP_659499	Q96AP4	ZUFSP_HUMAN	zinc finger with UFM1-specific peptidase domain	306						intracellular	zinc ion binding			skin(1)	1				GBM - Glioblastoma multiforme(226;0.0258)|all cancers(137;0.0368)|OV - Ovarian serous cystadenocarcinoma(136;0.0464)|Epithelial(106;0.186)		GCTAATGATTCCATCATATCA	0.348													172	362	---	---	---	---	PASS
L3MBTL3	84456	broad.mit.edu	37	6	130387610	130387610	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130387610G>A	uc003qbt.2	+	11	1147	c.977G>A	c.(976-978)GGC>GAC	p.G326D	L3MBTL3_uc003qbu.2_Missense_Mutation_p.G301D	NM_032438	NP_115814	Q96JM7	LMBL3_HUMAN	l(3)mbt-like 3 isoform a	326	MBT 1.				chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(5)|skin(1)	6				GBM - Glioblastoma multiforme(226;0.0266)|OV - Ovarian serous cystadenocarcinoma(155;0.154)		GAGAAAACCGGCCACAAACTC	0.388													5	225	---	---	---	---	PASS
HGC6.3	100128124	broad.mit.edu	37	6	168377094	168377094	+	Missense_Mutation	SNP	G	A	A	rs9364375		TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168377094G>A	uc010kks.1	-	1	526	c.239C>T	c.(238-240)CCC>CTC	p.P80L		NM_001129895	NP_001123367	Q9UM08	Q9UM08_HUMAN	hypothetical protein LOC100128124	80											0						TGCAGTGTGGGGGGAGGAGAA	0.627													4	3	---	---	---	---	PASS
TAX1BP1	8887	broad.mit.edu	37	7	27833958	27833958	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27833958T>C	uc003szl.2	+	11	1585	c.1427T>C	c.(1426-1428)GTC>GCC	p.V476A	TAX1BP1_uc011jzo.1_Missense_Mutation_p.V476A|TAX1BP1_uc003szk.2_Missense_Mutation_p.V476A|TAX1BP1_uc011jzp.1_Missense_Mutation_p.V319A	NM_006024	NP_006015	Q86VP1	TAXB1_HUMAN	Tax1 (human T-cell leukemia virus type I)	476	Potential.				anti-apoptosis|apoptosis|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production	cytosol	identical protein binding|kinase binding|zinc ion binding			breast(1)	1			GBM - Glioblastoma multiforme(3;0.0823)			AATAATAATGTCTTCACAAAG	0.333													6	243	---	---	---	---	PASS
TYW1	55253	broad.mit.edu	37	7	66514943	66514943	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66514943A>G	uc003tvn.2	+	8	1141	c.992A>G	c.(991-993)AAG>AGG	p.K331R	TYW1_uc010lai.2_RNA	NM_018264	NP_060734	Q9NV66	TYW1_HUMAN	radical S-adenosyl methionine and flavodoxin	331					tRNA processing		4 iron, 4 sulfur cluster binding|FMN binding|iron ion binding|oxidoreductase activity			skin(1)	1		Lung NSC(55;0.0846)|all_lung(88;0.183)				CAGAGAGAAAAGGAACAGCAG	0.388													7	369	---	---	---	---	PASS
WBSCR28	135886	broad.mit.edu	37	7	73280191	73280191	+	Silent	SNP	T	C	C			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73280191T>C	uc003tzk.2	+	3	822	c.786T>C	c.(784-786)ACT>ACC	p.T262T	RFC2_uc011kfa.1_Intron|WBSCR28_uc003tzl.2_Silent_p.T161T	NM_182504	NP_872310	Q6UE05	WBS28_HUMAN	hypothetical protein LOC135886	262						integral to membrane				breast(1)	1		Lung NSC(55;0.159)				AGCAAGAAACTCCCAGAGAAT	0.542													4	33	---	---	---	---	PASS
SMURF1	57154	broad.mit.edu	37	7	98654861	98654861	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98654861A>G	uc003upu.1	-	5	690	c.370T>C	c.(370-372)TCA>CCA	p.S124P	SMURF1_uc003upv.1_Missense_Mutation_p.S124P|SMURF1_uc003upt.2_Missense_Mutation_p.S124P	NM_020429	NP_065162	Q9HCE7	SMUF1_HUMAN	Smad ubiquitination regulatory factor 1 isoform	124					BMP signaling pathway|cell differentiation|ectoderm development|negative regulation of BMP signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of protein ubiquitination|proteasomal ubiquitin-dependent protein catabolic process|protein export from nucleus|protein localization at cell surface|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|receptor catabolic process|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent SMAD protein catabolic process	cytosol|plasma membrane	activin binding|I-SMAD binding|R-SMAD binding|ubiquitin-protein ligase activity			skin(2)|ovary(1)|lung(1)	4	all_cancers(62;1.05e-08)|all_epithelial(64;4.34e-09)|Lung NSC(181;0.00902)|all_lung(186;0.0145)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)|Lung(104;0.224)			TCAGTATCTGAGGGGTTTAGT	0.428													6	224	---	---	---	---	PASS
DPY19L2P2	349152	broad.mit.edu	37	7	102825947	102825947	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102825947A>G	uc003vbh.3	-	20	3239	c.1048T>C	c.(1048-1050)TGT>CGT	p.C350R	DPY19L2P2_uc003vbg.3_RNA|DPY19L2P2_uc010lit.2_RNA	NR_003561				RecName: Full=Protein dpy-19 homolog 2-like 2; AltName: Full=Dpy-19-like protein 2 pseudogene 2;												0						ACAGCTTGACACTTGCCATTG	0.373													4	50	---	---	---	---	PASS
DNAJC2	27000	broad.mit.edu	37	7	102957409	102957409	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102957409C>T	uc003vbo.2	-	13	1546	c.1295G>A	c.(1294-1296)CGT>CAT	p.R432H	PMPCB_uc011kll.1_Intron|DNAJC2_uc003vbn.2_Missense_Mutation_p.R57H|DNAJC2_uc010lix.2_Missense_Mutation_p.R379H|DNAJC2_uc003vbp.2_Missense_Mutation_p.R57H	NM_014377	NP_055192	Q99543	DNJC2_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 2	432					'de novo' cotranslational protein folding|chromatin modification|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nuclear membrane	chromatin binding|DNA binding|histone binding|Hsp70 protein binding|ubiquitin binding			kidney(1)	1						TTGTCGCATACGAGCCTCAGC	0.363													6	298	---	---	---	---	PASS
CUL1	8454	broad.mit.edu	37	7	148485659	148485659	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148485659G>A	uc010lpg.2	+	14	2016	c.1490G>A	c.(1489-1491)GGG>GAG	p.G497E	CUL1_uc003wey.2_Missense_Mutation_p.G497E|CUL1_uc003wez.2_Missense_Mutation_p.G387E|CUL1_uc003wfa.2_Missense_Mutation_p.G158E	NM_003592	NP_003583	Q13616	CUL1_HUMAN	cullin 1	497					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell cycle arrest|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|negative regulation of cell proliferation|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein ubiquitination|S phase of mitotic cell cycle|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	cytosol|nucleoplasm|SCF ubiquitin ligase complex	ubiquitin protein ligase binding			lung(1)	1	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00291)			CAAGCTTGCGGGTTCGAGTAC	0.388													40	91	---	---	---	---	PASS
CRISPLD1	83690	broad.mit.edu	37	8	75926309	75926309	+	Missense_Mutation	SNP	G	T	T			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75926309G>T	uc003yan.2	+	5	973	c.598G>T	c.(598-600)GTC>TTC	p.V200F	CRISPLD1_uc011lfk.1_Missense_Mutation_p.V12F|CRISPLD1_uc011lfl.1_Intron	NM_031461	NP_113649	Q9H336	CRLD1_HUMAN	cysteine-rich secretory protein LCCL domain	200						extracellular region				ovary(1)|central_nervous_system(1)	2	Breast(64;0.0799)		Epithelial(68;0.155)|BRCA - Breast invasive adenocarcinoma(89;0.161)			GCCCAAAGCTGTCTACCTGGT	0.398													10	164	---	---	---	---	PASS
PIGO	84720	broad.mit.edu	37	9	35095479	35095479	+	Silent	SNP	G	A	A			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35095479G>A	uc003zwd.2	-	2	480	c.84C>T	c.(82-84)TTC>TTT	p.F28F	PIGO_uc003zwc.1_Silent_p.F28F|PIGO_uc003zwe.2_Silent_p.F28F|PIGO_uc003zwf.2_Silent_p.F28F|PIGO_uc003zwg.1_5'UTR	NM_032634	NP_116023	Q8TEQ8	PIGO_HUMAN	phosphatidylinositol glycan anchor biosynthesis,	28					C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	transferase activity			large_intestine(1)|ovary(1)|skin(1)	3			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			GGGTGAGCAGGAAGCCACTGG	0.617													6	14	---	---	---	---	PASS
SLC16A9	220963	broad.mit.edu	37	10	61414026	61414026	+	Missense_Mutation	SNP	A	T	T			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61414026A>T	uc010qig.1	-	5	1207	c.758T>A	c.(757-759)CTT>CAT	p.L253H		NM_194298	NP_919274	Q7RTY1	MOT9_HUMAN	solute carrier family 16 (monocarboxylic acid	253	Extracellular (Potential).				urate metabolic process	integral to membrane|plasma membrane	symporter activity			skin(2)|ovary(1)	3						GTTTTTATGAAGTAGGCTGTC	0.403													78	140	---	---	---	---	PASS
SGPL1	8879	broad.mit.edu	37	10	72610951	72610951	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72610951C>T	uc001jrm.2	+	4	467	c.245C>T	c.(244-246)CCC>CTC	p.P82L		NM_003901	NP_003892	O95470	SGPL1_HUMAN	sphingosine-1-phosphate lyase 1	82	Cytoplasmic (Potential).				apoptosis|carboxylic acid metabolic process|ceramide metabolic process|sphingolipid catabolic process	integral to endoplasmic reticulum membrane	carboxy-lyase activity|pyridoxal phosphate binding|sphinganine-1-phosphate aldolase activity				0					Pyridoxal Phosphate(DB00114)	AGGAAGATGCCCATTATTGGT	0.313													10	495	---	---	---	---	PASS
PPP3CB	5532	broad.mit.edu	37	10	75231340	75231340	+	Silent	SNP	T	C	C			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75231340T>C	uc001jue.2	-	5	690	c.555A>G	c.(553-555)GAA>GAG	p.E185E	PPP3CB_uc001juf.2_Silent_p.E185E|PPP3CB_uc001jug.2_Silent_p.E185E|PPP3CB_uc001jui.2_Silent_p.E203E|PPP3CB_uc001juh.2_Silent_p.E99E	NM_021132	NP_066955	P16298	PP2BB_HUMAN	protein phosphatase 3, catalytic subunit, beta	185	Catalytic.									skin(1)	1	Prostate(51;0.0119)					CCATACAAGCTTCATAGACTC	0.338													7	251	---	---	---	---	PASS
PDCD4	27250	broad.mit.edu	37	10	112647425	112647425	+	Silent	SNP	A	G	G			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112647425A>G	uc001kzh.2	+	6	801	c.558A>G	c.(556-558)GAA>GAG	p.E186E	PDCD4_uc001kzg.2_Silent_p.E175E|PDCD4_uc010qre.1_Silent_p.E172E	NM_014456	NP_055271	Q53EL6	PDCD4_HUMAN	programmed cell death 4 isoform 1	186	MI 1.				apoptosis|cell aging|negative regulation of cell cycle|negative regulation of JUN kinase activity|negative regulation of transcription, DNA-dependent	cytosol|nucleus	protein binding|RNA binding			ovary(1)|breast(1)|skin(1)	3		Breast(234;0.0848)|Lung NSC(174;0.238)		Epithelial(162;0.000526)|all cancers(201;0.00794)|BRCA - Breast invasive adenocarcinoma(275;0.125)		ttGAACAGGAAATGTTAAGAG	0.284													5	200	---	---	---	---	PASS
RAB11FIP2	22841	broad.mit.edu	37	10	119805451	119805451	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:119805451C>T	uc001ldj.1	-	1	664	c.224G>A	c.(223-225)GGA>GAA	p.G75E	RAB11FIP2_uc009xyz.1_Missense_Mutation_p.G75E|CASC2_uc001ldm.3_5'Flank|CASC2_uc009xzc.2_5'Flank|CASC2_uc001ldk.2_5'Flank|CASC2_uc009xza.2_5'Flank|CASC2_uc009xzb.2_5'Flank	NM_014904	NP_055719	Q7L804	RFIP2_HUMAN	RAB11 family interacting protein 2	75	C2.|Necessary for its cellular translocation to the plasma membrane.				protein transport	plasma membrane|recycling endosome membrane	protein homodimerization activity				0		Colorectal(252;0.235)		all cancers(201;0.0238)		CTCTGGACTTCCCTGAATTAG	0.463													90	157	---	---	---	---	PASS
C10orf137	26098	broad.mit.edu	37	10	127412440	127412440	+	Missense_Mutation	SNP	C	A	A			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127412440C>A	uc001liq.1	+	4	738	c.445C>A	c.(445-447)CGC>AGC	p.R149S	C10orf137_uc001lin.2_Missense_Mutation_p.R149S|C10orf137_uc001lio.1_Missense_Mutation_p.R149S|C10orf137_uc001lip.1_5'UTR	NM_015608	NP_056423	Q3B7T1	EDRF1_HUMAN	erythroid differentiation-related factor 1	149					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	binding			ovary(5)|large_intestine(3)|lung(2)	10		all_lung(145;0.0096)|Lung NSC(174;0.0145)|Colorectal(57;0.0846)|all_neural(114;0.0936)				GGCAGTACACCGCATAGGAAG	0.348													4	186	---	---	---	---	PASS
TRIM22	10346	broad.mit.edu	37	11	5729821	5729821	+	Nonsense_Mutation	SNP	C	T	T			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5729821C>T	uc001mbr.2	+	7	1166	c.889C>T	c.(889-891)CAG>TAG	p.Q297*	TRIM5_uc001mbq.1_Intron|TRIM22_uc009yet.1_Nonsense_Mutation_p.Q265*|TRIM22_uc009yes.2_Nonsense_Mutation_p.Q293*|TRIM22_uc010qzm.1_Nonsense_Mutation_p.Q125*|TRIM22_uc009yeu.2_Nonsense_Mutation_p.Q108*|OR56B1_uc001mbs.1_5'UTR|OR56B1_uc009yev.1_5'UTR	NM_006074	NP_006065	Q8IYM9	TRI22_HUMAN	tripartite motif-containing 22	297	B30.2/SPRY.				immune response|interspecies interaction between organisms|protein trimerization|response to virus	Cajal body|Golgi apparatus|nuclear speck	ligase activity|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding				0		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;7.54e-09)|BRCA - Breast invasive adenocarcinoma(625;0.14)		GACAGATGTCCAGTACTACTG	0.403													5	324	---	---	---	---	PASS
OR56A4	120793	broad.mit.edu	37	11	6024124	6024124	+	Silent	SNP	G	A	A			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6024124G>A	uc010qzv.1	-	1	255	c.255C>T	c.(253-255)CCC>CCT	p.P85P		NM_001005179	NP_001005179	Q8NGH8	O56A4_HUMAN	olfactory receptor, family 56, subfamily A,	33	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)|skin(1)	2		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;7.01e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GAAGGCTGAGGGGCAGAGACA	0.582													12	115	---	---	---	---	PASS
DNHD1	144132	broad.mit.edu	37	11	6585252	6585252	+	Silent	SNP	C	T	T			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6585252C>T	uc001mdw.3	+	31	10746	c.10182C>T	c.(10180-10182)TGC>TGT	p.C3394C	DNHD1_uc001mea.3_5'UTR|DNHD1_uc001meb.2_5'Flank|DNHD1_uc001mec.2_5'Flank|DNHD1_uc010rao.1_5'Flank	NM_144666	NP_653267	Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1 isoform 1	3394					microtubule-based movement	dynein complex	microtubule motor activity			ovary(2)	2		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		CCCACAACTGCGTGGCAAAGA	0.582													8	16	---	---	---	---	PASS
MICALCL	84953	broad.mit.edu	37	11	12376331	12376331	+	Missense_Mutation	SNP	G	T	T			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12376331G>T	uc001mkg.1	+	8	2121	c.1830G>T	c.(1828-1830)ATG>ATT	p.M610I		NM_032867	NP_116256	Q6ZW33	MICLK_HUMAN	MICAL C-terminal like	610	Potential.				cell differentiation|multicellular organismal development|spermatogenesis	cytoplasm	mitogen-activated protein kinase binding			skin(1)	1				Epithelial(150;0.00177)		TCTCACCCAGGGCCCAGGAAC	0.403													76	149	---	---	---	---	PASS
STX3	6809	broad.mit.edu	37	11	59560912	59560912	+	Silent	SNP	C	T	T			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59560912C>T	uc001nog.2	+	8	790	c.600C>T	c.(598-600)GAC>GAT	p.D200D	STX3_uc010rkx.1_Silent_p.D200D|STX3_uc010rky.1_Silent_p.D103D|STX3_uc009ymt.1_Silent_p.D103D	NM_004177	NP_004168	Q13277	STX3_HUMAN	syntaxin 3	200	t-SNARE coiled-coil homology.|Cytoplasmic (Potential).				cellular response to oxidative stress|intracellular protein transport|neuron projection development|neurotransmitter transport	apical plasma membrane|azurophil granule|cell-cell junction|growth cone|integral to membrane|plasma membrane enriched fraction|SNARE complex|specific granule	arachidonic acid binding|SNAP receptor activity			ovary(2)	2						GACACAAGGACATTGTGAGGC	0.517													5	112	---	---	---	---	PASS
SUV420H1	51111	broad.mit.edu	37	11	67941331	67941331	+	Missense_Mutation	SNP	A	C	C			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67941331A>C	uc001onm.1	-	6	849	c.593T>G	c.(592-594)TTG>TGG	p.L198W	SUV420H1_uc009yse.1_Translation_Start_Site|SUV420H1_uc001onn.1_Missense_Mutation_p.L26W|SUV420H1_uc009ysf.2_Translation_Start_Site|SUV420H1_uc001ono.1_Missense_Mutation_p.L198W|SUV420H1_uc001onp.2_Missense_Mutation_p.L198W|SUV420H1_uc010rqa.1_Missense_Mutation_p.L175W|SUV420H1_uc001onq.2_Missense_Mutation_p.L198W	NM_017635	NP_060105	Q4FZB7	SV421_HUMAN	suppressor of variegation 4-20 homolog 1 isoform	198	SET.				regulation of transcription, DNA-dependent|transcription, DNA-dependent		protein binding			ovary(2)|kidney(1)	3						ATTACATGGCAATATTTCAAA	0.289													7	564	---	---	---	---	PASS
KIAA0528	9847	broad.mit.edu	37	12	22637818	22637818	+	Nonsense_Mutation	SNP	C	A	A	rs77626615		TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22637818C>A	uc001rfq.2	-	13	1591	c.1363G>T	c.(1363-1365)GAA>TAA	p.E455*	KIAA0528_uc010sir.1_Nonsense_Mutation_p.E270*|KIAA0528_uc010sis.1_Nonsense_Mutation_p.E455*|KIAA0528_uc010sit.1_Nonsense_Mutation_p.E457*|KIAA0528_uc010siu.1_Nonsense_Mutation_p.E455*|KIAA0528_uc001rfr.2_Nonsense_Mutation_p.E446*|KIAA0528_uc009ziy.1_Nonsense_Mutation_p.E457*	NM_014802	NP_055617	Q86YS7	K0528_HUMAN	hypothetical protein LOC9847	455							protein binding			ovary(1)|large_intestine(1)|breast(1)|central_nervous_system(1)	4						AAATTTTCTTCAAGCCtatat	0.264													9	187	---	---	---	---	PASS
ITPR2	3709	broad.mit.edu	37	12	26551917	26551917	+	Missense_Mutation	SNP	T	G	G			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26551917T>G	uc001rhg.2	-	54	8005	c.7588A>C	c.(7588-7590)ATT>CTT	p.I2530L	ITPR2_uc009zjg.1_Missense_Mutation_p.I681L	NM_002223	NP_002214	Q14571	ITPR2_HUMAN	inositol 1,4,5-triphosphate receptor, type 2	2530	Helical; (Potential).				activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity			kidney(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	14	Colorectal(261;0.0847)					AGAACAATAATGATAACAATG	0.313													7	358	---	---	---	---	PASS
STAB2	55576	broad.mit.edu	37	12	104107496	104107496	+	Missense_Mutation	SNP	G	A	A	rs141685549	by1000genomes	TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104107496G>A	uc001tjw.2	+	42	4673	c.4487G>A	c.(4486-4488)CGA>CAA	p.R1496Q	STAB2_uc009zug.2_RNA	NM_017564	NP_060034	Q8WWQ8	STAB2_HUMAN	stabilin 2 precursor	1496	Extracellular (Potential).|EGF-like 12.				angiogenesis|cell adhesion|defense response to bacterium|receptor-mediated endocytosis	cytoplasm|external side of plasma membrane|integral to plasma membrane	Gram-negative bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			ovary(9)|skin(5)	14						CCAGGAAGGCGAGTGTGCACG	0.522													54	78	---	---	---	---	PASS
THSD1P1	374500	broad.mit.edu	37	13	52857470	52857470	+	RNA	SNP	A	G	G			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52857470A>G	uc001vgm.1	-	3		c.224T>C								Homo sapiens cDNA FLJ14630 fis, clone NT2RP2000459.												0						ATGTTAAGTAAATCAGAAAAA	0.318													5	16	---	---	---	---	PASS
SYNE2	23224	broad.mit.edu	37	14	64683102	64683102	+	Silent	SNP	C	G	G			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64683102C>G	uc001xgm.2	+	107	19700	c.19470C>G	c.(19468-19470)CCC>CCG	p.P6490P	SYNE2_uc001xgl.2_Silent_p.P6513P|SYNE2_uc010apy.2_Silent_p.P2875P|SYNE2_uc001xgn.2_Silent_p.P1452P|SYNE2_uc001xgo.2_RNA|SYNE2_uc010aqa.2_Silent_p.P460P|SYNE2_uc001xgq.2_Silent_p.P855P|SYNE2_uc001xgr.2_Silent_p.P273P|SYNE2_uc010tsi.1_Silent_p.P147P|SYNE2_uc001xgs.2_Silent_p.P147P|SYNE2_uc001xgt.2_Silent_p.P21P	NM_015180	NP_055995	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	6490	Cytoplasmic (Potential).				centrosome localization|cytoskeletal anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration	cytoskeleton|filopodium membrane|focal adhesion|integral to membrane|lamellipodium membrane|mitochondrial part|nuclear outer membrane|nucleoplasm|sarcoplasmic reticulum membrane|SUN-KASH complex|Z disc	actin binding|protein binding			ovary(8)|breast(4)|central_nervous_system(1)|pancreas(1)	14				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		ATAAACCACCCTATGTAAGTC	0.473													26	78	---	---	---	---	PASS
SYNJ2BP	55333	broad.mit.edu	37	14	70839819	70839819	+	Missense_Mutation	SNP	A	T	T			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70839819A>T	uc001xmc.3	-	4	454	c.327T>A	c.(325-327)CAT>CAA	p.H109Q	SYNJ2BP_uc010arc.2_RNA	NM_018373	NP_060843	P57105	SYJ2B_HUMAN	synaptojanin 2 binding protein	109	Cytoplasmic (Potential).					integral to membrane|mitochondrial outer membrane					0				all cancers(60;0.00367)|BRCA - Breast invasive adenocarcinoma(234;0.00716)|OV - Ovarian serous cystadenocarcinoma(108;0.0377)		CTTCACCTCGATGTCCTATAG	0.483													33	88	---	---	---	---	PASS
PTPN21	11099	broad.mit.edu	37	14	88983531	88983531	+	Silent	SNP	C	T	T			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88983531C>T	uc001xwv.3	-	3	586	c.255G>A	c.(253-255)AAG>AAA	p.K85K	PTPN21_uc010twc.1_5'UTR|PTPN21_uc010atf.1_Silent_p.K85K	NM_007039	NP_008970	Q16825	PTN21_HUMAN	protein tyrosine phosphatase, non-receptor type	85	FERM.					cytoplasm|cytoskeleton	binding|protein tyrosine phosphatase activity			ovary(3)|skin(1)	4						CCAGCTGCTTCTTCAAAGGTT	0.453													59	144	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106757720	106757720	+	RNA	SNP	T	A	A			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106757720T>A	uc010tyt.1	-	472		c.16345A>T								Parts of antibodies, mostly variable regions.												0						CACCTGGCTTTTGGAGGTGTC	0.527													5	96	---	---	---	---	PASS
WHAMML2	440253	broad.mit.edu	37	15	28986303	28986303	+	RNA	SNP	A	G	G			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28986303A>G	uc010azf.2	+	2		c.651A>G			WHAMML2_uc010uap.1_RNA|WHAMML2_uc010azg.1_RNA|WHAMML2_uc010azh.1_RNA|WHAMML2_uc001zci.1_RNA					Homo sapiens WAS protein homology region 2 domain containing 1-like 2, mRNA (cDNA clone IMAGE:5261987).												0						CATTAATGAAAGTTTACCAAG	0.433													5	121	---	---	---	---	PASS
RYR3	6263	broad.mit.edu	37	15	34156384	34156384	+	Silent	SNP	G	T	T			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34156384G>T	uc001zhi.2	+	103	14581	c.14511G>T	c.(14509-14511)ACG>ACT	p.T4837T	RYR3_uc010bar.2_Silent_p.T4832T	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	4837					cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		CAGAGCACACGGGTCAGGTGA	0.383													6	244	---	---	---	---	PASS
SPG11	80208	broad.mit.edu	37	15	44943831	44943831	+	Silent	SNP	C	T	T			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44943831C>T	uc001ztx.2	-	6	1345	c.1314G>A	c.(1312-1314)CTG>CTA	p.L438L	SPG11_uc010ueh.1_Silent_p.L438L|SPG11_uc010uei.1_Silent_p.L438L|SPG11_uc001zua.1_Silent_p.L438L	NM_025137	NP_079413	Q96JI7	SPTCS_HUMAN	spatacsin isoform 1	438	Extracellular (Potential).				cell death	cytosol|integral to membrane|nucleus	protein binding			ovary(4)|skin(1)	5		all_cancers(109;1.29e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;1.34e-07)|all_lung(180;1.21e-06)|Melanoma(134;0.0122)		all cancers(107;2.93e-22)|GBM - Glioblastoma multiforme(94;1.55e-06)|COAD - Colon adenocarcinoma(120;0.0432)|Colorectal(105;0.0484)|Lung(196;0.104)|LUSC - Lung squamous cell carcinoma(244;0.214)		CCCAAGTAAACAGTGCAGTGA	0.458													5	212	---	---	---	---	PASS
DIS3L	115752	broad.mit.edu	37	15	66618393	66618393	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66618393A>G	uc010ujm.1	+	12	1907	c.1892A>G	c.(1891-1893)AAG>AGG	p.K631R	DIS3L_uc010ujl.1_Missense_Mutation_p.K261R|DIS3L_uc002app.2_Missense_Mutation_p.K548R|DIS3L_uc002apq.2_Missense_Mutation_p.K631R|DIS3L_uc010bho.2_Missense_Mutation_p.K497R	NM_001143688	NP_001137160	Q8TF46	DI3L1_HUMAN	DIS3 mitotic control homolog (S.	631					rRNA catabolic process	cytoplasm|exosome (RNase complex)	exonuclease activity|protein binding|ribonuclease activity|RNA binding			ovary(2)	2						GCAATTGGAAAGCTGACCGAC	0.483													5	106	---	---	---	---	PASS
PDE8A	5151	broad.mit.edu	37	15	85634296	85634296	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85634296A>G	uc002blh.2	+	8	925	c.736A>G	c.(736-738)ACA>GCA	p.T246A	PDE8A_uc002bli.2_Intron|PDE8A_uc010bnc.2_5'UTR|PDE8A_uc010bnd.2_5'UTR|PDE8A_uc002blj.2_Intron|PDE8A_uc002blk.2_Intron	NM_002605	NP_002596	O60658	PDE8A_HUMAN	phosphodiesterase 8A isoform 1	246	PAS.				cyclic nucleotide metabolic process|regulation of transcription, DNA-dependent	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding|two-component response regulator activity			ovary(2)|pancreas(1)|skin(1)	4	Colorectal(223;0.227)		BRCA - Breast invasive adenocarcinoma(143;0.0608)			TGCATTTGAAACAACAATGGG	0.353													6	265	---	---	---	---	PASS
SHISA9	729993	broad.mit.edu	37	16	13329151	13329151	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:13329151G>A	uc010uyy.1	+	5	1605	c.1283G>A	c.(1282-1284)GGC>GAC	p.G428D		NM_001145204	NP_001138676	B4DS77	SHSA9_HUMAN	shisa homolog 9 isoform 1	387	Cytoplasmic (Potential).				regulation of short-term neuronal synaptic plasticity	cell junction|dendritic spine membrane|ionotropic glutamate receptor complex|synapse					0						AGCAACAAGGGCAAGCTTGGC	0.612													32	52	---	---	---	---	PASS
KIAA0556	23247	broad.mit.edu	37	16	27689189	27689189	+	Missense_Mutation	SNP	G	T	T			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27689189G>T	uc002dow.2	+	7	704	c.680G>T	c.(679-681)AGA>ATA	p.R227I	KIAA0556_uc002dox.1_Missense_Mutation_p.R135I	NM_015202	NP_056017	O60303	K0556_HUMAN	hypothetical protein LOC23247	227										ovary(4)|large_intestine(2)|upper_aerodigestive_tract(1)|skin(1)	8						GGCCATCCCAGACATGACCGC	0.557													10	16	---	---	---	---	PASS
KIAA0895L	653319	broad.mit.edu	37	16	67214015	67214015	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67214015C>T	uc002ert.2	-	2	1274	c.499G>A	c.(499-501)GAG>AAG	p.E167K	KIAA0895L_uc002err.2_5'Flank|KIAA0895L_uc002ers.2_5'Flank|KIAA0895L_uc002eru.2_Missense_Mutation_p.E167K|EXOC3L_uc002erv.1_RNA	NM_001040715	NP_001035805	Q68EN5	K895L_HUMAN	hypothetical protein LOC653319	167											0						TCCTGGTACTCAAACTGTGGA	0.577													28	73	---	---	---	---	PASS
ELMO3	79767	broad.mit.edu	37	16	67235520	67235520	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67235520G>A	uc002esa.2	+	10	1095	c.1052G>A	c.(1051-1053)CGG>CAG	p.R351Q	ELMO3_uc002esb.2_Missense_Mutation_p.R334Q|ELMO3_uc002esc.2_Missense_Mutation_p.R185Q	NM_024712	NP_078988	Q96BJ8	ELMO3_HUMAN	engulfment and cell motility 3	298					apoptosis|phagocytosis	cytoplasm|cytoskeleton	SH3 domain binding				0		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00067)|Epithelial(162;0.00442)|all cancers(182;0.0417)		CCGCGCATGCGGACGCCCCTG	0.587													11	21	---	---	---	---	PASS
MYH8	4626	broad.mit.edu	37	17	10299727	10299727	+	Nonsense_Mutation	SNP	G	A	A			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10299727G>A	uc002gmm.2	-	33	4668	c.4573C>T	c.(4573-4575)CAA>TAA	p.Q1525*	uc002gml.1_Intron	NM_002472	NP_002463	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle,	1525	Potential.				muscle filament sliding	cytosol|muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			skin(6)|ovary(3)|breast(2)	11						TCATGAATTTGCTTTCCTCCC	0.408									Trismus-Pseudocamptodactyly_Syndrome_with_Cardiac_Myxoma_and_Freckling				156	332	---	---	---	---	PASS
C17orf79	55352	broad.mit.edu	37	17	30179187	30179187	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30179187T>C	uc002hgp.2	-	4	634	c.526A>G	c.(526-528)ACA>GCA	p.T176A	C17orf79_uc010css.2_RNA	NM_018405	NP_060875	Q9NQ92	COPR5_HUMAN	chromosome 17 open reading frame 79	176					histone H4-R3 methylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	histone binding				0		all_cancers(10;4.54e-07)|all_hematologic(16;0.0216)|Acute lymphoblastic leukemia(14;0.0255)|Myeloproliferative disorder(56;0.0393)|Ovarian(249;0.1)				AACTGTCCTGTTTCAAAGACC	0.517													7	187	---	---	---	---	PASS
CLTC	1213	broad.mit.edu	37	17	57761080	57761080	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57761080G>A	uc002ixq.1	+	27	4729	c.4286G>A	c.(4285-4287)CGG>CAG	p.R1429Q	CLTC_uc002ixp.2_Missense_Mutation_p.R1429Q|CLTC_uc002ixr.1_Missense_Mutation_p.R1433Q	NM_004859	NP_004850	Q00610	CLH1_HUMAN	clathrin heavy chain 1	1429	Heavy chain arm.|Proximal segment.|Involved in binding clathrin light chain (By similarity).				axon guidance|epidermal growth factor receptor signaling pathway|intracellular protein transport|mitosis|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|post-Golgi vesicle-mediated transport|receptor internalization|transferrin transport	clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|cytosol|melanosome|spindle	protein binding|structural molecule activity		CLTC/ALK(44)|CLTC/TFE3(2)	haematopoietic_and_lymphoid_tissue(33)|soft_tissue(11)|kidney(2)|ovary(1)|breast(1)	48	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					CTGTCTCCACGGTTGGATCAC	0.373			T	ALK|TFE3	ALCL|renal 								6	373	---	---	---	---	PASS
HEATR6	63897	broad.mit.edu	37	17	58137396	58137396	+	Missense_Mutation	SNP	G	C	C			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58137396G>C	uc002iyk.1	-	10	1495	c.1478C>G	c.(1477-1479)TCT>TGT	p.S493C	HEATR6_uc010ddk.1_Missense_Mutation_p.S32C|HEATR6_uc010wos.1_Missense_Mutation_p.S325C	NM_022070	NP_071353	Q6AI08	HEAT6_HUMAN	HEAT repeat containing 6	493							binding			ovary(1)|skin(1)	2	all_cancers(5;2.25e-13)|Breast(5;4.84e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		BRCA - Breast invasive adenocarcinoma(1;5.93e-19)|Epithelial(12;7.59e-12)|all cancers(12;1.26e-10)			TTCAGCAACAGAAAGAAACTG	0.433													33	93	---	---	---	---	PASS
KIF19	124602	broad.mit.edu	37	17	72345372	72345372	+	Missense_Mutation	SNP	G	T	T			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72345372G>T	uc002jkm.3	+	10	1235	c.1097G>T	c.(1096-1098)AGC>ATC	p.S366I	KIF19_uc002jkj.2_Missense_Mutation_p.S366I|KIF19_uc002jkk.2_Missense_Mutation_p.S324I|KIF19_uc002jkl.2_Missense_Mutation_p.S324I	NM_153209	NP_694941	Q2TAC6	KIF19_HUMAN	kinesin family member 19	366	Potential.				microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity				0						CAGTACACCAGCATCATCGCT	0.637													11	28	---	---	---	---	PASS
TMEM104	54868	broad.mit.edu	37	17	72787124	72787124	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72787124A>G	uc002jls.3	+	6	538	c.376A>G	c.(376-378)ATC>GTC	p.I126V	TMEM104_uc010wrf.1_Missense_Mutation_p.I126V|TMEM104_uc010wrg.1_Missense_Mutation_p.I139V|TMEM104_uc010dfx.2_Missense_Mutation_p.I126V	NM_017728	NP_060198	Q8NE00	TM104_HUMAN	transmembrane protein 104	126	Cytoplasmic (Potential).					integral to membrane					0	all_lung(278;0.23)					CCCGTTTGAAATCACAGACCG	0.527													5	118	---	---	---	---	PASS
KIAA0802	23255	broad.mit.edu	37	18	8825236	8825236	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8825236C>T	uc002knr.2	+	15	3870	c.3728C>T	c.(3727-3729)CCC>CTC	p.P1243L	KIAA0802_uc002knq.2_Missense_Mutation_p.P1202L|KIAA0802_uc002kns.2_Missense_Mutation_p.P583L	NM_015210	NP_056025	Q9Y4B5	CC165_HUMAN	hypothetical protein LOC23255	1553											0						TGCACCTCCCCCAGGCACTCC	0.662													4	5	---	---	---	---	PASS
SBNO2	22904	broad.mit.edu	37	19	1112193	1112193	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1112193T>C	uc002lrk.3	-	22	2861	c.2623A>G	c.(2623-2625)AGT>GGT	p.S875G	SBNO2_uc002lrj.3_Missense_Mutation_p.S818G|SBNO2_uc010dse.2_Missense_Mutation_p.S858G|SBNO2_uc010xgj.1_Intron	NM_014963	NP_055778	Q9Y2G9	SBNO2_HUMAN	strawberry notch homolog 2 isoform 1	875					macrophage activation involved in immune response|negative regulation of transcription, DNA-dependent|regulation of inflammatory response|transcription, DNA-dependent						0		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|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)		CTCACCAGACTCTCCAGGCGC	0.657													3	9	---	---	---	---	PASS
ACSBG2	81616	broad.mit.edu	37	19	6183057	6183057	+	Missense_Mutation	SNP	A	C	C			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6183057A>C	uc002mef.1	+	10	1323	c.1096A>C	c.(1096-1098)AAT>CAT	p.N366H	ACSBG2_uc002mee.1_Missense_Mutation_p.N179H|ACSBG2_uc002meg.1_Missense_Mutation_p.N366H|ACSBG2_uc002meh.1_Missense_Mutation_p.N366H|ACSBG2_uc002mei.1_Missense_Mutation_p.N316H|ACSBG2_uc010xiz.1_Missense_Mutation_p.N366H	NM_030924	NP_112186	Q5FVE4	ACBG2_HUMAN	bubblegum-related acyl-CoA synthetase 2	366					cell differentiation|fatty acid metabolic process|multicellular organismal development|spermatogenesis	membrane|microsome|mitochondrion	acyl-CoA thioesterase activity|ATP binding|long-chain fatty acid-CoA ligase activity			ovary(1)	1						CAGGAAATATAATACTCCCGT	0.522													17	35	---	---	---	---	PASS
DENND1C	79958	broad.mit.edu	37	19	6467892	6467892	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6467892C>T	uc002mfe.2	-	23	2121	c.2029G>A	c.(2029-2031)GAG>AAG	p.E677K	DENND1C_uc002mfb.2_Missense_Mutation_p.E227K|DENND1C_uc002mfc.2_Missense_Mutation_p.E227K|DENND1C_uc002mfd.2_Missense_Mutation_p.E227K|DENND1C_uc010xje.1_Missense_Mutation_p.E633K	NM_024898	NP_079174	Q8IV53	DEN1C_HUMAN	DENN/MADD domain containing 1C	677						clathrin-coated vesicle|cytosol	guanyl-nucleotide exchange factor activity			large_intestine(1)	1						ATTAGGGGCTCTGTGAGAGGA	0.577													6	115	---	---	---	---	PASS
DNM2	1785	broad.mit.edu	37	19	10935788	10935788	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10935788A>G	uc002mps.1	+	18	2113	c.1949A>G	c.(1948-1950)GAG>GGG	p.E650G	DNM2_uc010dxk.2_Intron|DNM2_uc002mpt.1_Missense_Mutation_p.E650G|DNM2_uc002mpv.1_Missense_Mutation_p.E646G|DNM2_uc002mpu.1_Missense_Mutation_p.E646G|DNM2_uc010dxl.1_Missense_Mutation_p.E650G|DNM2_uc002mpw.2_Missense_Mutation_p.E379G|DNM2_uc002mpx.1_Missense_Mutation_p.E6G	NM_001005361	NP_001005361	P50570	DYN2_HUMAN	dynamin 2 isoform 2	650			E -> K (in ADCNM; COS7 cells show a reduced uptake of transferrin and low- density lipoprotein complex).		G2/M transition of mitotic cell cycle|positive regulation of apoptosis|positive regulation of transcription, DNA-dependent|post-Golgi vesicle-mediated transport|receptor internalization|signal transduction|synaptic vesicle transport|transferrin transport	cell junction|cytosol|Golgi membrane|microtubule|postsynaptic density|postsynaptic membrane	GTP binding|GTPase activity|microtubule binding			central_nervous_system(2)|skin(2)|ovary(1)|breast(1)	6			Epithelial(33;4.17e-05)|all cancers(31;8.48e-05)			CCCCAACTGGAGCGGCAGGTG	0.602													3	8	---	---	---	---	PASS
ZNF91	7644	broad.mit.edu	37	19	23545264	23545264	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23545264T>C	uc002nre.2	-	4	630	c.517A>G	c.(517-519)ACG>GCG	p.T173A	ZNF91_uc010xrj.1_Missense_Mutation_p.T141A	NM_003430	NP_003421	Q05481	ZNF91_HUMAN	zinc finger protein 91	173	C2H2-type 1; degenerate.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)				TGTCTTATCGTATGTCTGTTT	0.308													10	263	---	---	---	---	PASS
PDCD5	9141	broad.mit.edu	37	19	33077874	33077874	+	Intron	SNP	G	T	T			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33077874G>T	uc002ntm.2	+						PDCD5_uc002ntl.2_3'UTR|PDCD5_uc010ede.2_Intron	NM_004708	NP_004699	O14737	PDCD5_HUMAN	programmed cell death 5						apoptosis|induction of apoptosis	cytoplasm|nucleus	DNA binding			ovary(1)|lung(1)	2	Esophageal squamous(110;0.137)					TGAAAAGATGGATACTTTAAA	0.353													58	156	---	---	---	---	PASS
ZNF382	84911	broad.mit.edu	37	19	37117562	37117562	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37117562C>T	uc002oek.2	+	5	876	c.763C>T	c.(763-765)CTC>TTC	p.L255F	ZNF382_uc010efa.2_Missense_Mutation_p.L206F|ZNF382_uc010efb.2_Missense_Mutation_p.L254F|ZNF382_uc002oel.2_Missense_Mutation_p.L254F	NM_032825	NP_116214	Q96SR6	ZN382_HUMAN	zinc finger protein 382	255					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			AAAGTCAAGCCTCAGTGTCCA	0.393													3	46	---	---	---	---	PASS
HKR1	284459	broad.mit.edu	37	19	37854193	37854193	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37854193G>A	uc002ogb.2	+	6	1765	c.1496G>A	c.(1495-1497)TGT>TAT	p.C499Y	HKR1_uc002ofx.2_Missense_Mutation_p.C215Y|HKR1_uc002ofy.2_Missense_Mutation_p.C215Y|HKR1_uc002oga.2_Missense_Mutation_p.C481Y|HKR1_uc010xto.1_Missense_Mutation_p.C481Y|HKR1_uc002ogc.2_Missense_Mutation_p.C480Y|HKR1_uc010xtp.1_Missense_Mutation_p.C438Y|HKR1_uc002ogd.2_Missense_Mutation_p.C438Y	NM_181786	NP_861451	P10072	HKR1_HUMAN	GLI-Kruppel family member HKR1	499	C2H2-type 8.				multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CCATTTGTATGTACGGAGTGT	0.527													20	42	---	---	---	---	PASS
ZNF227	7770	broad.mit.edu	37	19	44740521	44740521	+	Silent	SNP	T	C	C			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44740521T>C	uc002oyu.2	+	6	2143	c.1938T>C	c.(1936-1938)GGT>GGC	p.G646G	ZNF227_uc010xwu.1_Silent_p.G595G|ZNF227_uc002oyv.2_Silent_p.G646G|ZNF227_uc010xwv.1_Silent_p.G595G|ZNF227_uc010xww.1_Silent_p.G567G|ZNF227_uc002oyw.2_Silent_p.G618G|ZNF227_uc010ejh.2_Silent_p.G639G|ZNF235_uc002oyx.1_Intron|ZNF235_uc010eji.2_3'UTR	NM_182490	NP_872296	Q86WZ6	ZN227_HUMAN	zinc finger protein 227	646	C2H2-type 14.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Prostate(69;0.0435)				AGTCCTCTGGTCTTCAATCCC	0.463													10	63	---	---	---	---	PASS
GLTSCR2	29997	broad.mit.edu	37	19	48258011	48258011	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48258011G>A	uc002phm.2	+	8	940	c.916G>A	c.(916-918)GAT>AAT	p.D306N	GLTSCR2_uc002phk.2_Missense_Mutation_p.D306N|GLTSCR2_uc002phl.2_Missense_Mutation_p.D306N|GLTSCR2_uc010elj.2_Missense_Mutation_p.D306N|GLTSCR2_uc010elk.1_RNA|SNORD23_uc010ell.2_5'Flank	NM_015710	NP_056525	Q9NZM5	GSCR2_HUMAN	glioma tumor suppressor candidate region gene 2	306						nucleolus				central_nervous_system(1)	1		all_cancers(25;1.47e-06)|all_lung(116;6.89e-05)|all_epithelial(76;0.000108)|Lung NSC(112;0.000117)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000301)|OV - Ovarian serous cystadenocarcinoma(262;0.00031)|Epithelial(262;0.0149)|GBM - Glioblastoma multiforme(486;0.0278)		GGAGGAGTCGGATGGTGAGGG	0.716													3	9	---	---	---	---	PASS
NOSIP	51070	broad.mit.edu	37	19	50060397	50060397	+	Missense_Mutation	SNP	C	G	G			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50060397C>G	uc002pok.2	-	6	520	c.368G>C	c.(367-369)AGC>ACC	p.S123T	NOSIP_uc002pol.2_Missense_Mutation_p.S123T|NOSIP_uc010yay.1_RNA	NM_015953	NP_057037	Q9Y314	NOSIP_HUMAN	nitric oxide synthase interacting protein	123					negative regulation of nitric-oxide synthase activity|nitric oxide metabolic process	cytosol|nucleus	protein binding			skin(1)	1		all_lung(116;7.84e-06)|Lung NSC(112;2.8e-05)|all_neural(266;0.0966)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00321)|GBM - Glioblastoma multiforme(134;0.0133)		GAGGGGCCGGCTCACGATAGC	0.592													5	11	---	---	---	---	PASS
KLK14	43847	broad.mit.edu	37	19	51585845	51585845	+	Missense_Mutation	SNP	T	G	G			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51585845T>G	uc002pvs.1	-	3	294	c.75A>C	c.(73-75)CAA>CAC	p.Q25H		NM_022046	NP_071329	Q9P0G3	KLK14_HUMAN	kallikrein 14 preproprotein	25					epidermis morphogenesis|fertilization|negative regulation of G-protein coupled receptor protein signaling pathway|positive regulation of G-protein coupled receptor protein signaling pathway|proteolysis|seminal clot liquefaction	extracellular space	serine-type endopeptidase activity			skin(1)	1		all_neural(266;0.0199)		OV - Ovarian serous cystadenocarcinoma(262;0.00328)|GBM - Glioblastoma multiforme(134;0.00422)		TAGCCAGGACTTGAAGTGCTG	0.542													35	180	---	---	---	---	PASS
ZNF600	162966	broad.mit.edu	37	19	53270292	53270292	+	Silent	SNP	A	G	G			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53270292A>G	uc002qab.3	-	3	1003	c.717T>C	c.(715-717)CTT>CTC	p.L239L		NM_198457	NP_940859	Q6ZNG1	ZN600_HUMAN	zinc finger protein 600	239	C2H2-type 3.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				OV - Ovarian serous cystadenocarcinoma(262;0.0241)|GBM - Glioblastoma multiforme(134;0.0404)		CTGCAGTGTGAAGTCTACGAT	0.408													6	172	---	---	---	---	PASS
MBOAT7	79143	broad.mit.edu	37	19	54682431	54682431	+	Intron	SNP	C	A	A			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54682431C>A	uc002qdq.2	-						MBOAT7_uc010erg.2_Intron|MBOAT7_uc010yem.1_Intron|MBOAT7_uc002qdr.2_Intron|MBOAT7_uc002qds.2_Intron|MBOAT7_uc010yen.1_Intron|MBOAT7_uc002qdt.3_3'UTR	NM_024298	NP_077274	Q96N66	MBOA7_HUMAN	membrane bound O-acyltransferase domain						phospholipid biosynthetic process	integral to membrane	acyltransferase activity				0	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					CTGGGGCCTGCTGGGAGATGT	0.502													10	7	---	---	---	---	PASS
LILRA6	79168	broad.mit.edu	37	19	54742661	54742661	+	3'UTR	SNP	A	T	T			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54742661A>T	uc002qeu.1	-	8					LILRB3_uc002qeh.1_Intron|LILRB3_uc002qeg.1_Intron|LILRB3_uc002qei.1_Intron|LILRA6_uc002qek.1_Intron|LILRB3_uc010erh.1_Intron|LILRB3_uc002qej.1_Intron|LILRA6_uc002qel.1_Intron|LILRA6_uc002qem.1_Intron|LILRB3_uc002qen.1_Intron|LILRB3_uc002qeo.1_Intron|LILRB3_uc002qep.1_Intron|LILRB3_uc002qeq.1_Intron|LILRB3_uc002qer.1_Intron|LILRB3_uc002qes.1_Intron|LILRA6_uc010yep.1_Intron|LILRA6_uc010yeq.1_Intron|LILRA6_uc002qet.3_Intron	NM_024318	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor,							integral to membrane	receptor activity			skin(2)	2	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		attggaagtaaggtggagacc	0.219													3	12	---	---	---	---	PASS
NLRP5	126206	broad.mit.edu	37	19	56530712	56530712	+	Missense_Mutation	SNP	T	G	G			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56530712T>G	uc002qmj.2	+	5	570	c.570T>G	c.(568-570)ATT>ATG	p.I190M	NLRP5_uc002qmi.2_Intron	NM_153447	NP_703148	P59047	NALP5_HUMAN	NACHT, LRR and PYD containing protein 5	190						mitochondrion|nucleolus	ATP binding			ovary(3)|skin(2)|kidney(1)|central_nervous_system(1)	7		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0326)		TTGCAGAAATTTCACAAGCTA	0.398													9	263	---	---	---	---	PASS
TBC1D20	128637	broad.mit.edu	37	20	422492	422492	+	Intron	SNP	T	C	C			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:422492T>C	uc002wds.2	-						TBC1D20_uc002wdv.2_5'UTR|TBC1D20_uc002wdt.2_Intron|TBC1D20_uc002wdu.2_Intron	NM_144628	NP_653229	Q96BZ9	TBC20_HUMAN	TBC1 domain family, member 20						interspecies interaction between organisms	integral to membrane|intracellular	Rab GTPase activator activity			central_nervous_system(1)	1		all_epithelial(17;0.228)|Breast(17;0.231)				TGTTCCTCTCTACTGGTACCT	0.527													21	38	---	---	---	---	PASS
REM1	28954	broad.mit.edu	37	20	30064350	30064350	+	Missense_Mutation	SNP	C	G	G			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30064350C>G	uc002wwa.2	+	2	386	c.102C>G	c.(100-102)AGC>AGG	p.S34R		NM_014012	NP_054731	O75628	REM1_HUMAN	RAS-like GTP-binding protein REM	34					small GTPase mediated signal transduction	membrane	calmodulin binding|GTP binding|GTPase activity			lung(2)|pancreas(2)	4	all_cancers(5;0.000119)|Lung NSC(7;1.32e-05)|all_lung(7;2.14e-05)|all_hematologic(12;0.158)|Ovarian(7;0.198)		Colorectal(19;0.00254)|COAD - Colon adenocarcinoma(19;0.0347)			GCCGCCTGAGCACAGTGCCTT	0.642													21	31	---	---	---	---	PASS
CBR1	873	broad.mit.edu	37	21	37443282	37443282	+	Silent	SNP	A	G	G			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37443282A>G	uc002yvb.1	+	2	453	c.324A>G	c.(322-324)GAA>GAG	p.E108E	uc011aea.1_Intron|SETD4_uc002yva.2_Intron|CBR1_uc010gmx.1_Silent_p.E108E|CBR1_uc010gmy.1_Silent_p.E108E	NM_001757	NP_001748	P16152	CBR1_HUMAN	carbonyl reductase 1	108					drug metabolic process|vitamin K metabolic process	cytoplasm	15-hydroxyprostaglandin dehydrogenase (NADP+) activity|carbonyl reductase (NADPH) activity|prostaglandin-E2 9-reductase activity|protein binding				0					Acetohexamide(DB00414)|Lubiprostone(DB01046)	TTCAAGCTGAAGTGACGATGA	0.398													6	272	---	---	---	---	PASS
LIMK2	3985	broad.mit.edu	37	22	31644701	31644701	+	Intron	SNP	A	G	G			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31644701A>G	uc003akh.2	+						LIMK2_uc003akg.2_Intron|LIMK2_uc003aki.2_Intron|LIMK2_uc003akj.2_5'UTR|LIMK2_uc003akk.2_5'UTR|LIMK2_uc011aln.1_5'UTR	NM_005569	NP_005560	P53671	LIMK2_HUMAN	LIM domain kinase 2 isoform 2a							mitochondrion|nucleus	ATP binding|protein serine/threonine kinase activity|zinc ion binding			ovary(2)	2						TGTGGGAAGAAGATGGGGAGT	0.602													5	161	---	---	---	---	PASS
RFPL2	10739	broad.mit.edu	37	22	32587083	32587083	+	Silent	SNP	G	C	C			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32587083G>C	uc003amg.3	-	5	1749	c.813C>G	c.(811-813)ACC>ACG	p.T271T	RFPL2_uc003ame.3_Silent_p.T210T|RFPL2_uc003amf.3_Silent_p.T181T|RFPL2_uc003amh.3_Silent_p.T181T	NM_001098527	NP_001091997	O75678	RFPL2_HUMAN	ret finger protein-like 2 isoform 2	271	B30.2/SPRY.						zinc ion binding			skin(1)	1						CAAGCTCTGTGGTCAGCTGGA	0.587													24	89	---	---	---	---	PASS
NHS	4810	broad.mit.edu	37	X	17746842	17746842	+	Silent	SNP	C	T	T			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:17746842C>T	uc004cxx.2	+	7	4571	c.4233C>T	c.(4231-4233)TTC>TTT	p.F1411F	NHS_uc011mix.1_Silent_p.F1432F|NHS_uc004cxy.2_Silent_p.F1255F|NHS_uc004cxz.2_Silent_p.F1234F|NHS_uc004cya.2_Silent_p.F1134F	NM_198270	NP_938011	Q6T4R5	NHS_HUMAN	Nance-Horan syndrome protein isoform 1	1411						nucleus				skin(3)|ovary(2)|breast(1)|central_nervous_system(1)	7	Hepatocellular(33;0.183)					AGGGTGTGTTCGTGTCTCCAA	0.418													16	13	---	---	---	---	PASS
ARX	170302	broad.mit.edu	37	X	25022841	25022841	+	Missense_Mutation	SNP	C	A	A			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:25022841C>A	uc004dbp.3	-	5	1846	c.1635G>T	c.(1633-1635)CAG>CAT	p.Q545H		NM_139058	NP_620689	Q96QS3	ARX_HUMAN	aristaless related homeobox	545						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						GCTGCGTGAGCTGCGCCGCGT	0.612													2	0	---	---	---	---	PASS
DMD	1756	broad.mit.edu	37	X	31196785	31196785	+	Splice_Site	SNP	C	A	A			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:31196785C>A	uc004dda.1	-	70	10467	c.10223_splice	c.e70+1	p.T3408_splice	DMD_uc004dcq.1_Splice_Site_p.T679_splice|DMD_uc004dcr.1_Intron|DMD_uc004dcs.1_Splice_Site_p.T948_splice|DMD_uc004dct.1_Splice_Site_p.T948_splice|DMD_uc004dcu.1_Splice_Site_p.T948_splice|DMD_uc004dcv.1_Splice_Site_p.T948_splice|DMD_uc004dcw.2_Splice_Site_p.T2064_splice|DMD_uc004dcx.2_Splice_Site_p.T2067_splice|DMD_uc004dcz.2_Splice_Site_p.T3285_splice|DMD_uc004dcy.1_Splice_Site_p.T3404_splice|DMD_uc004ddb.1_Splice_Site_p.T3400_splice|DMD_uc004dcm.1_Splice_Site_p.T340_splice|DMD_uc004dcn.1_Splice_Site_p.T340_splice|DMD_uc004dco.1_Splice_Site_p.T340_splice|DMD_uc004dcp.1_Splice_Site_p.T340_splice|DMD_uc011mkb.1_Splice_Site_p.T340_splice|DMD_uc010ngm.2_Silent_p.T340T	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)				CTACTACTCACGTTTCCATGT	0.438													80	61	---	---	---	---	PASS
SLC35A2	7355	broad.mit.edu	37	X	48762340	48762340	+	Silent	SNP	C	T	T			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48762340C>T	uc004dlo.1	-	4	850	c.846G>A	c.(844-846)GGG>GGA	p.G282G	SLC35A2_uc011mml.1_Silent_p.G295G|SLC35A2_uc004dlp.1_Silent_p.G282G|SLC35A2_uc011mmm.1_Silent_p.G310G|SLC35A2_uc011mmn.1_Silent_p.G221G|SLC35A2_uc004dlr.1_Missense_Mutation_p.G136D|SLC35A2_uc004dlq.2_Intron	NM_005660	NP_005651	P78381	S35A2_HUMAN	solute carrier family 35, member A2 isoform a	282	Helical; (Potential).				galactose metabolic process	Golgi membrane|integral to membrane|nucleus	sugar:hydrogen symporter activity|UDP-galactose transmembrane transporter activity			breast(1)	1						CCACCAGTAGCCCGCCGAAGG	0.597													6	7	---	---	---	---	PASS
VSIG4	11326	broad.mit.edu	37	X	65252420	65252420	+	Missense_Mutation	SNP	G	A	A	rs139911916		TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:65252420G>A	uc004dwh.2	-	3	711	c.584C>T	c.(583-585)ACC>ATC	p.T195I	VSIG4_uc004dwi.2_Intron|VSIG4_uc010nkq.1_Missense_Mutation_p.T195I|VSIG4_uc004dwj.2_Missense_Mutation_p.T195I|VSIG4_uc011moy.1_Intron|VSIG4_uc004dwk.2_Missense_Mutation_p.T195I|VSIG4_uc004dwl.2_Missense_Mutation_p.T91I	NM_007268	NP_009199	Q9Y279	VSIG4_HUMAN	V-set and immunoglobulin domain containing 4	195	Ig-like 2.|Extracellular (Potential).				complement activation, alternative pathway	integral to membrane	protein binding				0						GAAGAGTAAGGTACTTAGGGT	0.498													17	165	---	---	---	---	PASS
DCAF12L1	139170	broad.mit.edu	37	X	125685459	125685459	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:125685459C>T	uc004eul.2	-	1	1384	c.1133G>A	c.(1132-1134)CGG>CAG	p.R378Q		NM_178470	NP_848565	Q5VU92	DC121_HUMAN	DDB1 and CUL4 associated factor 12-like 1	378	WD 4.									skin(3)|ovary(1)	4						TTTCTGGGCCCGGACGTCATA	0.627													10	3	---	---	---	---	PASS
ZNF280C	55609	broad.mit.edu	37	X	129339369	129339369	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129339369A>G	uc004evm.2	-	17	2217	c.2063T>C	c.(2062-2064)CTT>CCT	p.L688P		NM_017666	NP_060136	Q8ND82	Z280C_HUMAN	zinc finger protein 280C	688					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(2)|ovary(1)	3						ATCACATTTAAGGCACACTAG	0.333													8	174	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	6924	6924	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:6924G>A	uc011mfh.1	+	1	1071	c.23G>A	c.(22-24)AGC>AAC	p.S8N	uc004cou.3_5'Flank|uc011mfi.1_5'Flank					Homo sapiens cDNA: FLJ22894 fis, clone KAT04907.																		CAGTGCTCTGAGCCCTAGGAT	0.483													11	29	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	12940	12940	+	RNA	SNP	G	A	A			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:12940G>A	uc004cox.3	+	1		c.604G>A			uc004coy.2_5'Flank					Homo sapiens NADH dehydrogenase subunit 5 (MTND5) mRNA, RNA 5, complete cds; mitochondrial gene for mitochondrial product.																		CACAACAAATAGCCCTTCTAA	0.507													3	42	---	---	---	---	PASS
KAZ	23254	broad.mit.edu	37	1	15440945	15440945	+	Intron	SNP	G	T	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15440945G>T	uc001avm.3	+						C1orf126_uc001avv.3_RNA|C1orf126_uc009voh.2_RNA|KAZ_uc001avs.3_Intron	NM_201628	NP_963922	Q674X7	KAZRN_HUMAN	kazrin isoform E						keratinization	cornified envelope|cytoplasm|desmosome|nucleus					0						CCTGTCCTTTGATCATATTCT	0.358													3	16	---	---	---	---	PASS
NBPF1	55672	broad.mit.edu	37	1	16918727	16918727	+	5'UTR	SNP	G	C	C			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16918727G>C	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)		CGAGGTGCCTGAACTCAGAGC	0.463													3	32	---	---	---	---	PASS
CDC42	998	broad.mit.edu	37	1	22417987	22417987	+	Missense_Mutation	SNP	A	T	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22417987A>T	uc001bfq.2	+	7	845	c.553A>T	c.(553-555)AGC>TGC	p.S185C	CDC42_uc001bfr.2_Missense_Mutation_p.S185C|CDC42_uc010odr.1_Missense_Mutation_p.S230C|CDC42_uc010ods.1_Missense_Mutation_p.S227C|CDC42_uc009vqh.2_Missense_Mutation_p.S144C	NM_001039802	NP_001034891	P60953	CDC42_HUMAN	cell division cycle 42 isoform 1	185					actin cytoskeleton organization|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|establishment or maintenance of cell polarity|macrophage differentiation|muscle cell differentiation|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of protein complex assembly|positive regulation of muscle cell differentiation|positive regulation of pseudopodium assembly|regulation of filopodium assembly|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction|T cell costimulation	cytosol|filopodium|plasma membrane	GTP binding|GTPase activity|protein binding|thioesterase binding			haematopoietic_and_lymphoid_tissue(1)	1		Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;6.55e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)|Prostate(1639;0.0792)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0452)|OV - Ovarian serous cystadenocarcinoma(117;7.32e-26)|Colorectal(126;1.35e-07)|COAD - Colon adenocarcinoma(152;7.73e-06)|GBM - Glioblastoma multiforme(114;8.62e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000649)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00767)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.207)		ACCGAAGAAGAGCCGCAGGTG	0.453													12	58	---	---	---	---	PASS
PTPRF	5792	broad.mit.edu	37	1	44087698	44087698	+	3'UTR	SNP	A	C	C			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44087698A>C	uc001cjr.2	+	34					PTPRF_uc001cjs.2_3'UTR|PTPRF_uc001cju.2_3'UTR|PTPRF_uc009vwt.2_3'UTR|PTPRF_uc001cjv.2_3'UTR|PTPRF_uc001cjw.2_3'UTR	NM_002840	NP_002831	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F						transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|skin(3)|lung(1)|kidney(1)|central_nervous_system(1)	10	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				CTCCTCCGCCACCCCCGCCGT	0.652													8	16	---	---	---	---	PASS
KDM4A	9682	broad.mit.edu	37	1	44128741	44128741	+	Silent	SNP	T	C	C			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44128741T>C	uc001cjx.2	+	5	772	c.606T>C	c.(604-606)TTT>TTC	p.F202F	KDM4A_uc010oki.1_Silent_p.F202F	NM_014663	NP_055478	O75164	KDM4A_HUMAN	jumonji domain containing 2A	202	JmjC.				interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	centrosome|nucleolus	histone demethylase activity (H3-K36 specific)|nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|zinc ion binding			skin(1)	1						ACCTGCACTTTGGAGAACCAA	0.453													60	162	---	---	---	---	PASS
TMEM69	51249	broad.mit.edu	37	1	46156752	46156752	+	Silent	SNP	C	T	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46156752C>T	uc001cor.1	+	2	208	c.12C>T	c.(10-12)TTC>TTT	p.F4F		NM_016486	NP_057570	Q5SWH9	TMM69_HUMAN	transmembrane protein 69	4						integral to membrane				ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)					TGCTTCGCTTCATCCAGAAGT	0.308													28	81	---	---	---	---	PASS
LRRC7	57554	broad.mit.edu	37	1	70502282	70502282	+	Missense_Mutation	SNP	G	C	C			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70502282G>C	uc001dep.2	+	18	2179	c.2149G>C	c.(2149-2151)GTA>CTA	p.V717L	LRRC7_uc009wbg.2_Intron|LRRC7_uc001deq.2_5'UTR	NM_020794	NP_065845	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	717						centrosome|focal adhesion|nucleolus	protein binding			ovary(9)|breast(2)|central_nervous_system(2)|liver(1)	14						TAAAGATGCAGTACATAATTC	0.423													11	194	---	---	---	---	PASS
LOC400759	400759	broad.mit.edu	37	1	89890132	89890132	+	RNA	SNP	G	A	A			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89890132G>A	uc009wcy.1	+	5		c.873G>A				NR_003133				Homo sapiens cDNA, FLJ17004.												0						TTGCTTACTTGTACTTTTCAA	0.453													8	35	---	---	---	---	PASS
LPPR5	163404	broad.mit.edu	37	1	99380412	99380412	+	Missense_Mutation	SNP	T	A	A			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:99380412T>A	uc001dsb.2	-	5	1085	c.863A>T	c.(862-864)AAT>ATT	p.N288I	LPPR5_uc001dsc.2_Missense_Mutation_p.N288I	NM_001037317	NP_001032394	Q32ZL2	LPPR5_HUMAN	phosphatidic acid phosphatase type 2d isoform 1	288						integral to membrane	hydrolase activity				0						CTGTGCCAGATTATCCATGTG	0.358													8	238	---	---	---	---	PASS
DCLRE1B	64858	broad.mit.edu	37	1	114454032	114454032	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114454032A>G	uc001eeg.2	+	4	989	c.818A>G	c.(817-819)TAC>TGC	p.Y273C	DCLRE1B_uc001eeh.2_Missense_Mutation_p.Y147C|DCLRE1B_uc001eei.2_Missense_Mutation_p.Y147C	NM_022836	NP_073747	Q9H816	DCR1B_HUMAN	DNA cross-link repair 1B (PSO2 homolog, S.	273					cell cycle checkpoint|DNA repair|protection from non-homologous end joining at telomere|telomeric 3' overhang formation|telomeric loop formation	centrosome|chromosome, telomeric region|nucleus	5'-3' exonuclease activity|protein binding				0	Lung SC(450;0.184)	all_cancers(81;1.46e-05)|all_epithelial(167;2.42e-05)|all_lung(203;0.000353)|Lung NSC(69;0.000518)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		GTCATCCCTTACTCTGACCAT	0.552								Direct_reversal_of_damage|Other_identified_genes_with_known_or_suspected_DNA_repair_function					5	165	---	---	---	---	PASS
BCL9	607	broad.mit.edu	37	1	147091647	147091647	+	Silent	SNP	C	T	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:147091647C>T	uc001epq.2	+	8	2426	c.1686C>T	c.(1684-1686)CTC>CTT	p.L562L	BCL9_uc010ozr.1_Silent_p.L488L	NM_004326	NP_004317	O00512	BCL9_HUMAN	B-cell CLL/lymphoma 9	562	Pro-rich.				Wnt receptor signaling pathway	nucleus	protein binding			ovary(2)|large_intestine(2)|breast(1)|skin(1)	6	all_hematologic(923;0.115)					AGATGCGCCTCCCTGGATTTG	0.557			T	IGH@|IGL@	B-ALL								7	218	---	---	---	---	PASS
LASS2	29956	broad.mit.edu	37	1	150939585	150939585	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150939585T>C	uc001evy.2	-	8	1093	c.706A>G	c.(706-708)ATG>GTG	p.M236V	LASS2_uc001evz.2_Missense_Mutation_p.M236V|LASS2_uc009wmh.2_Missense_Mutation_p.M86V	NM_181746	NP_859530	Q96G23	CERS2_HUMAN	LAG1 longevity assurance 2	236	Lumenal (Potential).|TLC.					endoplasmic reticulum membrane|integral to membrane|nuclear membrane	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sphingosine N-acyltransferase activity				0	all_lung(15;8.07e-35)|Lung NSC(24;7.93e-31)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			TGCAGAGCCATGATTAGAGTC	0.488													46	96	---	---	---	---	PASS
RYR2	6262	broad.mit.edu	37	1	237895427	237895427	+	Silent	SNP	C	A	A			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237895427C>A	uc001hyl.1	+	78	11137	c.11017C>A	c.(11017-11019)CGG>AGG	p.R3673R	RYR2_uc010pya.1_Silent_p.R69R	NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	3673					cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			TCTGTTTAGTCGGACAGCTTT	0.443													33	70	---	---	---	---	PASS
ZNF238	10472	broad.mit.edu	37	1	244218338	244218338	+	Missense_Mutation	SNP	G	T	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244218338G>T	uc001iae.2	+	1	1757	c.1235G>T	c.(1234-1236)TGC>TTC	p.C412F	ZNF238_uc001iad.3_Missense_Mutation_p.C421F|ZNF238_uc001iaf.1_3'UTR	NM_006352	NP_006343	Q99592	ZN238_HUMAN	zinc finger protein 238 isoform 2	412	C2H2-type 2.|Interaction with DNMT3A.				negative regulation of transcription from RNA polymerase II promoter|skeletal muscle tissue development	nuclear chromosome	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)|pancreas(2)	5	all_cancers(71;6.42e-05)|all_epithelial(71;7e-05)|Breast(184;0.0333)|Ovarian(71;0.0619)|all_lung(81;0.089)|all_neural(11;0.101)|Lung NSC(105;0.123)		all cancers(7;1.35e-08)|GBM - Glioblastoma multiforme(7;1e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00223)			GTGCCCACGTGCTCGCTGTGT	0.632													49	80	---	---	---	---	PASS
MYT1L	23040	broad.mit.edu	37	2	1926721	1926721	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1926721C>T	uc002qxe.2	-	10	1647	c.820G>A	c.(820-822)GTT>ATT	p.V274I	MYT1L_uc002qxd.2_Missense_Mutation_p.V274I|MYT1L_uc010ewl.1_RNA	NM_015025	NP_055840	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	274					cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|central_nervous_system(1)	6	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)		GAGAGCACAACACCGTGTCCT	0.428													108	211	---	---	---	---	PASS
GTF2A1L	11036	broad.mit.edu	37	2	48960052	48960052	+	Silent	SNP	G	A	A			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48960052G>A	uc002rwt.2	+	9	1416	c.1350G>A	c.(1348-1350)TCG>TCA	p.S450S	LHCGR_uc002rwu.3_Intron|LHCGR_uc002rwv.2_Intron	NM_172196	NP_751946	Q9UNN4	TF2AY_HUMAN	general transcription factor IIA, 1-like isoform	Error:Variant_position_missing_in_Q9UNN4_after_alignment					regulation of transcription, DNA-dependent|transcription initiation from RNA polymerase II promoter	transcription factor TFIIA complex	DNA binding|transcription coactivator activity				0		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			GAAGGACATCGTTTAACACCT	0.244													63	139	---	---	---	---	PASS
ASTL	431705	broad.mit.edu	37	2	96803405	96803405	+	Silent	SNP	G	A	A			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96803405G>A	uc010yui.1	-	2	90	c.90C>T	c.(88-90)TGC>TGT	p.C30C		NM_001002036	NP_001002036	Q6HA08	ASTL_HUMAN	astacin-like metalloendopeptidase precursor	30					proteolysis		metalloendopeptidase activity|zinc ion binding				0						AGGCTCCTGCGCAGCTGGAGG	0.627													7	172	---	---	---	---	PASS
MAP4K4	9448	broad.mit.edu	37	2	102505356	102505356	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102505356A>G	uc002tbg.2	+	29	3650	c.3595A>G	c.(3595-3597)AGG>GGG	p.R1199G	MAP4K4_uc002tbc.2_Missense_Mutation_p.R1280G|MAP4K4_uc002tbd.2_Missense_Mutation_p.R1172G|MAP4K4_uc002tbe.2_Missense_Mutation_p.R1126G|MAP4K4_uc002tbf.2_Missense_Mutation_p.R1233G|MAP4K4_uc010yvy.1_Missense_Mutation_p.R1195G|MAP4K4_uc002tbh.2_Missense_Mutation_p.R1125G|MAP4K4_uc002tbi.2_Missense_Mutation_p.R1002G|MAP4K4_uc010yvz.1_Missense_Mutation_p.R1239G|MAP4K4_uc002tbk.2_Missense_Mutation_p.R654G|MAP4K4_uc002tbl.2_Missense_Mutation_p.R385G	NM_145687	NP_663720	O95819	M4K4_HUMAN	mitogen-activated protein kinase kinase kinase	1199	CNH.|Mediates interaction with RAP2A.				intracellular protein kinase cascade|regulation of JNK cascade|response to stress	cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			stomach(1)|lung(1)|central_nervous_system(1)|skin(1)	4						CATGCACAAAAGGGCTCAAAG	0.403													3	50	---	---	---	---	PASS
PABPC1P2	728773	broad.mit.edu	37	2	147345348	147345348	+	5'UTR	SNP	G	A	A			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:147345348G>A	uc002twf.3	+	1						NR_026904				RecName: Full=Putative protein PABPC1-like; AltName: Full=Polyadenylate-binding protein pseudogene 2;												0						GCGATCTATCGCTGCGCAAAA	0.493													8	13	---	---	---	---	PASS
DNAH7	56171	broad.mit.edu	37	2	196723250	196723250	+	Missense_Mutation	SNP	G	T	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196723250G>T	uc002utj.3	-	43	8116	c.8015C>A	c.(8014-8016)GCC>GAC	p.A2672D		NM_018897	NP_061720	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	2672	Stalk (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			skin(10)|ovary(2)	12						TATTGGCAAGGCACCTGCCAG	0.453													7	76	---	---	---	---	PASS
CFLAR	8837	broad.mit.edu	37	2	201994484	201994484	+	5'UTR	SNP	T	C	C			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201994484T>C	uc002uxb.3	+	2					CFLAR_uc002uwy.2_5'UTR|CFLAR_uc002uwz.2_5'UTR|CFLAR_uc002uxa.3_5'UTR|CFLAR_uc010zhk.1_Intron|CFLAR_uc002uxc.3_5'UTR|CFLAR_uc010zhl.1_Intron|CFLAR_uc010fsw.1_RNA|CFLAR_uc002uxd.3_5'UTR|CFLAR_uc002uxe.2_5'UTR|CFLAR_uc002uxf.2_5'UTR|CFLAR_uc010fsy.2_RNA|CFLAR_uc010fsx.2_5'UTR	NM_003879	NP_003870	O15519	CFLAR_HUMAN	CASP8 and FADD-like apoptosis regulator isoform						anti-apoptosis|apoptosis|induction of apoptosis by extracellular signals|interspecies interaction between organisms|positive regulation of I-kappaB kinase/NF-kappaB cascade|proteolysis		cysteine-type endopeptidase activity|protein binding				0						CTGAAAGAAATGAAGTCAGCC	0.443													38	62	---	---	---	---	PASS
ABCA12	26154	broad.mit.edu	37	2	215815770	215815770	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215815770C>T	uc002vew.2	-	45	6905	c.6685G>A	c.(6685-6687)GAG>AAG	p.E2229K	ABCA12_uc002vev.2_Missense_Mutation_p.E1911K|ABCA12_uc010zjn.1_Missense_Mutation_p.E1156K	NM_173076	NP_775099	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A, member 12	2229					cellular homeostasis|lipid transport	integral to membrane	ATP binding|ATPase activity			ovary(6)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	11		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		TCTATTGTCTCCCTTACATGT	0.373													7	249	---	---	---	---	PASS
ACCN4	55515	broad.mit.edu	37	2	220401850	220401850	+	Missense_Mutation	SNP	G	T	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220401850G>T	uc002vma.2	+	6	1630	c.1616G>T	c.(1615-1617)CGA>CTA	p.R539L	ACCN4_uc002vlz.2_Missense_Mutation_p.R558L|ACCN4_uc002vmb.2_Missense_Mutation_p.R212L	NM_182847	NP_878267	Q96FT7	ACCN4_HUMAN	amiloride-sensitive cation channel 4 isoform 2	539	Extracellular (Potential).					integral to plasma membrane	sodium channel activity|sodium ion transmembrane transporter activity			ovary(2)	2		Renal(207;0.0183)		Epithelial(149;5.47e-10)|all cancers(144;9e-08)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.0086)|READ - Rectum adenocarcinoma(5;0.156)		ATGGAGCAGCGAGCAGCCTAT	0.627													3	82	---	---	---	---	PASS
KIF1A	547	broad.mit.edu	37	2	241660401	241660401	+	Missense_Mutation	SNP	C	A	A			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241660401C>A	uc002vzy.2	-	43	4641	c.4495G>T	c.(4495-4497)GTG>TTG	p.V1499L	KIF1A_uc010fzk.2_Missense_Mutation_p.V1600L|KIF1A_uc002vzw.2_Missense_Mutation_p.V160L|KIF1A_uc002vzx.2_Missense_Mutation_p.V226L	NM_004321	NP_004312	Q12756	KIF1A_HUMAN	axonal transport of synaptic vesicles	1499					anterograde axon cargo transport	cytoplasm|microtubule|nucleus	ATP binding|microtubule motor activity			lung(1)	1		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176)		AGAGTGGCCACCCCTAGAGGG	0.647													4	18	---	---	---	---	PASS
SLC4A7	9497	broad.mit.edu	37	3	27451006	27451006	+	Silent	SNP	C	T	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27451006C>T	uc003cdv.2	-	13	1826	c.1755G>A	c.(1753-1755)TTG>TTA	p.L585L	SLC4A7_uc011awu.1_Intron|SLC4A7_uc011awv.1_Intron|SLC4A7_uc003cdu.3_Silent_p.L466L|SLC4A7_uc011aww.1_Silent_p.L594L|SLC4A7_uc011awx.1_Silent_p.L581L|SLC4A7_uc011awy.1_Silent_p.L577L|SLC4A7_uc011awz.1_Intron|SLC4A7_uc011axa.1_Silent_p.L466L|SLC4A7_uc011axb.1_Silent_p.L581L|SLC4A7_uc010hfl.2_Silent_p.L135L|SLC4A7_uc003cdw.2_Silent_p.L461L	NM_003615	NP_003606	Q9Y6M7	S4A7_HUMAN	solute carrier family 4, sodium bicarbonate	585	Extracellular (Potential).					apical plasma membrane|basolateral plasma membrane|integral to membrane|stereocilium	inorganic anion exchanger activity|protein binding|sodium:bicarbonate symporter activity			ovary(3)|central_nervous_system(1)|skin(1)	5						TGTCAAGTATCAAACCACCAA	0.408													15	90	---	---	---	---	PASS
C3orf45	132228	broad.mit.edu	37	3	50324620	50324620	+	Missense_Mutation	SNP	A	T	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50324620A>T	uc003cyz.2	+	4	509	c.482A>T	c.(481-483)CAA>CTA	p.Q161L		NM_153215	NP_694947	Q8N112	CC045_HUMAN	hypothetical protein LOC132228	161						integral to membrane				ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		AGTGAGGCCCAAGCACCCAGC	0.612													28	27	---	---	---	---	PASS
GLYCTK	132158	broad.mit.edu	37	3	52324497	52324497	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52324497G>A	uc003ddo.2	+	2	235	c.139G>A	c.(139-141)GGT>AGT	p.G47S	GLYCTK_uc003ddq.2_Missense_Mutation_p.G47S|GLYCTK_uc003ddm.2_Intron|GLYCTK_uc003ddn.2_RNA|GLYCTK_uc003ddp.1_Missense_Mutation_p.G47S|GLYCTK_uc003ddr.2_5'Flank	NM_145262	NP_660305	Q8IVS8	GLCTK_HUMAN	glycerate kinase isoform 1	47					protein phosphorylation	Golgi apparatus|mitochondrion	ATP binding|glycerate kinase activity|protein binding				0				BRCA - Breast invasive adenocarcinoma(193;3.56e-05)|Kidney(197;0.00171)|KIRC - Kidney renal clear cell carcinoma(197;0.00194)|OV - Ovarian serous cystadenocarcinoma(275;0.235)		GAGTGCTGTAGGTGCAGTGCT	0.642													19	34	---	---	---	---	PASS
ALCAM	214	broad.mit.edu	37	3	105243461	105243461	+	Intron	SNP	C	A	A			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:105243461C>A	uc003dvx.2	+						ALCAM_uc003dvv.2_3'UTR|ALCAM_uc003dvw.1_Intron|ALCAM_uc003dvy.2_Intron|ALCAM_uc011bhh.1_Intron	NM_001627	NP_001618	Q13740	CD166_HUMAN	activated leukocyte cell adhesion molecule						cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(2)|breast(1)	3						TAGCAGGTATCTATATAAGGG	0.388													3	31	---	---	---	---	PASS
RUFY3	22902	broad.mit.edu	37	4	71648807	71648807	+	Splice_Site	SNP	G	T	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71648807G>T	uc003hfq.2	+	9	1490	c.895_splice	c.e9-1	p.L299_splice	RUFY3_uc003hfp.3_Splice_Site_p.L359_splice|RUFY3_uc011cax.1_Splice_Site_p.L317_splice|RUFY3_uc003hfr.2_Splice_Site_p.L299_splice|RUFY3_uc011cay.1_Splice_Site_p.L235_splice	NM_014961	NP_055776	Q7L099	RUFY3_HUMAN	RUN and FYVE domain containing 3 isoform 2						negative regulation of axonogenesis	filopodium|growth cone					0		all_hematologic(202;0.248)	Lung(101;0.235)			tttatCCACAGCTTGCAGTTG	0.308													22	41	---	---	---	---	PASS
PF4	5196	broad.mit.edu	37	4	74847209	74847209	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:74847209G>A	uc003hhi.2	-	2	188	c.143C>T	c.(142-144)TCC>TTC	p.S48F		NM_002619	NP_002610	P02776	PLF4_HUMAN	platelet factor 4 (chemokine (C-X-C motif)	48					cytokine-mediated signaling pathway|immune response|leukocyte chemotaxis|negative regulation of angiogenesis|negative regulation of apoptosis|negative regulation of cytolysis|negative regulation of megakaryocyte differentiation|negative regulation of MHC class II biosynthetic process|platelet activation|platelet degranulation|positive regulation of gene expression|positive regulation of macrophage derived foam cell differentiation|positive regulation of macrophage differentiation|positive regulation of tumor necrosis factor production	extracellular space|platelet alpha granule lumen	chemokine activity|heparin binding				0	Breast(15;0.00136)		all cancers(17;0.0034)|Lung(101;0.196)		Drotrecogin alfa(DB00055)	ACGGACCTGGGAGGTGGTCTT	0.602													6	67	---	---	---	---	PASS
PTPN13	5783	broad.mit.edu	37	4	87696460	87696460	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87696460C>T	uc003hpz.2	+	34	6125	c.5645C>T	c.(5644-5646)CCG>CTG	p.P1882L	PTPN13_uc003hpy.2_Missense_Mutation_p.P1887L|PTPN13_uc003hqa.2_Missense_Mutation_p.P1863L|PTPN13_uc003hqb.2_Missense_Mutation_p.P1691L|PTPN13_uc003hqc.1_Missense_Mutation_p.P248L	NM_080683	NP_542414	Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type	1882	PDZ 5.					cytoplasm|cytoskeleton|plasma membrane	protein binding|protein binding|protein tyrosine phosphatase activity			ovary(4)|breast(1)|kidney(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		CATTTGCTACCGGACATAACA	0.383													26	66	---	---	---	---	PASS
MAD2L1	4085	broad.mit.edu	37	4	120981284	120981284	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:120981284C>T	uc003idl.2	-	5	731	c.607G>A	c.(607-609)GTC>ATC	p.V203I	MAD2L1_uc003idm.2_3'UTR	NM_002358	NP_002349	Q13257	MD2L1_HUMAN	MAD2-like 1	203	Required for assuming the closed conformation and for interaction with CDC20.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|negative regulation of apoptosis|negative regulation of mitotic anaphase-promoting complex activity|positive regulation of mitotic cell cycle spindle assembly checkpoint	condensed chromosome kinetochore|cytosol|nucleus|perinuclear region of cytoplasm	protein homodimerization activity				0						CAGTCATTGACAGGAATTTTG	0.353													37	139	---	---	---	---	PASS
TMEM184C	55751	broad.mit.edu	37	4	148545115	148545115	+	Missense_Mutation	SNP	G	C	C			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:148545115G>C	uc003ila.3	+	2	823	c.254G>C	c.(253-255)AGG>ACG	p.R85T		NM_018241	NP_060711	Q9NVA4	T184C_HUMAN	transmembrane protein 184C	85						integral to membrane					0						CCAATAATAAGGTATGTCTTA	0.308													44	108	---	---	---	---	PASS
ADAM29	11086	broad.mit.edu	37	4	175898846	175898846	+	Nonsense_Mutation	SNP	C	T	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:175898846C>T	uc003iuc.2	+	5	2840	c.2170C>T	c.(2170-2172)CGA>TGA	p.R724*	ADAM29_uc003iud.2_Nonsense_Mutation_p.R724*|ADAM29_uc010irr.2_Nonsense_Mutation_p.R724*|ADAM29_uc011cki.1_Nonsense_Mutation_p.R724*	NM_014269	NP_055084	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29 preproprotein	724	Cytoplasmic (Potential).				proteolysis|spermatogenesis	integral to plasma membrane	metalloendopeptidase activity|zinc ion binding			skin(5)|central_nervous_system(3)|ovary(3)|large_intestine(2)|lung(2)|pancreas(1)	16		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		AATTCAGCGTCGACCTCATGA	0.438													45	79	---	---	---	---	PASS
CDH18	1016	broad.mit.edu	37	5	19520813	19520813	+	Missense_Mutation	SNP	C	A	A			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19520813C>A	uc003jgc.2	-	9	1842	c.1465G>T	c.(1465-1467)GCC>TCC	p.A489S	CDH18_uc003jgd.2_Missense_Mutation_p.A489S|CDH18_uc011cnm.1_Missense_Mutation_p.A489S	NM_004934	NP_004925	Q13634	CAD18_HUMAN	cadherin 18, type 2 preproprotein	489	Extracellular (Potential).|Cadherin 5.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|large_intestine(1)|skin(1)	7	Lung NSC(1;0.00734)|all_lung(1;0.0197)					TATTCCCTGGCAAGTTCGGGT	0.393													56	146	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	5	23980775	23980775	+	RNA	SNP	G	A	A			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:23980775G>A	uc003jgq.1	+	4		c.1382G>A								Homo sapiens cDNA FLJ34836 fis, clone NT2NE2010400.																		AGGAGATAGAGGTGGCACCCC	0.512													3	8	---	---	---	---	PASS
FNIP1	96459	broad.mit.edu	37	5	131008580	131008580	+	Missense_Mutation	SNP	T	G	G			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131008580T>G	uc003kvs.1	-	14	1699	c.1557A>C	c.(1555-1557)TTA>TTC	p.L519F	RAPGEF6_uc003kvp.1_Intron|FNIP1_uc003kvt.1_Missense_Mutation_p.L491F|FNIP1_uc010jdm.1_Missense_Mutation_p.L474F	NM_133372	NP_588613	Q8TF40	FNIP1_HUMAN	folliculin interacting protein 1 isoform 1	519					regulation of protein phosphorylation	cytoplasm	protein binding			pancreas(1)|skin(1)	2		all_cancers(142;0.00347)|Lung NSC(810;0.106)|all_lung(232;0.123)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0665)		CAGTCCTTGCTAACCGTACGG	0.403													59	161	---	---	---	---	PASS
TGFBI	7045	broad.mit.edu	37	5	135379760	135379760	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135379760G>A	uc003lbf.3	+	3	408	c.247G>A	c.(247-249)GAG>AAG	p.E83K	TGFBI_uc003lbg.3_5'UTR|TGFBI_uc003lbh.3_5'UTR|TGFBI_uc011cyb.1_5'Flank	NM_000358	NP_000349	Q15582	BGH3_HUMAN	transforming growth factor, beta-induced, 68kDa	83	EMI.				angiogenesis|cell adhesion|cell proliferation|negative regulation of cell adhesion|response to stimulus|visual perception	extracellular space|proteinaceous extracellular matrix	integrin binding			breast(3)|ovary(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CATCAGCTACGAGTGCTGTCC	0.537													94	281	---	---	---	---	PASS
PCDHB6	56130	broad.mit.edu	37	5	140532190	140532190	+	Silent	SNP	C	A	A	rs146937630		TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140532190C>A	uc003lir.2	+	1	2352	c.2352C>A	c.(2350-2352)ACC>ACA	p.T784T	PCDHB6_uc011dah.1_Silent_p.T648T	NM_018939	NP_061762	Q9Y5E3	PCDB6_HUMAN	protocadherin beta 6 precursor	784	Cytoplasmic (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to plasma membrane	calcium ion binding	p.T784T(1)		skin(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TGGAAGAAACCCCCACCTCTC	0.433													50	141	---	---	---	---	PASS
PCDHGA8	9708	broad.mit.edu	37	5	140774176	140774176	+	Missense_Mutation	SNP	G	T	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140774176G>T	uc003lkd.1	+	1	2694	c.1796G>T	c.(1795-1797)GGC>GTC	p.G599V	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkb.3_Missense_Mutation_p.G599V	NM_032088	NP_114477	Q9Y5G5	PCDG8_HUMAN	protocadherin gamma subfamily A, 8 isoform 1	599	Extracellular (Potential).|Cadherin 6.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGAGACTCGGGCCAGAACGCC	0.706													7	77	---	---	---	---	PASS
NSD1	64324	broad.mit.edu	37	5	176665505	176665505	+	Missense_Mutation	SNP	C	G	G			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176665505C>G	uc003mfr.3	+	7	4327	c.4189C>G	c.(4189-4191)CCA>GCA	p.P1397A	NSD1_uc003mft.3_Missense_Mutation_p.P1128A|NSD1_uc003mfs.1_Missense_Mutation_p.P1294A|NSD1_uc011dfx.1_Missense_Mutation_p.P1045A	NM_022455	NP_071900	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	1397				P -> Q (in Ref. 3; AAK92049).	negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	androgen receptor binding|chromatin binding|estrogen receptor binding|histone methyltransferase activity (H3-K36 specific)|histone methyltransferase activity (H4-K20 specific)|ligand-dependent nuclear receptor binding|retinoid X receptor binding|thyroid hormone receptor binding|transcription corepressor activity|zinc ion binding			ovary(2)|kidney(1)	3	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)		AGTTAAAACGCCAGGTAAGGT	0.478			T	NUP98	AML		Sotos Syndrome		Beckwith-Wiedemann_syndrome|Sotos_syndrome|Weaver_syndrome	HNSCC(47;0.14)			104	142	---	---	---	---	PASS
HIST1H3I	8354	broad.mit.edu	37	6	27839911	27839911	+	Silent	SNP	C	T	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27839911C>T	uc003njy.2	-	1	189	c.183G>A	c.(181-183)CTG>CTA	p.L61L		NM_003533	NP_003524	P68431	H31_HUMAN	histone cluster 1, H3i	61					blood coagulation|nucleosome assembly|regulation of gene silencing|S phase	nucleoplasm|nucleosome	DNA binding|protein binding			ovary(1)	1						TCCGGATTAGCAGCTCGGTCG	0.652													14	146	---	---	---	---	PASS
HMGN3	9324	broad.mit.edu	37	6	79944257	79944257	+	Intron	SNP	A	C	C			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:79944257A>C	uc003pit.2	-						HMGN3_uc003pis.2_Intron|HMGN3_uc003piu.1_Intron|uc003piv.1_RNA	NM_004242	NP_004233	Q15651	HMGN3_HUMAN	high mobility group nucleosomal binding domain 3						chromatin modification	chromatin|cytoplasm|nucleus	DNA binding|thyroid hormone receptor binding				0		all_cancers(76;0.000116)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.0393)		BRCA - Breast invasive adenocarcinoma(397;0.125)		TTTTGGTAAGACTTACCTTTC	0.498													67	202	---	---	---	---	PASS
C6orf167	253714	broad.mit.edu	37	6	97676875	97676875	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97676875T>C	uc003ppb.2	-	14	2200	c.1934A>G	c.(1933-1935)CAT>CGT	p.H645R	C6orf167_uc011eaf.1_Missense_Mutation_p.H605R	NM_198468	NP_940870	Q6ZRQ5	MMS22_HUMAN	hypothetical protein LOC253714	645					double-strand break repair via homologous recombination|replication fork processing	nuclear replication fork	protein binding				0		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;7.02e-10)|all_hematologic(75;1.23e-06)|all_epithelial(107;0.148)|Colorectal(196;0.198)		BRCA - Breast invasive adenocarcinoma(108;0.0457)		CAGTTTTTCATGGGAAGGATA	0.423													5	215	---	---	---	---	PASS
ZUFSP	221302	broad.mit.edu	37	6	116977892	116977892	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116977892C>T	uc003pxf.1	-	5	1162	c.916G>A	c.(916-918)GAA>AAA	p.E306K	ZUFSP_uc010kef.1_Missense_Mutation_p.E110K	NM_145062	NP_659499	Q96AP4	ZUFSP_HUMAN	zinc finger with UFM1-specific peptidase domain	306						intracellular	zinc ion binding			skin(1)	1				GBM - Glioblastoma multiforme(226;0.0258)|all cancers(137;0.0368)|OV - Ovarian serous cystadenocarcinoma(136;0.0464)|Epithelial(106;0.186)		GCTAATGATTCCATCATATCA	0.348													23	70	---	---	---	---	PASS
CLDN3	1365	broad.mit.edu	37	7	73183930	73183930	+	Silent	SNP	C	G	G			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73183930C>G	uc003tzg.3	-	1	671	c.450G>C	c.(448-450)GTG>GTC	p.V150V	RFC2_uc011kfa.1_Intron	NM_001306	NP_001297	O15551	CLD3_HUMAN	claudin 3	150	Extracellular (Potential).				response to hypoxia	integral to plasma membrane|tight junction	structural molecule activity|transmembrane receptor activity				0		Lung NSC(55;0.159)				CCTCGGGCACCACGGGGTTGT	0.706													14	33	---	---	---	---	PASS
MUC17	140453	broad.mit.edu	37	7	100676256	100676256	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100676256C>T	uc003uxp.1	+	3	1612	c.1559C>T	c.(1558-1560)ACC>ATC	p.T520I	MUC17_uc010lho.1_RNA	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17 precursor	520	Extracellular (Potential).|Ser-rich.|59 X approximate tandem repeats.|6.					extracellular region|integral to membrane|plasma membrane	extracellular matrix constituent, lubricant activity			ovary(14)|skin(8)|breast(3)|lung(2)	27	Lung NSC(181;0.136)|all_lung(186;0.182)					TCTGTCAGCACCATGCCGGTG	0.493													13	651	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	142180683	142180683	+	Intron	SNP	C	T	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142180683C>T	uc011kro.1	+						uc011krp.1_Intron|uc011krr.1_Intron|uc011krx.1_Intron|uc011ksa.1_RNA|uc011krz.1_Missense_Mutation_p.G59D					SubName: Full=V_segment translation product; Flags: Fragment;																		CAGCCCCATGCCTGGGTCTTG	0.502													15	729	---	---	---	---	PASS
CUL1	8454	broad.mit.edu	37	7	148485659	148485659	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148485659G>A	uc010lpg.2	+	14	2016	c.1490G>A	c.(1489-1491)GGG>GAG	p.G497E	CUL1_uc003wey.2_Missense_Mutation_p.G497E|CUL1_uc003wez.2_Missense_Mutation_p.G387E|CUL1_uc003wfa.2_Missense_Mutation_p.G158E	NM_003592	NP_003583	Q13616	CUL1_HUMAN	cullin 1	497					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell cycle arrest|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|negative regulation of cell proliferation|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein ubiquitination|S phase of mitotic cell cycle|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	cytosol|nucleoplasm|SCF ubiquitin ligase complex	ubiquitin protein ligase binding			lung(1)	1	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00291)			CAAGCTTGCGGGTTCGAGTAC	0.388													48	144	---	---	---	---	PASS
CRISPLD1	83690	broad.mit.edu	37	8	75926309	75926309	+	Missense_Mutation	SNP	G	T	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75926309G>T	uc003yan.2	+	5	973	c.598G>T	c.(598-600)GTC>TTC	p.V200F	CRISPLD1_uc011lfk.1_Missense_Mutation_p.V12F|CRISPLD1_uc011lfl.1_Intron	NM_031461	NP_113649	Q9H336	CRLD1_HUMAN	cysteine-rich secretory protein LCCL domain	200						extracellular region				ovary(1)|central_nervous_system(1)	2	Breast(64;0.0799)		Epithelial(68;0.155)|BRCA - Breast invasive adenocarcinoma(89;0.161)			GCCCAAAGCTGTCTACCTGGT	0.398													5	170	---	---	---	---	PASS
C10orf128	170371	broad.mit.edu	37	10	50374802	50374802	+	Intron	SNP	C	T	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50374802C>T	uc001jhn.3	-						C10orf128_uc001jhl.3_RNA|C10orf128_uc001jhm.3_Intron|C10orf128_uc010qgo.1_Intron|C10orf128_uc001jho.3_Intron	NM_001010863	NP_001010863	Q5T292	CJ128_HUMAN	hypothetical protein LOC170371 precursor							integral to membrane				lung(1)	1						TCCTTTACAGCCTGTTGGGCT	0.463													16	24	---	---	---	---	PASS
SLC16A9	220963	broad.mit.edu	37	10	61414026	61414026	+	Missense_Mutation	SNP	A	T	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61414026A>T	uc010qig.1	-	5	1207	c.758T>A	c.(757-759)CTT>CAT	p.L253H		NM_194298	NP_919274	Q7RTY1	MOT9_HUMAN	solute carrier family 16 (monocarboxylic acid	253	Extracellular (Potential).				urate metabolic process	integral to membrane|plasma membrane	symporter activity			skin(2)|ovary(1)	3						GTTTTTATGAAGTAGGCTGTC	0.403													160	336	---	---	---	---	PASS
RAB11FIP2	22841	broad.mit.edu	37	10	119805451	119805451	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:119805451C>T	uc001ldj.1	-	1	664	c.224G>A	c.(223-225)GGA>GAA	p.G75E	RAB11FIP2_uc009xyz.1_Missense_Mutation_p.G75E|CASC2_uc001ldm.3_5'Flank|CASC2_uc009xzc.2_5'Flank|CASC2_uc001ldk.2_5'Flank|CASC2_uc009xza.2_5'Flank|CASC2_uc009xzb.2_5'Flank	NM_014904	NP_055719	Q7L804	RFIP2_HUMAN	RAB11 family interacting protein 2	75	C2.|Necessary for its cellular translocation to the plasma membrane.				protein transport	plasma membrane|recycling endosome membrane	protein homodimerization activity				0		Colorectal(252;0.235)		all cancers(201;0.0238)		CTCTGGACTTCCCTGAATTAG	0.463													81	104	---	---	---	---	PASS
OR56A4	120793	broad.mit.edu	37	11	6024124	6024124	+	Silent	SNP	G	A	A			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6024124G>A	uc010qzv.1	-	1	255	c.255C>T	c.(253-255)CCC>CCT	p.P85P		NM_001005179	NP_001005179	Q8NGH8	O56A4_HUMAN	olfactory receptor, family 56, subfamily A,	33	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)|skin(1)	2		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;7.01e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GAAGGCTGAGGGGCAGAGACA	0.582													7	97	---	---	---	---	PASS
CYB5R2	51700	broad.mit.edu	37	11	7689781	7689781	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7689781T>C	uc001mfm.2	-	6	638	c.400A>G	c.(400-402)ATC>GTC	p.I134V	CYB5R2_uc001mfn.2_RNA|CYB5R2_uc009yfk.2_Missense_Mutation_p.I134V|CYB5R2_uc009yfl.1_3'UTR	NM_016229	NP_057313	Q6BCY4	NB5R2_HUMAN	cytochrome b5 reductase b5R.2	134	FAD (By similarity).				sterol biosynthetic process	membrane|soluble fraction	cytochrome-b5 reductase activity				0				Epithelial(150;5.48e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		TCTGGTCTGATTCCAAGATTC	0.502													7	260	---	---	---	---	PASS
MICALCL	84953	broad.mit.edu	37	11	12376331	12376331	+	Missense_Mutation	SNP	G	T	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12376331G>T	uc001mkg.1	+	8	2121	c.1830G>T	c.(1828-1830)ATG>ATT	p.M610I		NM_032867	NP_116256	Q6ZW33	MICLK_HUMAN	MICAL C-terminal like	610	Potential.				cell differentiation|multicellular organismal development|spermatogenesis	cytoplasm	mitogen-activated protein kinase binding			skin(1)	1				Epithelial(150;0.00177)		TCTCACCCAGGGCCCAGGAAC	0.403													17	41	---	---	---	---	PASS
NTF3	4908	broad.mit.edu	37	12	5541411	5541411	+	5'UTR	SNP	T	G	G			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5541411T>G	uc001qnk.3	+	1						NM_001102654	NP_001096124	P20783	NTF3_HUMAN	neurotrophin 3 isoform 1 preproprotein						signal transduction	extracellular region	growth factor activity|neurotrophin receptor binding			pancreas(1)	1						TGCGGCGGGGTGGGGGAGACT	0.597													4	6	---	---	---	---	PASS
LARP4	113251	broad.mit.edu	37	12	50794655	50794655	+	5'UTR	SNP	A	G	G			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50794655A>G	uc001rwp.1	+	1					LARP4_uc001rwo.1_5'UTR|LARP4_uc001rwq.1_5'UTR|LARP4_uc001rwr.1_5'UTR|LARP4_uc001rws.1_5'UTR|LARP4_uc001rwm.2_5'UTR|LARP4_uc001rwn.2_5'UTR	NM_052879	NP_443111	Q71RC2	LARP4_HUMAN	c-Mpl binding protein isoform a								nucleotide binding|RNA binding			ovary(1)	1						GCAGCGGCTGACGGCAGGGGA	0.627													14	52	---	---	---	---	PASS
STAB2	55576	broad.mit.edu	37	12	104107496	104107496	+	Missense_Mutation	SNP	G	A	A	rs141685549	by1000genomes	TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104107496G>A	uc001tjw.2	+	42	4673	c.4487G>A	c.(4486-4488)CGA>CAA	p.R1496Q	STAB2_uc009zug.2_RNA	NM_017564	NP_060034	Q8WWQ8	STAB2_HUMAN	stabilin 2 precursor	1496	Extracellular (Potential).|EGF-like 12.				angiogenesis|cell adhesion|defense response to bacterium|receptor-mediated endocytosis	cytoplasm|external side of plasma membrane|integral to plasma membrane	Gram-negative bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			ovary(9)|skin(5)	14						CCAGGAAGGCGAGTGTGCACG	0.522													125	258	---	---	---	---	PASS
ANKLE2	23141	broad.mit.edu	37	12	133331621	133331621	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133331621T>C	uc001ukx.2	-	2	347	c.280A>G	c.(280-282)ATT>GTT	p.I94V	ANKLE2_uc001uky.3_Missense_Mutation_p.I32V	NM_015114	NP_055929	Q86XL3	ANKL2_HUMAN	ankyrin repeat and LEM domain containing 2	94	LEM.					cytoplasm|integral to membrane|nuclear envelope					0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.3e-08)|Epithelial(86;1.56e-07)|all cancers(50;4.94e-06)		GTTGATGTAATGGGTCCACAT	0.433													9	202	---	---	---	---	PASS
NOVA1	4857	broad.mit.edu	37	14	27066701	27066701	+	5'UTR	SNP	C	T	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:27066701C>T	uc001wpy.2	-	1					NOVA1_uc001wpz.2_5'UTR|NOVA1_uc001wqa.2_5'UTR|NOVA1_uc001wqb.2_5'UTR	NM_002515	NP_002506	P51513	NOVA1_HUMAN	neuro-oncological ventral antigen 1 isoform 1						locomotory behavior|RNA splicing|synaptic transmission	nucleus	RNA binding			skin(2)|upper_aerodigestive_tract(1)|breast(1)|liver(1)	5				GBM - Glioblastoma multiforme(265;0.0135)		TTGGCtttttcttttcttttt	0.363													3	7	---	---	---	---	PASS
SYNE2	23224	broad.mit.edu	37	14	64683102	64683102	+	Silent	SNP	C	G	G			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64683102C>G	uc001xgm.2	+	107	19700	c.19470C>G	c.(19468-19470)CCC>CCG	p.P6490P	SYNE2_uc001xgl.2_Silent_p.P6513P|SYNE2_uc010apy.2_Silent_p.P2875P|SYNE2_uc001xgn.2_Silent_p.P1452P|SYNE2_uc001xgo.2_RNA|SYNE2_uc010aqa.2_Silent_p.P460P|SYNE2_uc001xgq.2_Silent_p.P855P|SYNE2_uc001xgr.2_Silent_p.P273P|SYNE2_uc010tsi.1_Silent_p.P147P|SYNE2_uc001xgs.2_Silent_p.P147P|SYNE2_uc001xgt.2_Silent_p.P21P	NM_015180	NP_055995	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	6490	Cytoplasmic (Potential).				centrosome localization|cytoskeletal anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration	cytoskeleton|filopodium membrane|focal adhesion|integral to membrane|lamellipodium membrane|mitochondrial part|nuclear outer membrane|nucleoplasm|sarcoplasmic reticulum membrane|SUN-KASH complex|Z disc	actin binding|protein binding			ovary(8)|breast(4)|central_nervous_system(1)|pancreas(1)	14				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		ATAAACCACCCTATGTAAGTC	0.473													32	70	---	---	---	---	PASS
SYNJ2BP	55333	broad.mit.edu	37	14	70839819	70839819	+	Missense_Mutation	SNP	A	T	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70839819A>T	uc001xmc.3	-	4	454	c.327T>A	c.(325-327)CAT>CAA	p.H109Q	SYNJ2BP_uc010arc.2_RNA	NM_018373	NP_060843	P57105	SYJ2B_HUMAN	synaptojanin 2 binding protein	109	Cytoplasmic (Potential).					integral to membrane|mitochondrial outer membrane					0				all cancers(60;0.00367)|BRCA - Breast invasive adenocarcinoma(234;0.00716)|OV - Ovarian serous cystadenocarcinoma(108;0.0377)		CTTCACCTCGATGTCCTATAG	0.483													35	125	---	---	---	---	PASS
PTPN21	11099	broad.mit.edu	37	14	88983531	88983531	+	Silent	SNP	C	T	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88983531C>T	uc001xwv.3	-	3	586	c.255G>A	c.(253-255)AAG>AAA	p.K85K	PTPN21_uc010twc.1_5'UTR|PTPN21_uc010atf.1_Silent_p.K85K	NM_007039	NP_008970	Q16825	PTN21_HUMAN	protein tyrosine phosphatase, non-receptor type	85	FERM.					cytoplasm|cytoskeleton	binding|protein tyrosine phosphatase activity			ovary(3)|skin(1)	4						CCAGCTGCTTCTTCAAAGGTT	0.453													38	90	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106757720	106757720	+	RNA	SNP	T	A	A			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106757720T>A	uc010tyt.1	-	472		c.16345A>T								Parts of antibodies, mostly variable regions.												0						CACCTGGCTTTTGGAGGTGTC	0.527													17	229	---	---	---	---	PASS
GOLGA6L10	647042	broad.mit.edu	37	15	82635117	82635117	+	RNA	SNP	T	C	C			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:82635117T>C	uc002bgx.2	-	5		c.463A>G						A6NI86	GG6LA_HUMAN	Homo sapiens cDNA FLJ40113 fis, clone TESTI2008621.												0						TTTTTCAATTTCTTGACCCGC	0.383													4	24	---	---	---	---	PASS
KIAA0556	23247	broad.mit.edu	37	16	27689189	27689189	+	Missense_Mutation	SNP	G	T	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27689189G>T	uc002dow.2	+	7	704	c.680G>T	c.(679-681)AGA>ATA	p.R227I	KIAA0556_uc002dox.1_Missense_Mutation_p.R135I	NM_015202	NP_056017	O60303	K0556_HUMAN	hypothetical protein LOC23247	227										ovary(4)|large_intestine(2)|upper_aerodigestive_tract(1)|skin(1)	8						GGCCATCCCAGACATGACCGC	0.557													22	71	---	---	---	---	PASS
SETD1A	9739	broad.mit.edu	37	16	30982880	30982880	+	Silent	SNP	G	A	A			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30982880G>A	uc002ead.1	+	13	3884	c.3198G>A	c.(3196-3198)GAG>GAA	p.E1066E		NM_014712	NP_055527	O15047	SET1A_HUMAN	SET domain containing 1A	1066					regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nuclear speck|Set1C/COMPASS complex	histone-lysine N-methyltransferase activity|nucleotide binding|protein binding|RNA binding			ovary(2)|skin(1)	3						AAGATGAAGAGGAAGAGGAGC	0.478													4	92	---	---	---	---	PASS
KIAA0895L	653319	broad.mit.edu	37	16	67214015	67214015	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67214015C>T	uc002ert.2	-	2	1274	c.499G>A	c.(499-501)GAG>AAG	p.E167K	KIAA0895L_uc002err.2_5'Flank|KIAA0895L_uc002ers.2_5'Flank|KIAA0895L_uc002eru.2_Missense_Mutation_p.E167K|EXOC3L_uc002erv.1_RNA	NM_001040715	NP_001035805	Q68EN5	K895L_HUMAN	hypothetical protein LOC653319	167											0						TCCTGGTACTCAAACTGTGGA	0.577													61	142	---	---	---	---	PASS
ELMO3	79767	broad.mit.edu	37	16	67235520	67235520	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67235520G>A	uc002esa.2	+	10	1095	c.1052G>A	c.(1051-1053)CGG>CAG	p.R351Q	ELMO3_uc002esb.2_Missense_Mutation_p.R334Q|ELMO3_uc002esc.2_Missense_Mutation_p.R185Q	NM_024712	NP_078988	Q96BJ8	ELMO3_HUMAN	engulfment and cell motility 3	298					apoptosis|phagocytosis	cytoplasm|cytoskeleton	SH3 domain binding				0		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00067)|Epithelial(162;0.00442)|all cancers(182;0.0417)		CCGCGCATGCGGACGCCCCTG	0.587													33	90	---	---	---	---	PASS
MYH8	4626	broad.mit.edu	37	17	10299727	10299727	+	Nonsense_Mutation	SNP	G	A	A			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10299727G>A	uc002gmm.2	-	33	4668	c.4573C>T	c.(4573-4575)CAA>TAA	p.Q1525*	uc002gml.1_Intron	NM_002472	NP_002463	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle,	1525	Potential.				muscle filament sliding	cytosol|muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			skin(6)|ovary(3)|breast(2)	11						TCATGAATTTGCTTTCCTCCC	0.408									Trismus-Pseudocamptodactyly_Syndrome_with_Cardiac_Myxoma_and_Freckling				21	48	---	---	---	---	PASS
SREBF1	6720	broad.mit.edu	37	17	17720979	17720979	+	Intron	SNP	T	G	G			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17720979T>G	uc002gru.1	-						SREBF1_uc002grp.1_Silent_p.P48P|SREBF1_uc002grq.1_Intron|SREBF1_uc002grr.1_Intron|SREBF1_uc002grs.1_Intron|SREBF1_uc002grt.1_Intron|SREBF1_uc010cpp.1_Intron|SREBF1_uc010cpq.1_Intron	NM_004176	NP_004167	P36956	SRBP1_HUMAN	sterol regulatory element binding transcription						cellular response to starvation|cholesterol metabolic process|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter	endoplasmic reticulum|endoplasmic reticulum membrane|ER to Golgi transport vesicle membrane|Golgi membrane|integral to membrane|nuclear envelope|nucleus	protein binding|protein binding|sequence-specific DNA binding transcription factor activity|sterol response element binding			skin(1)	1						TGGCTGGGAGTGGGGAAGGGG	0.413													4	19	---	---	---	---	PASS
TUBG2	27175	broad.mit.edu	37	17	40815012	40815012	+	Missense_Mutation	SNP	A	T	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40815012A>T	uc010wgr.1	+	5	677	c.421A>T	c.(421-423)ATC>TTC	p.I141F	TUBG2_uc002iaq.2_5'UTR|TUBG2_uc002iar.2_Intron|TUBG2_uc002ias.2_5'UTR|TUBG2_uc002iap.2_Intron	NM_016437	NP_057521	Q9NRH3	TBG2_HUMAN	tubulin, gamma 2	141					G2/M transition of mitotic cell cycle|microtubule-based process|protein polymerization	cytosol	GTP binding|GTPase activity|structural molecule activity			ovary(1)	1		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.141)		GTGTCACTCCATCGCTGGGGG	0.388													7	215	---	---	---	---	PASS
GFAP	2670	broad.mit.edu	37	17	42990657	42990657	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42990657C>T	uc002ihq.2	-	4	820	c.760G>A	c.(760-762)GAA>AAA	p.E254K	GFAP_uc002ihr.2_Missense_Mutation_p.E254K|GFAP_uc010wjg.1_RNA	NM_002055	NP_002046	P14136	GFAP_HUMAN	glial fibrillary acidic protein isoform 1	254	Linker 2.|Rod.					cytoplasm|intermediate filament	structural constituent of cytoskeleton			ovary(1)|pancreas(1)	2		Prostate(33;0.0959)				TACCACTCTTCGGCTTCATGC	0.607													7	264	---	---	---	---	PASS
HEATR6	63897	broad.mit.edu	37	17	58137396	58137396	+	Missense_Mutation	SNP	G	C	C			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58137396G>C	uc002iyk.1	-	10	1495	c.1478C>G	c.(1477-1479)TCT>TGT	p.S493C	HEATR6_uc010ddk.1_Missense_Mutation_p.S32C|HEATR6_uc010wos.1_Missense_Mutation_p.S325C	NM_022070	NP_071353	Q6AI08	HEAT6_HUMAN	HEAT repeat containing 6	493							binding			ovary(1)|skin(1)	2	all_cancers(5;2.25e-13)|Breast(5;4.84e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		BRCA - Breast invasive adenocarcinoma(1;5.93e-19)|Epithelial(12;7.59e-12)|all cancers(12;1.26e-10)			TTCAGCAACAGAAAGAAACTG	0.433													70	205	---	---	---	---	PASS
ABCA8	10351	broad.mit.edu	37	17	66871821	66871821	+	Missense_Mutation	SNP	G	T	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66871821G>T	uc002jhp.2	-	34	4483	c.4304C>A	c.(4303-4305)ACC>AAC	p.T1435N	ABCA8_uc002jhq.2_Missense_Mutation_p.T1475N|ABCA8_uc010wqq.1_Missense_Mutation_p.T1470N	NM_007168	NP_009099	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A member 8	1435	ABC transporter 2.					integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(2)|skin(1)	3	Breast(10;4.56e-13)					CATGTAGTGGGTGGTTAGGAG	0.522													7	99	---	---	---	---	PASS
KIF19	124602	broad.mit.edu	37	17	72345372	72345372	+	Missense_Mutation	SNP	G	T	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72345372G>T	uc002jkm.3	+	10	1235	c.1097G>T	c.(1096-1098)AGC>ATC	p.S366I	KIF19_uc002jkj.2_Missense_Mutation_p.S366I|KIF19_uc002jkk.2_Missense_Mutation_p.S324I|KIF19_uc002jkl.2_Missense_Mutation_p.S324I	NM_153209	NP_694941	Q2TAC6	KIF19_HUMAN	kinesin family member 19	366	Potential.				microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity				0						CAGTACACCAGCATCATCGCT	0.637													11	38	---	---	---	---	PASS
PYCR1	5831	broad.mit.edu	37	17	79894640	79894640	+	Missense_Mutation	SNP	C	G	G			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79894640C>G	uc002kcr.1	-	1	329	c.51G>C	c.(49-51)AAG>AAC	p.K17N	PYCR1_uc002kcq.1_Missense_Mutation_p.K17N|PYCR1_uc002kcp.2_Missense_Mutation_p.K17N|PYCR1_uc002kcs.1_Missense_Mutation_p.K17N|PYCR1_uc010wvd.1_Missense_Mutation_p.K44N|PYCR1_uc002kct.1_Missense_Mutation_p.K17N|PYCR1_uc002kcu.1_Missense_Mutation_p.K17N|PYCR1_uc010wve.1_5'Flank	NM_006907	NP_008838	P32322	P5CR1_HUMAN	pyrroline-5-carboxylate reductase 1 isoform 1	17					cellular response to oxidative stress|proline biosynthetic process	mitochondrial matrix	binding|pyrroline-5-carboxylate reductase activity				0	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.0165)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)		L-Proline(DB00172)|NADH(DB00157)	CTGTGAAGCCCTTGGCCAGGG	0.672													6	12	---	---	---	---	PASS
KIAA0802	23255	broad.mit.edu	37	18	8825236	8825236	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8825236C>T	uc002knr.2	+	15	3870	c.3728C>T	c.(3727-3729)CCC>CTC	p.P1243L	KIAA0802_uc002knq.2_Missense_Mutation_p.P1202L|KIAA0802_uc002kns.2_Missense_Mutation_p.P583L	NM_015210	NP_056025	Q9Y4B5	CC165_HUMAN	hypothetical protein LOC23255	1553											0						TGCACCTCCCCCAGGCACTCC	0.662													23	31	---	---	---	---	PASS
SETBP1	26040	broad.mit.edu	37	18	42531405	42531405	+	Silent	SNP	T	G	G			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:42531405T>G	uc010dni.2	+	4	2396	c.2100T>G	c.(2098-2100)CCT>CCG	p.P700P		NM_015559	NP_056374	Q9Y6X0	SETBP_HUMAN	SET binding protein 1 isoform a	700						nucleus	DNA binding			upper_aerodigestive_tract(2)|large_intestine(1)	3				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)		AGACCAGCCCTGGGGCAGCAG	0.507									Schinzel-Giedion_syndrome				4	55	---	---	---	---	PASS
PSTPIP2	9050	broad.mit.edu	37	18	43579500	43579500	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43579500C>T	uc002lbp.3	-	7	514	c.418G>A	c.(418-420)GCA>ACA	p.A140T	PSTPIP2_uc002lbq.3_Missense_Mutation_p.A140T	NM_024430	NP_077748	Q9H939	PPIP2_HUMAN	proline-serine-threonine phosphatase interacting	140	Potential.					membrane				ovary(1)	1						TTCTTCTTTGCCTTTGTCATT	0.502													5	114	---	---	---	---	PASS
SBNO2	22904	broad.mit.edu	37	19	1112193	1112193	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1112193T>C	uc002lrk.3	-	22	2861	c.2623A>G	c.(2623-2625)AGT>GGT	p.S875G	SBNO2_uc002lrj.3_Missense_Mutation_p.S818G|SBNO2_uc010dse.2_Missense_Mutation_p.S858G|SBNO2_uc010xgj.1_Intron	NM_014963	NP_055778	Q9Y2G9	SBNO2_HUMAN	strawberry notch homolog 2 isoform 1	875					macrophage activation involved in immune response|negative regulation of transcription, DNA-dependent|regulation of inflammatory response|transcription, DNA-dependent						0		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|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)		CTCACCAGACTCTCCAGGCGC	0.657													4	10	---	---	---	---	PASS
ACSBG2	81616	broad.mit.edu	37	19	6183057	6183057	+	Missense_Mutation	SNP	A	C	C			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6183057A>C	uc002mef.1	+	10	1323	c.1096A>C	c.(1096-1098)AAT>CAT	p.N366H	ACSBG2_uc002mee.1_Missense_Mutation_p.N179H|ACSBG2_uc002meg.1_Missense_Mutation_p.N366H|ACSBG2_uc002meh.1_Missense_Mutation_p.N366H|ACSBG2_uc002mei.1_Missense_Mutation_p.N316H|ACSBG2_uc010xiz.1_Missense_Mutation_p.N366H	NM_030924	NP_112186	Q5FVE4	ACBG2_HUMAN	bubblegum-related acyl-CoA synthetase 2	366					cell differentiation|fatty acid metabolic process|multicellular organismal development|spermatogenesis	membrane|microsome|mitochondrion	acyl-CoA thioesterase activity|ATP binding|long-chain fatty acid-CoA ligase activity			ovary(1)	1						CAGGAAATATAATACTCCCGT	0.522													58	108	---	---	---	---	PASS
ZNF91	7644	broad.mit.edu	37	19	23545264	23545264	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23545264T>C	uc002nre.2	-	4	630	c.517A>G	c.(517-519)ACG>GCG	p.T173A	ZNF91_uc010xrj.1_Missense_Mutation_p.T141A	NM_003430	NP_003421	Q05481	ZNF91_HUMAN	zinc finger protein 91	173	C2H2-type 1; degenerate.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)				TGTCTTATCGTATGTCTGTTT	0.308													5	134	---	---	---	---	PASS
PDCD5	9141	broad.mit.edu	37	19	33077874	33077874	+	Intron	SNP	G	T	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33077874G>T	uc002ntm.2	+						PDCD5_uc002ntl.2_3'UTR|PDCD5_uc010ede.2_Intron	NM_004708	NP_004699	O14737	PDCD5_HUMAN	programmed cell death 5						apoptosis|induction of apoptosis	cytoplasm|nucleus	DNA binding			ovary(1)|lung(1)	2	Esophageal squamous(110;0.137)					TGAAAAGATGGATACTTTAAA	0.353													19	49	---	---	---	---	PASS
HKR1	284459	broad.mit.edu	37	19	37854193	37854193	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37854193G>A	uc002ogb.2	+	6	1765	c.1496G>A	c.(1495-1497)TGT>TAT	p.C499Y	HKR1_uc002ofx.2_Missense_Mutation_p.C215Y|HKR1_uc002ofy.2_Missense_Mutation_p.C215Y|HKR1_uc002oga.2_Missense_Mutation_p.C481Y|HKR1_uc010xto.1_Missense_Mutation_p.C481Y|HKR1_uc002ogc.2_Missense_Mutation_p.C480Y|HKR1_uc010xtp.1_Missense_Mutation_p.C438Y|HKR1_uc002ogd.2_Missense_Mutation_p.C438Y	NM_181786	NP_861451	P10072	HKR1_HUMAN	GLI-Kruppel family member HKR1	499	C2H2-type 8.				multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CCATTTGTATGTACGGAGTGT	0.527													42	66	---	---	---	---	PASS
ZNF227	7770	broad.mit.edu	37	19	44740521	44740521	+	Silent	SNP	T	C	C			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44740521T>C	uc002oyu.2	+	6	2143	c.1938T>C	c.(1936-1938)GGT>GGC	p.G646G	ZNF227_uc010xwu.1_Silent_p.G595G|ZNF227_uc002oyv.2_Silent_p.G646G|ZNF227_uc010xwv.1_Silent_p.G595G|ZNF227_uc010xww.1_Silent_p.G567G|ZNF227_uc002oyw.2_Silent_p.G618G|ZNF227_uc010ejh.2_Silent_p.G639G|ZNF235_uc002oyx.1_Intron|ZNF235_uc010eji.2_3'UTR	NM_182490	NP_872296	Q86WZ6	ZN227_HUMAN	zinc finger protein 227	646	C2H2-type 14.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Prostate(69;0.0435)				AGTCCTCTGGTCTTCAATCCC	0.463													13	85	---	---	---	---	PASS
NOSIP	51070	broad.mit.edu	37	19	50060397	50060397	+	Missense_Mutation	SNP	C	G	G			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50060397C>G	uc002pok.2	-	6	520	c.368G>C	c.(367-369)AGC>ACC	p.S123T	NOSIP_uc002pol.2_Missense_Mutation_p.S123T|NOSIP_uc010yay.1_RNA	NM_015953	NP_057037	Q9Y314	NOSIP_HUMAN	nitric oxide synthase interacting protein	123					negative regulation of nitric-oxide synthase activity|nitric oxide metabolic process	cytosol|nucleus	protein binding			skin(1)	1		all_lung(116;7.84e-06)|Lung NSC(112;2.8e-05)|all_neural(266;0.0966)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00321)|GBM - Glioblastoma multiforme(134;0.0133)		GAGGGGCCGGCTCACGATAGC	0.592													5	30	---	---	---	---	PASS
KLK14	43847	broad.mit.edu	37	19	51585845	51585845	+	Missense_Mutation	SNP	T	G	G			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51585845T>G	uc002pvs.1	-	3	294	c.75A>C	c.(73-75)CAA>CAC	p.Q25H		NM_022046	NP_071329	Q9P0G3	KLK14_HUMAN	kallikrein 14 preproprotein	25					epidermis morphogenesis|fertilization|negative regulation of G-protein coupled receptor protein signaling pathway|positive regulation of G-protein coupled receptor protein signaling pathway|proteolysis|seminal clot liquefaction	extracellular space	serine-type endopeptidase activity			skin(1)	1		all_neural(266;0.0199)		OV - Ovarian serous cystadenocarcinoma(262;0.00328)|GBM - Glioblastoma multiforme(134;0.00422)		TAGCCAGGACTTGAAGTGCTG	0.542													15	77	---	---	---	---	PASS
MBOAT7	79143	broad.mit.edu	37	19	54682431	54682431	+	Intron	SNP	C	A	A			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54682431C>A	uc002qdq.2	-						MBOAT7_uc010erg.2_Intron|MBOAT7_uc010yem.1_Intron|MBOAT7_uc002qdr.2_Intron|MBOAT7_uc002qds.2_Intron|MBOAT7_uc010yen.1_Intron|MBOAT7_uc002qdt.3_3'UTR	NM_024298	NP_077274	Q96N66	MBOA7_HUMAN	membrane bound O-acyltransferase domain						phospholipid biosynthetic process	integral to membrane	acyltransferase activity				0	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					CTGGGGCCTGCTGGGAGATGT	0.502													6	17	---	---	---	---	PASS
ZNF580	51157	broad.mit.edu	37	19	56153817	56153817	+	Intron	SNP	A	T	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56153817A>T	uc002qlo.2	+						ZNF580_uc002qlm.2_Intron|ZNF581_uc002qln.2_Intron|ZNF580_uc002qlp.2_5'UTR|ZNF580_uc010ygd.1_Intron|ZNF581_uc002qlq.2_5'Flank	NM_207115	NP_996998	Q9UK33	ZN580_HUMAN	zinc finger protein 580						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0			BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.105)		AACTTTTCCTAAAAGGAAGTG	0.537													19	32	---	---	---	---	PASS
NLRP5	126206	broad.mit.edu	37	19	56530712	56530712	+	Missense_Mutation	SNP	T	G	G			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56530712T>G	uc002qmj.2	+	5	570	c.570T>G	c.(568-570)ATT>ATG	p.I190M	NLRP5_uc002qmi.2_Intron	NM_153447	NP_703148	P59047	NALP5_HUMAN	NACHT, LRR and PYD containing protein 5	190						mitochondrion|nucleolus	ATP binding			ovary(3)|skin(2)|kidney(1)|central_nervous_system(1)	7		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0326)		TTGCAGAAATTTCACAAGCTA	0.398													3	80	---	---	---	---	PASS
TBC1D20	128637	broad.mit.edu	37	20	422492	422492	+	Intron	SNP	T	C	C			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:422492T>C	uc002wds.2	-						TBC1D20_uc002wdv.2_5'UTR|TBC1D20_uc002wdt.2_Intron|TBC1D20_uc002wdu.2_Intron	NM_144628	NP_653229	Q96BZ9	TBC20_HUMAN	TBC1 domain family, member 20						interspecies interaction between organisms	integral to membrane|intracellular	Rab GTPase activator activity			central_nervous_system(1)	1		all_epithelial(17;0.228)|Breast(17;0.231)				TGTTCCTCTCTACTGGTACCT	0.527													51	130	---	---	---	---	PASS
ZNF343	79175	broad.mit.edu	37	20	2464182	2464182	+	Silent	SNP	A	G	G			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2464182A>G	uc002wge.1	-	6	1913	c.1425T>C	c.(1423-1425)AGT>AGC	p.S475S	ZNF343_uc010gao.1_Silent_p.S475S|ZNF343_uc002wgd.1_Silent_p.S385S	NM_024325	NP_077301	Q6P1L6	ZN343_HUMAN	zinc finger protein 343	475	C2H2-type 8.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3						GTGATTTCCGACTAAAGCCTC	0.527													4	130	---	---	---	---	PASS
REM1	28954	broad.mit.edu	37	20	30064350	30064350	+	Missense_Mutation	SNP	C	G	G			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30064350C>G	uc002wwa.2	+	2	386	c.102C>G	c.(100-102)AGC>AGG	p.S34R		NM_014012	NP_054731	O75628	REM1_HUMAN	RAS-like GTP-binding protein REM	34					small GTPase mediated signal transduction	membrane	calmodulin binding|GTP binding|GTPase activity			lung(2)|pancreas(2)	4	all_cancers(5;0.000119)|Lung NSC(7;1.32e-05)|all_lung(7;2.14e-05)|all_hematologic(12;0.158)|Ovarian(7;0.198)		Colorectal(19;0.00254)|COAD - Colon adenocarcinoma(19;0.0347)			GCCGCCTGAGCACAGTGCCTT	0.642													35	61	---	---	---	---	PASS
LOC96610	96610	broad.mit.edu	37	22	22661478	22661478	+	RNA	SNP	T	G	G			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22661478T>G	uc011aim.1	+	28		c.1702T>G			LOC96610_uc011aiq.1_RNA|LOC96610_uc011aip.1_RNA|LOC96610_uc010gto.2_RNA					Parts of antibodies, mostly variable regions.												0						CAGATGCGTCTGAAGAAACAT	0.488													3	94	---	---	---	---	PASS
LOC96610	96610	broad.mit.edu	37	22	22664606	22664606	+	RNA	SNP	A	G	G			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22664606A>G	uc011aim.1	+	31		c.2121A>G			LOC96610_uc011aiq.1_RNA					Parts of antibodies, mostly variable regions.												0						GTCTTCATGCAAACTTGGTAT	0.398													3	40	---	---	---	---	PASS
POM121L9P	29774	broad.mit.edu	37	22	24659591	24659591	+	RNA	SNP	A	G	G			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24659591A>G	uc002zzs.3	+	7		c.3323A>G			uc011ajp.1_5'Flank	NR_003714				Homo sapiens mRNA; cDNA DKFZp434P211 (from clone DKFZp434P211).												0						ACTCACTGACATCGAAGGCTG	0.632													3	31	---	---	---	---	PASS
POM121L9P	29774	broad.mit.edu	37	22	24659593	24659593	+	RNA	SNP	C	T	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24659593C>T	uc002zzs.3	+	7		c.3325C>T			uc011ajp.1_5'Flank	NR_003714				Homo sapiens mRNA; cDNA DKFZp434P211 (from clone DKFZp434P211).												0						TCACTGACATCGAAGGCTGCC	0.632													3	30	---	---	---	---	PASS
RFPL2	10739	broad.mit.edu	37	22	32587083	32587083	+	Silent	SNP	G	C	C			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32587083G>C	uc003amg.3	-	5	1749	c.813C>G	c.(811-813)ACC>ACG	p.T271T	RFPL2_uc003ame.3_Silent_p.T210T|RFPL2_uc003amf.3_Silent_p.T181T|RFPL2_uc003amh.3_Silent_p.T181T	NM_001098527	NP_001091997	O75678	RFPL2_HUMAN	ret finger protein-like 2 isoform 2	271	B30.2/SPRY.						zinc ion binding			skin(1)	1						CAAGCTCTGTGGTCAGCTGGA	0.587													38	108	---	---	---	---	PASS
NHS	4810	broad.mit.edu	37	X	17746842	17746842	+	Silent	SNP	C	T	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:17746842C>T	uc004cxx.2	+	7	4571	c.4233C>T	c.(4231-4233)TTC>TTT	p.F1411F	NHS_uc011mix.1_Silent_p.F1432F|NHS_uc004cxy.2_Silent_p.F1255F|NHS_uc004cxz.2_Silent_p.F1234F|NHS_uc004cya.2_Silent_p.F1134F	NM_198270	NP_938011	Q6T4R5	NHS_HUMAN	Nance-Horan syndrome protein isoform 1	1411						nucleus				skin(3)|ovary(2)|breast(1)|central_nervous_system(1)	7	Hepatocellular(33;0.183)					AGGGTGTGTTCGTGTCTCCAA	0.418													57	50	---	---	---	---	PASS
DMD	1756	broad.mit.edu	37	X	31196785	31196785	+	Splice_Site	SNP	C	A	A			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:31196785C>A	uc004dda.1	-	70	10467	c.10223_splice	c.e70+1	p.T3408_splice	DMD_uc004dcq.1_Splice_Site_p.T679_splice|DMD_uc004dcr.1_Intron|DMD_uc004dcs.1_Splice_Site_p.T948_splice|DMD_uc004dct.1_Splice_Site_p.T948_splice|DMD_uc004dcu.1_Splice_Site_p.T948_splice|DMD_uc004dcv.1_Splice_Site_p.T948_splice|DMD_uc004dcw.2_Splice_Site_p.T2064_splice|DMD_uc004dcx.2_Splice_Site_p.T2067_splice|DMD_uc004dcz.2_Splice_Site_p.T3285_splice|DMD_uc004dcy.1_Splice_Site_p.T3404_splice|DMD_uc004ddb.1_Splice_Site_p.T3400_splice|DMD_uc004dcm.1_Splice_Site_p.T340_splice|DMD_uc004dcn.1_Splice_Site_p.T340_splice|DMD_uc004dco.1_Splice_Site_p.T340_splice|DMD_uc004dcp.1_Splice_Site_p.T340_splice|DMD_uc011mkb.1_Splice_Site_p.T340_splice|DMD_uc010ngm.2_Silent_p.T340T	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)				CTACTACTCACGTTTCCATGT	0.438													58	53	---	---	---	---	PASS
SLC35A2	7355	broad.mit.edu	37	X	48762340	48762340	+	Silent	SNP	C	T	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48762340C>T	uc004dlo.1	-	4	850	c.846G>A	c.(844-846)GGG>GGA	p.G282G	SLC35A2_uc011mml.1_Silent_p.G295G|SLC35A2_uc004dlp.1_Silent_p.G282G|SLC35A2_uc011mmm.1_Silent_p.G310G|SLC35A2_uc011mmn.1_Silent_p.G221G|SLC35A2_uc004dlr.1_Missense_Mutation_p.G136D|SLC35A2_uc004dlq.2_Intron	NM_005660	NP_005651	P78381	S35A2_HUMAN	solute carrier family 35, member A2 isoform a	282	Helical; (Potential).				galactose metabolic process	Golgi membrane|integral to membrane|nucleus	sugar:hydrogen symporter activity|UDP-galactose transmembrane transporter activity			breast(1)	1						CCACCAGTAGCCCGCCGAAGG	0.597													12	9	---	---	---	---	PASS
VSIG4	11326	broad.mit.edu	37	X	65252420	65252420	+	Missense_Mutation	SNP	G	A	A	rs139911916		TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:65252420G>A	uc004dwh.2	-	3	711	c.584C>T	c.(583-585)ACC>ATC	p.T195I	VSIG4_uc004dwi.2_Intron|VSIG4_uc010nkq.1_Missense_Mutation_p.T195I|VSIG4_uc004dwj.2_Missense_Mutation_p.T195I|VSIG4_uc011moy.1_Intron|VSIG4_uc004dwk.2_Missense_Mutation_p.T195I|VSIG4_uc004dwl.2_Missense_Mutation_p.T91I	NM_007268	NP_009199	Q9Y279	VSIG4_HUMAN	V-set and immunoglobulin domain containing 4	195	Ig-like 2.|Extracellular (Potential).				complement activation, alternative pathway	integral to membrane	protein binding				0						GAAGAGTAAGGTACTTAGGGT	0.498													6	73	---	---	---	---	PASS
DCAF12L1	139170	broad.mit.edu	37	X	125685459	125685459	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:125685459C>T	uc004eul.2	-	1	1384	c.1133G>A	c.(1132-1134)CGG>CAG	p.R378Q		NM_178470	NP_848565	Q5VU92	DC121_HUMAN	DDB1 and CUL4 associated factor 12-like 1	378	WD 4.									skin(3)|ovary(1)	4						TTTCTGGGCCCGGACGTCATA	0.627													53	32	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	6924	6924	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:6924G>A	uc011mfh.1	+	1	1071	c.23G>A	c.(22-24)AGC>AAC	p.S8N	uc004cou.3_5'Flank|uc011mfi.1_5'Flank					Homo sapiens cDNA: FLJ22894 fis, clone KAT04907.																		CAGTGCTCTGAGCCCTAGGAT	0.483													6	38	---	---	---	---	PASS
CAMTA1	23261	broad.mit.edu	37	1	7676804	7676805	+	Intron	INS	-	C	C	rs147094934	by1000genomes	TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7676804_7676805insC	uc001aoi.2	+							NM_015215	NP_056030	Q9Y6Y1	CMTA1_HUMAN	calmodulin-binding transcription activator 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	calmodulin binding			ovary(5)|central_nervous_system(2)|breast(1)|pancreas(1)	9	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		GAGAGACGGGGCCCCCCCACCA	0.559													4	2	---	---	---	---	
KIF1B	23095	broad.mit.edu	37	1	10352529	10352529	+	Intron	DEL	C	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10352529delC	uc001aqx.3	+						KIF1B_uc001aqv.3_Intron|KIF1B_uc001aqw.3_Intron|KIF1B_uc001aqy.2_Intron|KIF1B_uc001aqz.2_Intron|KIF1B_uc001ara.2_Intron|KIF1B_uc001arb.2_Intron	NM_015074	NP_055889	O60333	KIF1B_HUMAN	kinesin family member 1B isoform b						anterograde axon cargo transport|apoptosis|neuromuscular synaptic transmission|neuron-neuron synaptic transmission	cytoplasmic vesicle membrane|microtubule|microtubule associated complex|mitochondrion	ATP binding|ATPase activity|kinesin binding|microtubule motor activity|protein binding			ovary(2)|upper_aerodigestive_tract(1)	3	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)		TGTAGATTTTCCCACAGAAGT	0.373													4	2	---	---	---	---	
CROCCL2	114819	broad.mit.edu	37	1	16804938	16804939	+	5'Flank	DEL	GG	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16804938_16804939delGG	uc001ayr.3	-						CROCCL2_uc001ayt.2_Intron|CROCCL2_uc001ays.2_Intron					Homo sapiens mRNA for KIAA1922 protein, partial cds.												0						TCTCCCTTCAGGACAAGCAGAG	0.629													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	19290557	19290557	+	IGR	DEL	G	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19290557delG								IFFO2 (7731 upstream) : UBR4 (108047 downstream)																							ttcttagtttggggctactag	0.000													4	2	---	---	---	---	
SFRS13A	10772	broad.mit.edu	37	1	24294450	24294451	+	Intron	INS	-	A	A	rs34887415		TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24294450_24294451insA	uc010oee.1	-						SFRS13A_uc001bij.1_Intron	NM_006625	NP_006616	O75494	SRS10_HUMAN	FUS interacting protein (serine-arginine rich) 1						assembly of spliceosomal tri-snRNP|cytoplasmic transport|mRNA export from nucleus|mRNA splice site selection|negative regulation of nuclear mRNA splicing, via spliceosome|regulation of transcription, DNA-dependent	cytoplasm|nuclear speck	nucleotide binding|RNA binding|RS domain binding|unfolded protein binding				0						TACTTGGCTTCAAAAAAAAAAA	0.297													10	9	---	---	---	---	
EXTL1	2134	broad.mit.edu	37	1	26349976	26349976	+	Intron	DEL	A	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26349976delA	uc001blf.2	+							NM_004455	NP_004446	Q92935	EXTL1_HUMAN	exostoses-like 1						skeletal system development	integral to membrane|intrinsic to endoplasmic reticulum membrane	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|protein binding			central_nervous_system(1)	1		Colorectal(325;3.46e-05)|Lung NSC(340;6.18e-05)|all_lung(284;9.43e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;6.44e-26)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|BRCA - Breast invasive adenocarcinoma(304;0.000954)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00594)|READ - Rectum adenocarcinoma(331;0.0649)		ACGCAAGCCCAAAAACGAGGG	0.502													4	2	---	---	---	---	
PHACTR4	65979	broad.mit.edu	37	1	28817721	28817721	+	Intron	DEL	A	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28817721delA	uc001bpw.2	+						PHACTR4_uc001bpv.1_Intron|PHACTR4_uc001bpx.2_Intron|PHACTR4_uc001bpy.2_Intron|PHACTR4_uc001bpz.2_5'Flank	NM_001048183	NP_001041648	Q8IZ21	PHAR4_HUMAN	phosphatase and actin regulator 4 isoform 1								actin binding|protein phosphatase inhibitor activity				0		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;7.01e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;1.35e-21)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0144)|READ - Rectum adenocarcinoma(331;0.0649)		tgtctacattaaaaaaaaaaa	0.040													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	30094676	30094676	+	IGR	DEL	G	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:30094676delG								PTPRU (441361 upstream) : None (None downstream)																							ggtcagcaacgccaggaggca	0.050													4	2	---	---	---	---	
CSMD2	114784	broad.mit.edu	37	1	34038465	34038465	+	Intron	DEL	T	-	-	rs68139900		TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34038465delT	uc001bxn.1	-						CSMD2_uc001bxm.1_Intron	NM_052896	NP_443128	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2							integral to membrane|plasma membrane	protein binding			ovary(6)|skin(5)|pancreas(1)	12		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				TTTTTTCTTCTTTTTTTTTTT	0.358													6	6	---	---	---	---	
LEPRE1	64175	broad.mit.edu	37	1	43218630	43218630	+	Intron	DEL	A	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43218630delA	uc001chv.2	-						LEPRE1_uc001chw.2_Intron|LEPRE1_uc001chx.3_Intron	NM_022356	NP_071751	Q32P28	P3H1_HUMAN	leprecan 1 isoform 1						negative regulation of cell proliferation	endoplasmic reticulum|proteinaceous extracellular matrix	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|procollagen-proline 3-dioxygenase activity			ovary(3)|lung(1)	4	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)			L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)	gggaacgaggaagaactgact	0.080													4	2	---	---	---	---	
ZCCHC11	23318	broad.mit.edu	37	1	52897141	52897141	+	Intron	DEL	A	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52897141delA	uc001ctx.2	-						ZCCHC11_uc001cty.2_Intron|ZCCHC11_uc001ctz.2_Intron|ZCCHC11_uc001cua.1_Intron	NM_015269	NP_056084	Q5TAX3	TUT4_HUMAN	zinc finger, CCHC domain containing 11 isoform						miRNA catabolic process|pre-miRNA processing|RNA 3'-end processing|stem cell maintenance	cytoplasm|nucleolus	nucleic acid binding|protein binding|protein binding|RNA uridylyltransferase activity|zinc ion binding			ovary(2)|skin(1)	3						GACTGCAGACaaaaaaaaaat	0.279													10	6	---	---	---	---	
ODF2L	57489	broad.mit.edu	37	1	86850155	86850160	+	Intron	DEL	AAAAAT	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86850155_86850160delAAAAAT	uc001dll.1	-						ODF2L_uc001dlm.1_Intron|ODF2L_uc001dln.2_Intron|ODF2L_uc001dlo.2_Intron|ODF2L_uc001dlp.2_Intron|ODF2L_uc010osg.1_Intron|ODF2L_uc001dlq.1_Intron|ODF2L_uc009wcr.1_Intron	NM_020729	NP_065780	Q9ULJ1	ODF2L_HUMAN	outer dense fiber of sperm tails 2-like isoform							centrosome				ovary(1)	1				all cancers(265;0.0313)|Epithelial(280;0.0611)		TTTTGAGATGAAAAATAAAAATACAT	0.248													11	9	---	---	---	---	
EPHX4	253152	broad.mit.edu	37	1	92495037	92495039	+	5'Flank	DEL	GCA	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92495037_92495039delGCA	uc001don.2	+							NM_173567	NP_775838	Q8IUS5	EPHX4_HUMAN	abhydrolase domain containing 7							integral to membrane	hydrolase activity			central_nervous_system(1)	1						CCCTGGGGTTGCAGCTCTCTGTA	0.517													4	2	---	---	---	---	
PSMA5	5686	broad.mit.edu	37	1	109955454	109955454	+	Intron	DEL	A	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109955454delA	uc001dxn.2	-						PSMA5_uc010ovj.1_Intron	NM_002790	NP_002781	P28066	PSA5_HUMAN	proteasome alpha 5 subunit						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome core complex, alpha-subunit complex	protein binding|threonine-type endopeptidase activity				0		all_epithelial(167;2.83e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Lung(183;0.045)|Colorectal(144;0.116)|Epithelial(280;0.187)|all cancers(265;0.196)|LUSC - Lung squamous cell carcinoma(189;0.235)		AGGCAAAGCCAAAAAAAAAAG	0.438													6	4	---	---	---	---	
ATXN7L2	127002	broad.mit.edu	37	1	110033134	110033134	+	Intron	DEL	C	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110033134delC	uc001dxr.2	+						ATXN7L2_uc001dxs.2_Intron|ATXN7L2_uc001dxt.2_5'Flank	NM_153340	NP_699171	Q5T6C5	AT7L2_HUMAN	ataxin 7-like 2											ovary(2)	2		all_epithelial(167;0.00197)|all_lung(203;0.00291)|Lung NSC(277;0.00453)		Colorectal(144;0.0129)|Lung(183;0.0426)|Epithelial(280;0.0675)|READ - Rectum adenocarcinoma(129;0.0693)|all cancers(265;0.071)|LUSC - Lung squamous cell carcinoma(189;0.228)		TGGCTATTTGCCAGCAGGACC	0.507											OREG0013635	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
PTPN22	26191	broad.mit.edu	37	1	114380072	114380072	+	Intron	DEL	A	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114380072delA	uc001eds.2	-						PTPN22_uc009wgq.2_Intron|PTPN22_uc010owo.1_Intron|PTPN22_uc001edt.2_Intron|PTPN22_uc009wgr.2_Intron|PTPN22_uc009wgs.2_Intron|PTPN22_uc001edu.2_Intron	NM_015967	NP_057051	Q9Y2R2	PTN22_HUMAN	protein tyrosine phosphatase, non-receptor type						negative regulation of T cell activation|negative regulation of T cell receptor signaling pathway|phosphoanandamide dephosphorylation|regulation of B cell receptor signaling pathway|regulation of natural killer cell proliferation|T cell differentiation	internal side of plasma membrane|nucleus|perinuclear region of cytoplasm	kinase binding|protein tyrosine phosphatase activity|SH3 domain binding			kidney(2)|lung(1)|skin(1)	4	Lung SC(450;0.184)	all_cancers(81;1.93e-08)|all_epithelial(167;4.37e-08)|all_lung(203;5.22e-06)|Lung NSC(69;8.94e-06)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		actccatctcaaaaaaaaaaa	0.035													7	5	---	---	---	---	
SYCP1	6847	broad.mit.edu	37	1	115418989	115418989	+	Intron	DEL	T	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115418989delT	uc001efr.2	+						SYCP1_uc010owt.1_Intron|SYCP1_uc001efq.2_Intron|SYCP1_uc009wgw.2_Intron	NM_003176	NP_003167	Q15431	SYCP1_HUMAN	synaptonemal complex protein 1						cell division|reciprocal meiotic recombination|spermatogenesis|synaptonemal complex assembly		DNA binding			skin(1)	1	Lung SC(450;0.211)	all_cancers(81;8.65e-08)|all_epithelial(167;3.32e-07)|all_lung(203;6.55e-06)|Lung NSC(69;1.11e-05)|Acute lymphoblastic leukemia(138;0.221)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		ACTAATTTTATTTTTTTTTTA	0.159													5	3	---	---	---	---	
NOTCH2	4853	broad.mit.edu	37	1	120510989	120510989	+	Intron	DEL	C	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120510989delC	uc001eik.2	-						NOTCH2_uc001eil.2_Intron|NOTCH2_uc001eim.3_Intron	NM_024408	NP_077719	Q04721	NOTC2_HUMAN	notch 2 preproprotein						anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity			lung(8)|haematopoietic_and_lymphoid_tissue(7)|ovary(4)|central_nervous_system(2)|skin(2)|kidney(2)|breast(1)|prostate(1)	27	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		TACGCAACTTCTGCTTTGCCT	0.498			N|F|Mis		marginal zone lymphoma|DLBCL				Alagille_Syndrome		OREG0013734	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	160076399	160076399	+	IGR	DEL	C	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160076399delC								IGSF8 (7781 upstream) : ATP1A2 (9121 downstream)																							TCATCTGAAGCCCTGCCTGGA	0.542													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	163378867	163378867	+	IGR	DEL	T	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:163378867delT								NUF2 (53314 upstream) : None (None downstream)																							AGGGTTTGGATTTATCATGCA	0.433													4	2	---	---	---	---	
KLHL20	27252	broad.mit.edu	37	1	173710877	173710877	+	Intron	DEL	A	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173710877delA	uc001gjc.2	+						KLHL20_uc010pmr.1_Intron|KLHL20_uc009wwf.2_Intron	NM_014458	NP_055273	Q9Y2M5	KLH20_HUMAN	kelch-like 20						cytoskeleton organization|negative regulation of apoptosis|proteasomal ubiquitin-dependent protein catabolic process|response to interferon-alpha	actin cytoskeleton|cell surface|Cul3-RING ubiquitin ligase complex|Golgi apparatus|perinuclear region of cytoplasm|PML body	actin binding|interferon-gamma binding|ubiquitin-protein ligase activity			ovary(1)	1						ACACAAGAAGAAATGCCTGGT	0.463													4	2	---	---	---	---	
CFHR1	3078	broad.mit.edu	37	1	196794449	196794450	+	Intron	INS	-	T	T	rs146000731	by1000genomes	TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196794449_196794450insT	uc001gtn.2	+						CFHR1_uc001gtm.2_Intron	NM_002113	NP_002104	Q03591	FHR1_HUMAN	complement factor H-related 1 precursor						complement activation	extracellular space					0						AGTTAGTGATGCTTTTCATTCC	0.282													6	9	---	---	---	---	
LGR6	59352	broad.mit.edu	37	1	202173671	202173672	+	Intron	INS	-	AC	AC	rs142174158	by1000genomes	TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202173671_202173672insAC	uc001gxu.2	+						LGR6_uc001gxv.2_Intron|LGR6_uc009xab.2_Intron	NM_001017403	NP_001017403	Q9HBX8	LGR6_HUMAN	leucine-rich repeat-containing G protein-coupled							integral to membrane|plasma membrane	protein-hormone receptor activity			large_intestine(4)|ovary(3)|skin(2)|pancreas(1)	10						acctccttcaaacacacacaca	0.000													5	3	---	---	---	---	
ERO1LB	56605	broad.mit.edu	37	1	236385071	236385072	+	Intron	INS	-	TTAATA	TTAATA	rs10647377		TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236385071_236385072insTTAATA	uc001hxt.2	-							NM_019891	NP_063944	Q86YB8	ERO1B_HUMAN	endoplasmic reticulum oxidoreductin 1-Lbeta						electron transport chain|protein thiol-disulfide exchange|transport	endoplasmic reticulum membrane	flavin adenine dinucleotide binding|oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor|unfolded protein binding				0	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.123)|Acute lymphoblastic leukemia(190;0.205)|Prostate(94;0.219)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)			ACACATATACTTTAATTTTTTC	0.282													32	15	---	---	---	---	
CNST	163882	broad.mit.edu	37	1	246810555	246810555	+	Frame_Shift_Del	DEL	T	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246810555delT	uc001ibp.2	+	9	1430	c.1052delT	c.(1051-1053)CTTfs	p.L351fs	CNST_uc001ibo.3_Frame_Shift_Del_p.L351fs	NM_152609	NP_689822	Q6PJW8	CNST_HUMAN	hypothetical protein LOC163882 isoform 1	351					positive regulation of Golgi to plasma membrane protein transport	integral to membrane|plasma membrane|protein complex|trans-Golgi network|transport vesicle	connexin binding				0						TCCCCAAGCCTTTCGGTAACT	0.582											OREG0014367	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	30	16	---	---	---	---	
PXDN	7837	broad.mit.edu	37	2	1683453	1683454	+	Intron	DEL	AT	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1683453_1683454delAT	uc002qxa.2	-						PXDN_uc002qxb.1_Intron|PXDN_uc002qxc.1_Intron	NM_012293	NP_036425	Q92626	PXDN_HUMAN	peroxidasin precursor						extracellular matrix organization|hydrogen peroxide catabolic process|immune response	endoplasmic reticulum|extracellular space|proteinaceous extracellular matrix	extracellular matrix structural constituent|heme binding|interleukin-1 receptor antagonist activity|peroxidase activity			pancreas(6)|ovary(2)	8	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		TGGATGGCACAtgtgtgtggtc	0.054													5	4	---	---	---	---	
SPAST	6683	broad.mit.edu	37	2	32362049	32362049	+	Intron	DEL	T	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32362049delT	uc002roc.2	+						SPAST_uc002rod.2_Intron	NM_014946	NP_055761	Q9UBP0	SPAST_HUMAN	spastin isoform 1						cell cycle|cell death|cell differentiation|cytokinesis, completion of separation|ER to Golgi vesicle-mediated transport|microtubule bundle formation|microtubule severing|nervous system development|protein hexamerization|protein homooligomerization	endoplasmic reticulum|endosome|integral to membrane|microtubule|microtubule organizing center|nucleus|perinuclear region of cytoplasm|spindle	alpha-tubulin binding|ATP binding|beta-tubulin binding|microtubule binding|microtubule-severing ATPase activity			breast(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					TAAGTGTTGATTATGATATTT	0.294													382	186	---	---	---	---	
FLJ40330	645784	broad.mit.edu	37	2	89104503	89104504	+	Intron	INS	-	C	C	rs149625899	by1000genomes	TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89104503_89104504insC	uc010fhg.2	+						FLJ40330_uc010fhh.2_Intron|FLJ40330_uc010fhi.1_Intron	NR_015424				Homo sapiens mRNA; cDNA DKFZp434J1630 (from clone DKFZp434J1630).												0						gtagatttttttcagattttgg	0.074													33	22	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	96617456	96617456	+	Intron	DEL	T	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96617456delT	uc010yug.1	-											Homo sapiens cDNA FLJ54441 complete cds, highly similar to Homo sapiens ankyrin repeat domain 36 (ANKRD36), mRNA.																		AAAAATGTACTCATATGTAAT	0.234													16	7	---	---	---	---	
NEURL3	93082	broad.mit.edu	37	2	97166139	97166139	+	Frame_Shift_Del	DEL	C	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97166139delC	uc010yuo.1	-	2	622	c.551delG	c.(550-552)GGAfs	p.G184fs	NEURL3_uc010fhx.2_Intron|NEURL3_uc002swc.2_Intron					SubName: Full=cDNA FLJ54814;												0						GCCCCCATCTCCCCACCTCCC	0.632													4	2	---	---	---	---	
ANKRD36B	57730	broad.mit.edu	37	2	98165711	98165716	+	Intron	DEL	CAGCAT	-	-	rs113435370		TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98165711_98165716delCAGCAT	uc010yvc.1	-						ANKRD36B_uc010yve.1_Intron	NM_025190	NP_079466	Q8N2N9	AN36B_HUMAN	ankyrin repeat domain 36B												0						TCCAGACCAGcagcatcagcatcagc	0.218													13	10	---	---	---	---	
TBC1D8	11138	broad.mit.edu	37	2	101624051	101624052	+	3'UTR	INS	-	GTAA	GTAA			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101624051_101624052insGTAA	uc010fiv.2	-	20					RPL31_uc010yvu.1_Intron|RPL31_uc010yvv.1_Intron|RPL31_uc010fiu.1_Intron|TBC1D8_uc002tau.3_3'UTR	NM_001102426	NP_001095896	O95759	TBCD8_HUMAN	TBC1 domain family, member 8						blood circulation|positive regulation of cell proliferation	intracellular|membrane	calcium ion binding|Rab GTPase activator activity			ovary(3)	3						CGGTAAAAATTGTAAGTTGGCA	0.431													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	103502127	103502127	+	IGR	DEL	T	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:103502127delT								TMEM182 (67991 upstream) : None (None downstream)																							aaaaaaaagcttttttttttt	0.050													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	118162205	118162205	+	IGR	DEL	T	-	-	rs75322796		TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:118162205delT								None (None upstream) : DDX18 (410050 downstream)																							TCTAAACAACTTTTTTTTGTT	0.358													7	4	---	---	---	---	
POLR2D	5433	broad.mit.edu	37	2	128605982	128605982	+	Intron	DEL	T	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128605982delT	uc002tpj.2	-						uc010fmc.2_5'Flank|POLR2D_uc002tpk.2_Intron	NM_004805	NP_004796	O15514	RPB4_HUMAN	DNA directed RNA polymerase II polypeptide D						mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of viral transcription|protein phosphorylation|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	DNA-directed RNA polymerase II, core complex	DNA-directed RNA polymerase activity|nucleotide binding				0	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0675)		GACTTAGAGGttttttttttt	0.139													6	5	---	---	---	---	
MCM6	4175	broad.mit.edu	37	2	136630022	136630023	+	Intron	INS	-	AAAC	AAAC	rs140829752	by1000genomes	TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136630022_136630023insAAAC	uc002tuw.2	-							NM_005915	NP_005906	Q14566	MCM6_HUMAN	minichromosome maintenance complex component 6						cell cycle checkpoint|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle	MCM complex	ATP binding|identical protein binding				0				BRCA - Breast invasive adenocarcinoma(221;0.166)	Atorvastatin(DB01076)	tccgtctcaaaaaacaaacaaa	0.134													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	164350017	164350017	+	IGR	DEL	T	-	-	rs77274994		TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:164350017delT								KCNH7 (654777 upstream) : FIGN (114101 downstream)																							TTTATAAAAATAAAATCCTGC	0.408													6	3	---	---	---	---	
TLK1	9874	broad.mit.edu	37	2	171923670	171923671	+	Intron	INS	-	T	T	rs146279997		TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171923670_171923671insT	uc002ugn.2	-						TLK1_uc002ugo.2_Intron|TLK1_uc002ugp.2_Intron|TLK1_uc002ugq.2_Intron|TLK1_uc010zdn.1_5'Flank	NM_012290	NP_036422	Q9UKI8	TLK1_HUMAN	tousled-like kinase 1 isoform 1						cell cycle|chromatin modification|intracellular protein transport|intracellular signal transduction|regulation of chromatin assembly or disassembly|response to DNA damage stimulus	nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(1)	1						gtgcacttaggttttttttttt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	175636868	175636869	+	Intron	INS	-	T	T	rs145883525	by1000genomes	TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175636868_175636869insT	uc002uiw.2	+											Homo sapiens cDNA FLJ11228 fis, clone PLACE1008329.																		AGTTTCTTCTGTTTTTTTTTTC	0.441											OREG0015080	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	2	4	---	---	---	---	
HECW2	57520	broad.mit.edu	37	2	197280335	197280336	+	Intron	INS	-	C	C	rs150111937	by1000genomes	TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197280335_197280336insC	uc002utm.1	-							NM_020760	NP_065811	Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm	ubiquitin-protein ligase activity			skin(5)|ovary(5)|lung(4)|pancreas(2)|central_nervous_system(1)|kidney(1)	18						agctgagctttcgtgcatgaca	0.084													5	4	---	---	---	---	
SF3B1	23451	broad.mit.edu	37	2	198262521	198262521	+	Intron	DEL	A	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198262521delA	uc002uue.2	-							NM_012433	NP_036565	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1 isoform 1						nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome|nuclear speck|U12-type spliceosomal complex	protein binding			pancreas(3)|ovary(1)|breast(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.246)			actccgtctcaaaaaaaaaaa	0.144													6	4	---	---	---	---	
MDH1B	130752	broad.mit.edu	37	2	207604137	207604137	+	Intron	DEL	A	-	-	rs141240854		TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207604137delA	uc002vbs.2	-						MDH1B_uc010ziw.1_Intron|MDH1B_uc010fui.2_Intron|MDH1B_uc010fuj.2_Intron|MDH1B_uc002vbt.2_Intron	NM_001039845	NP_001034934	Q5I0G3	MDH1B_HUMAN	malate dehydrogenase 1B, NAD (soluble)						carbohydrate metabolic process|malate metabolic process|tricarboxylic acid cycle		binding|malate dehydrogenase activity			ovary(3)|kidney(1)	4				LUSC - Lung squamous cell carcinoma(261;0.0763)|Epithelial(149;0.131)|Lung(261;0.145)		accttgtcttaaaaaaaaaaa	0.249													12	7	---	---	---	---	
RHBDD1	84236	broad.mit.edu	37	2	227773299	227773300	+	Intron	DEL	AC	-	-	rs10559846		TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227773299_227773300delAC	uc002voi.2	+						RHBDD1_uc010fxc.2_Intron|RHBDD1_uc002voj.2_Intron	NM_032276	NP_115652	Q8TEB9	RHBD1_HUMAN	rhomboid domain containing 1							integral to membrane	serine-type endopeptidase activity			ovary(1)	1		Renal(207;0.023)|all_lung(227;0.13)|Esophageal squamous(248;0.23)|all_hematologic(139;0.248)		Epithelial(121;1.47e-11)|all cancers(144;1.52e-08)|Lung(261;0.0128)|LUSC - Lung squamous cell carcinoma(224;0.0175)		ATTTTCCACTacacacacacac	0.371													14	8	---	---	---	---	
MFF	56947	broad.mit.edu	37	2	228204808	228204809	+	Intron	DEL	GT	-	-	rs112978620		TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228204808_228204809delGT	uc002vos.2	+						MFF_uc002vot.2_Intron|MFF_uc002vou.2_Intron|MFF_uc002vov.2_Intron|MFF_uc002vow.2_Intron|MFF_uc002vox.2_Intron|MFF_uc002voy.2_Intron|MFF_uc002voz.2_Intron	NM_020194	NP_064579	Q9GZY8	MFF_HUMAN	mitochondrial fission factor							integral to membrane|mitochondrial outer membrane				large_intestine(1)	1						AGTAAGTAGGGTGTGTGTGTGT	0.337													4	2	---	---	---	---	
AGFG1	3267	broad.mit.edu	37	2	228336468	228336469	+	5'Flank	DEL	GC	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228336468_228336469delGC	uc002vpc.2	+						AGFG1_uc002vpd.2_5'Flank|AGFG1_uc002vpe.2_5'Flank|AGFG1_uc002vpf.2_5'Flank	NM_004504	NP_004495	P52594	AGFG1_HUMAN	HIV-1 Rev binding protein isoform 2						cell differentiation|mRNA export from nucleus|multicellular organismal development|regulation of ARF GTPase activity|spermatogenesis	cytoplasmic membrane-bounded vesicle|Golgi apparatus|nuclear pore	ARF GTPase activator activity|DNA binding|protein binding|RNA binding|zinc ion binding			skin(2)|ovary(1)|central_nervous_system(1)	4						caaaggtcctgcaggagtcaga	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	228670597	228670605	+	IGR	DEL	CGCGGGGAA	-	-	rs66843448		TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228670597_228670605delCGCGGGGAA								SLC19A3 (87852 upstream) : CCL20 (7953 downstream)																							atcgagcaagcgcggggaacgtgactggg	0.000													4	2	---	---	---	---	
NCL	4691	broad.mit.edu	37	2	232325998	232325998	+	Intron	DEL	A	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232325998delA	uc002vru.2	-						SNORD82_uc010fxw.1_5'Flank	NM_005381	NP_005372	P19338	NUCL_HUMAN	nucleolin						angiogenesis	cell cortex|nucleolus|ribonucleoprotein complex	nucleotide binding|protein C-terminus binding|RNA binding|telomeric DNA binding			ovary(2)|pancreas(1)	3		Ovarian(221;1.34e-05)|Renal(207;0.0112)|Lung NSC(271;0.0339)|all_lung(227;0.0616)|all_hematologic(139;0.0748)|Hepatocellular(293;0.137)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.65e-111)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.014)|COAD - Colon adenocarcinoma(134;0.141)|STAD - Stomach adenocarcinoma(1183;0.18)		aaaaaaatttaaaaaaaaaaa	0.119													6	4	---	---	---	---	
VHL	7428	broad.mit.edu	37	3	10191649	10191650	+	3'UTR	DEL	AA	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10191649_10191650delAA	uc003bvc.2	+	3					VHL_uc003bvd.2_3'UTR	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1						anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.?(1)|p.*214C(1)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		TGGGAGATTGAAGATTTCTGTT	0.455		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				19	23	---	---	---	---	
WDR48	57599	broad.mit.edu	37	3	39107048	39107048	+	Intron	DEL	A	-	-	rs34404622		TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39107048delA	uc003cit.2	+						WDR48_uc011ayt.1_Intron|WDR48_uc011ayu.1_Intron|WDR48_uc011ayv.1_Intron|WDR48_uc003ciu.2_Intron	NM_020839	NP_065890	Q8TAF3	WDR48_HUMAN	WD repeat domain 48						interspecies interaction between organisms|protein deubiquitination	lysosome|nucleus	protein binding			ovary(1)|breast(1)	2				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		TTAACAAGGCAAAAAAAAAAA	0.363													3	6	---	---	---	---	
TGM4	7047	broad.mit.edu	37	3	44945571	44945572	+	Intron	INS	-	G	G			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44945571_44945572insG	uc003coc.3	+							NM_003241	NP_003232	P49221	TGM4_HUMAN	transglutaminase 4 (prostate)						peptide cross-linking|protein polyamination		acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.00963)|KIRC - Kidney renal clear cell carcinoma(197;0.0546)|Kidney(197;0.0686)	L-Glutamine(DB00130)	GCCAAGCAGGTGGGGAAAGTTT	0.515													4	2	---	---	---	---	
CCR3	1232	broad.mit.edu	37	3	46271345	46271345	+	Intron	DEL	A	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46271345delA	uc003cpg.1	+							NM_178329	NP_847899	P51677	CCR3_HUMAN	CC chemokine receptor 3 isoform 1						cell adhesion|cellular defense response|chemotaxis|elevation of cytosolic calcium ion concentration|G-protein signaling, coupled to cAMP nucleotide second messenger|inflammatory response|interspecies interaction between organisms|positive regulation of angiogenesis	integral to plasma membrane				ovary(3)|lung(3)|breast(1)|kidney(1)	8				BRCA - Breast invasive adenocarcinoma(193;0.00119)|KIRC - Kidney renal clear cell carcinoma(197;0.0183)|Kidney(197;0.0216)		atgtgctgagaaaaaaaaaca	0.055													3	3	---	---	---	---	
SETD2	29072	broad.mit.edu	37	3	47142941	47142943	+	Intron	DEL	TAC	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47142941_47142943delTAC	uc003cqs.2	-						SETD2_uc003cqv.2_Intron	NM_014159	NP_054878	Q9BYW2	SETD2_HUMAN	SET domain containing 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	DNA binding|histone-lysine N-methyltransferase activity|oxidoreductase activity|transition metal ion binding			kidney(24)|ovary(5)|skin(1)|central_nervous_system(1)|breast(1)	32		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		GTAGAAACAATACTTACCCATAT	0.355			N|F|S|Mis		clear cell renal carcinoma								144	63	---	---	---	---	
SMARCC1	6599	broad.mit.edu	37	3	47734484	47734484	+	Intron	DEL	A	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47734484delA	uc003crq.2	-						SMARCC1_uc011bbd.1_Intron	NM_003074	NP_003065	Q92922	SMRC1_HUMAN	SWI/SNF-related matrix-associated						chromatin remodeling|nervous system development|transcription, DNA-dependent	nBAF complex|npBAF complex|nucleoplasm|SWI/SNF complex|WINAC complex	DNA binding|protein N-terminus binding|transcription coactivator activity			skin(2)|lung(1)	3				BRCA - Breast invasive adenocarcinoma(193;7.47e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)		attccgtcttaaaaaaaaaag	0.000													5	3	---	---	---	---	
COL7A1	1294	broad.mit.edu	37	3	48626634	48626634	+	Intron	DEL	G	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48626634delG	uc003ctz.2	-							NM_000094	NP_000085	Q02388	CO7A1_HUMAN	alpha 1 type VII collagen precursor						cell adhesion|epidermis development	basement membrane|collagen type VII	protein binding|serine-type endopeptidase inhibitor activity			ovary(4)|breast(3)|skin(3)|central_nervous_system(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		TAATCAGTGTGGGGTGGGTCA	0.622													4	2	---	---	---	---	
ARIH2	10425	broad.mit.edu	37	3	48964875	48964875	+	Intron	DEL	T	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48964875delT	uc003cvb.2	+						ARIH2_uc003cvc.2_Intron|ARIH2_uc003cvf.2_5'UTR|ARIH2_uc010hkl.2_5'Flank|ARIH2_uc003cvd.1_Intron|ARIH2_uc003cve.1_Intron	NM_006321	NP_006312	O95376	ARI2_HUMAN	ariadne homolog 2						developmental cell growth|hemopoietic stem cell proliferation|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	nucleic acid binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;9.42e-05)|Kidney(197;0.00258)|KIRC - Kidney renal clear cell carcinoma(197;0.00269)		GTAACACTTATTTTTTTTTTC	0.408													3	3	---	---	---	---	
MON1A	84315	broad.mit.edu	37	3	49950989	49950990	+	Intron	INS	-	A	A			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49950989_49950990insA	uc003cxz.2	-						MON1A_uc003cya.2_Intron|MON1A_uc003cyb.2_Intron|MON1A_uc010hlb.2_Intron	NM_032355	NP_115731	Q86VX9	MON1A_HUMAN	MON1 homolog A isoform a								protein binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(193;4.62e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)		atattcattgtaaaaaaaagac	0.094													4	2	---	---	---	---	
POC1A	25886	broad.mit.edu	37	3	52181250	52181250	+	Intron	DEL	T	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52181250delT	uc003dcu.2	-						POC1A_uc003dcv.2_Intron|POC1A_uc003dcw.2_Intron	NM_015426	NP_056241	Q8NBT0	POC1A_HUMAN	WD repeat domain 51A isoform 1							centriole|microtubule basal body					0						CCTGCTGTGATTTTTTTTTTT	0.443													4	3	---	---	---	---	
COL8A1	1295	broad.mit.edu	37	3	99383811	99383811	+	Intron	DEL	C	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:99383811delC	uc003dtg.1	+						COL8A1_uc003dth.1_Intron|COL8A1_uc010hpe.1_Intron	NM_001850	NP_001841	P27658	CO8A1_HUMAN	alpha 1 type VIII collagen precursor						angiogenesis|cell adhesion	basement membrane|collagen type VIII					0						GATGCCAGGTCCCACCTGCAG	0.353													4	2	---	---	---	---	
LOC285205	285205	broad.mit.edu	37	3	107609946	107609946	+	Intron	DEL	A	-	-	rs147319621		TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:107609946delA	uc003dws.3	+							NR_015394				Homo sapiens cDNA clone IMAGE:5721886.												0						actcagtctcaaaaaaaaaaa	0.000													10	6	---	---	---	---	
SIDT1	54847	broad.mit.edu	37	3	113326743	113326743	+	Intron	DEL	G	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113326743delG	uc003eak.2	+						SIDT1_uc011bif.1_Intron|SIDT1_uc003eaj.1_Intron|SIDT1_uc011big.1_Intron|SIDT1_uc011bih.1_Intron|SIDT1_uc011bii.1_Intron	NM_017699	NP_060169	Q9NXL6	SIDT1_HUMAN	SID1 transmembrane family, member 1 precursor							integral to membrane				ovary(3)|pancreas(1)|skin(1)	5						CAGTCACGTTGTCACAGGCTA	0.418													4	2	---	---	---	---	
OSBPL11	114885	broad.mit.edu	37	3	125297615	125297615	+	Intron	DEL	A	-	-	rs67679539		TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125297615delA	uc003eic.2	-							NM_022776	NP_073613	Q9BXB4	OSB11_HUMAN	oxysterol binding protein-like 11						lipid transport		lipid binding			ovary(3)|breast(1)|kidney(1)	5						actccgtctcaaaaaaaaaaa	0.000													11	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	125624220	125624223	+	IGR	DEL	GATG	-	-	rs149876568		TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125624220_125624223delGATG								MIR548I1 (114825 upstream) : LOC100125556 (11221 downstream)																							ctacccgtgtgatggatggaacat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	129717843	129717844	+	IGR	DEL	AG	-	-	rs75643277		TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129717843_129717844delAG								TRH (21067 upstream) : ALG1L2 (82830 downstream)																							AAAAAAAAAAAGGAAGcagtct	0.183													4	2	---	---	---	---	
MECOM	2122	broad.mit.edu	37	3	168862968	168862981	+	Intron	DEL	ACACACACACAGAG	-	-	rs67598122		TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:168862968_168862981delACACACACACAGAG	uc003ffi.3	-						MECOM_uc003ffj.3_Intron|MECOM_uc011bpi.1_Intron|MECOM_uc003ffn.3_Intron|MECOM_uc003ffk.2_Intron|MECOM_uc003ffl.2_Intron|MECOM_uc011bpj.1_Intron|MECOM_uc011bpk.1_Intron|MECOM_uc010hwn.2_Intron|MECOM_uc003ffm.1_Splice_Site	NM_005241	NP_005232	Q03112	EVI1_HUMAN	MDS1 and EVI1 complex locus isoform b						apoptosis|cell differentiation|hemopoietic stem cell proliferation|negative regulation of JNK cascade|negative regulation of programmed cell death|negative regulation of transcription, DNA-dependent|regulation of cell cycle	nuclear speck	DNA binding|protein binding|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(5)|skin(5)|upper_aerodigestive_tract(1)|central_nervous_system(1)|ovary(1)|pancreas(1)	14						acacacacacacacacacacaGAGAGAAATCAAA	0.248													25	13	---	---	---	---	
VPS8	23355	broad.mit.edu	37	3	184560716	184560716	+	Intron	DEL	T	-	-	rs68026955		TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184560716delT	uc003fpb.1	+						VPS8_uc010hyd.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)			AGTTTTCCTCTTTTTTTTTTT	0.269													10	8	---	---	---	---	
RELL1	768211	broad.mit.edu	37	4	37636845	37636845	+	Intron	DEL	A	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37636845delA	uc003gsz.2	-						RELL1_uc010ifc.2_Intron	NM_001085399	NP_001078868	Q8IUW5	RELL1_HUMAN	receptor expressed in lymphoid tissues like 1							cytoplasm|integral to membrane|microtubule cytoskeleton|plasma membrane					0						AAATTGAAAGAAAAAAAAAAG	0.398													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49323455	49323456	+	IGR	DEL	AG	-	-	rs76831553	by1000genomes	TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49323455_49323456delAG								CWH43 (259362 upstream) : None (None downstream)																							ccgcacacacagaaacacacac	0.223													4	2	---	---	---	---	
UBA6	55236	broad.mit.edu	37	4	68529846	68529846	+	Intron	DEL	A	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68529846delA	uc003hdg.3	-						UBA6_uc003hdi.2_Intron|UBA6_uc003hdj.2_Intron	NM_018227	NP_060697	A0AVT1	UBA6_HUMAN	ubiquitin-activating enzyme E1-like 2						protein ubiquitination|ubiquitin-dependent protein catabolic process	cytoplasm	ATP binding|FAT10 activating enzyme activity|ligase activity|protein binding				0						GACCATACTTAAAAAAAAAAG	0.274													14	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	85405986	85405987	+	IGR	INS	-	T	T			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85405986_85405987insT								AGPAT9 (878961 upstream) : NKX6-1 (8449 downstream)																							ACACCTAAGGCTTTTTCTAGCC	0.480													4	2	---	---	---	---	
LOC285501	285501	broad.mit.edu	37	4	178882315	178882316	+	Intron	INS	-	A	A	rs143225684	by1000genomes	TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:178882315_178882316insA	uc010iru.2	+							NR_028342				Homo sapiens cDNA clone IMAGE:4828874.												0		all_lung(41;6.03e-08)|Lung NSC(41;4.26e-07)|Breast(14;0.00066)|Melanoma(52;0.00168)|Prostate(90;0.0129)|all_hematologic(60;0.0202)|Renal(120;0.0246)|Colorectal(36;0.0508)|Hepatocellular(41;0.236)		all cancers(43;9.24e-25)|Epithelial(43;6.28e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.29e-10)|LUSC - Lung squamous cell carcinoma(1;2.61e-05)|Lung(1;3.22e-05)|GBM - Glioblastoma multiforme(59;0.000185)|Colorectal(24;0.000244)|STAD - Stomach adenocarcinoma(60;0.000777)|COAD - Colon adenocarcinoma(29;0.000884)		GTTATTTTGGGAAAAATATTTT	0.292													11	11	---	---	---	---	
FRG1	2483	broad.mit.edu	37	4	190874469	190874470	+	Intron	INS	-	A	A	rs147303533	by1000genomes	TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190874469_190874470insA	uc003izs.2	+							NM_004477	NP_004468	Q14331	FRG1_HUMAN	FSHD region gene 1						rRNA processing	Cajal body|catalytic step 2 spliceosome|nuclear speck|nucleolus					0		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)		all cancers(3;1.73e-30)|Epithelial(3;5.85e-30)|OV - Ovarian serous cystadenocarcinoma(60;5.56e-15)|BRCA - Breast invasive adenocarcinoma(30;9.14e-06)|Lung(3;3.54e-05)|STAD - Stomach adenocarcinoma(60;8.83e-05)|LUSC - Lung squamous cell carcinoma(40;0.000198)|GBM - Glioblastoma multiforme(59;0.00892)|READ - Rectum adenocarcinoma(43;0.161)		TGCTAGGCTGGAAAAAAAATAA	0.262													12	7	---	---	---	---	
ADCY2	108	broad.mit.edu	37	5	7713286	7713286	+	Intron	DEL	A	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7713286delA	uc003jdz.1	+						ADCY2_uc011cmo.1_Intron	NM_020546	NP_065433	Q08462	ADCY2_HUMAN	adenylate cyclase 2						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	cytoplasm|dendrite|integral to membrane|plasma membrane	ATP binding|metal ion binding			ovary(5)|pancreas(1)|skin(1)	7						AATGTGTGGTAAAAAAAAAAG	0.234													6	3	---	---	---	---	
DNAH5	1767	broad.mit.edu	37	5	13842159	13842160	+	Intron	INS	-	A	A	rs147371351	by1000genomes	TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13842159_13842160insA	uc003jfd.2	-							NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5						microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|skin(13)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|pancreas(1)	31	Lung NSC(4;0.00476)					TTCAAAACAATAAAAAAAAAAG	0.183									Kartagener_syndrome				12	6	---	---	---	---	
GOLPH3	64083	broad.mit.edu	37	5	32168712	32168712	+	Intron	DEL	A	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32168712delA	uc003jhp.1	-							NM_022130	NP_071413	Q9H4A6	GOLP3_HUMAN	golgi phosphoprotein 3						cell proliferation|positive regulation of TOR signaling cascade|regulation of mitochondrion organization	cytosol|endosome|Golgi cisterna membrane|mitochondrial intermembrane space|plasma membrane|trans-Golgi network	protein binding			ovary(1)	1						ATCAGACTGGAAAAAAACAGT	0.413													4	2	---	---	---	---	
TTC23L	153657	broad.mit.edu	37	5	34866750	34866751	+	Intron	INS	-	T	T	rs146977766	by1000genomes	TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34866750_34866751insT	uc003jiu.2	+						TTC23L_uc003jiv.2_Intron|TTC23L_uc010iut.1_Intron	NM_144725	NP_653326	Q6PF05	TT23L_HUMAN	tetratricopeptide repeat domain 23-like								binding			central_nervous_system(1)	1						TTTCCATTTGCTTTTTAAAAAA	0.317													4	6	---	---	---	---	
SKIV2L2	23517	broad.mit.edu	37	5	54652998	54652998	+	Intron	DEL	G	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54652998delG	uc003jpy.3	+						SKIV2L2_uc011cqi.1_Intron	NM_015360	NP_056175	P42285	SK2L2_HUMAN	superkiller viralicidic activity 2-like 2						maturation of 5.8S rRNA	catalytic step 2 spliceosome|nucleolus	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			ovary(1)|skin(1)	2		Lung NSC(810;0.000744)|Breast(144;0.181)|Prostate(74;0.194)				TACCCCTCCTGGTACTTGATC	0.537													4	2	---	---	---	---	
ADAMTS6	11174	broad.mit.edu	37	5	64506454	64506454	+	Intron	DEL	A	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64506454delA	uc003jtp.2	-						ADAMTS6_uc003jto.2_Intron|ADAMTS6_uc003jtq.2_Intron	NM_197941	NP_922932	Q9UKP5	ATS6_HUMAN	ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding				0		Lung NSC(167;2.44e-06)|Prostate(74;0.014)|Ovarian(174;0.0549)|Breast(144;0.111)|Colorectal(97;0.235)		Lung(70;0.00942)		CTATGGATGGAGGCTTGTCTA	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	65537204	65537206	+	IGR	DEL	CAG	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:65537204_65537206delCAG								SFRS12 (60492 upstream) : MAST4 (354970 downstream)																							aaaagacacacagatgctttgga	0.000													4	2	---	---	---	---	
NAIP	4671	broad.mit.edu	37	5	70343688	70343688	+	Intron	DEL	T	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:70343688delT	uc003kat.1	-						GTF2H2_uc003kav.3_Intron|GTF2H2_uc003kau.3_Intron|GTF2H2_uc011crt.1_Intron	NM_022892	NP_075043	Q13075	BIRC1_HUMAN	NLR family, apoptosis inhibitory protein isoform						anti-apoptosis|apoptosis|nervous system development	basolateral plasma membrane|cytoplasm	caspase inhibitor activity|metal ion binding|nucleoside-triphosphatase activity|nucleotide binding			central_nervous_system(1)	1		Lung NSC(167;4.15e-05)|Prostate(74;0.00996)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;3.04e-60)|Epithelial(20;7.09e-58)|all cancers(19;1.13e-53)|Lung(70;0.0174)		gtagttttaattttttttttc	0.104													7	4	---	---	---	---	
ANKRA2	57763	broad.mit.edu	37	5	72857292	72857292	+	Intron	DEL	A	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72857292delA	uc003kcu.1	-						ANKRA2_uc003kcv.2_Intron	NM_023039	NP_075526	Q9H9E1	ANRA2_HUMAN	ankyrin repeat, family A (RFXANK-like), 2							cytoskeleton|cytosol|membrane	low-density lipoprotein particle binding				0		Lung NSC(167;0.0378)|Ovarian(174;0.0908)		OV - Ovarian serous cystadenocarcinoma(47;3.71e-54)		ATGGTTAGTCAAAAAAAAAAA	0.149													11	7	---	---	---	---	
SSBP2	23635	broad.mit.edu	37	5	80742368	80742369	+	Intron	INS	-	C	C			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80742368_80742369insC	uc003kho.2	-						RNU5E_uc011cto.1_Intron|SSBP2_uc010jar.2_Intron|SSBP2_uc003khn.2_Intron|SSBP2_uc003khp.2_Intron|SSBP2_uc011ctp.1_Intron|SSBP2_uc011ctq.1_Intron|SSBP2_uc011ctr.1_Intron	NM_012446	NP_036578	P81877	SSBP2_HUMAN	single-stranded DNA binding protein 2						regulation of transcription, DNA-dependent	cytoplasm|nucleus	single-stranded DNA binding		SSBP2/JAK2(4)	haematopoietic_and_lymphoid_tissue(4)|skin(1)	5		Lung NSC(167;0.00154)|all_lung(232;0.00179)|Ovarian(174;0.0338)		OV - Ovarian serous cystadenocarcinoma(54;1.07e-41)|Epithelial(54;2.79e-35)|all cancers(79;1.18e-29)		TTTATTCAGAAATTTTCTAAAT	0.277													3	4	---	---	---	---	
ERAP1	51752	broad.mit.edu	37	5	96100743	96100745	+	Intron	DEL	CTC	-	-	rs34365401		TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96100743_96100745delCTC	uc003kml.2	-						CAST_uc003klt.2_Intron|CAST_uc003klu.2_Intron|CAST_uc003klv.2_Intron|CAST_uc003klw.2_Intron|CAST_uc003klx.2_Intron|CAST_uc003kly.2_Intron|CAST_uc011cuo.1_Intron|CAST_uc003klz.1_Intron|CAST_uc011cur.1_Intron|CAST_uc011cus.1_Intron|CAST_uc003kma.1_Intron|CAST_uc011cut.1_Intron|CAST_uc003kmb.2_Intron|CAST_uc003kmc.2_Intron|CAST_uc003kmd.2_Intron|CAST_uc003kme.2_Intron|CAST_uc003kmf.2_Intron|CAST_uc003kmh.2_Intron|CAST_uc010jbj.2_Intron|CAST_uc010jbk.2_Intron|CAST_uc010jbl.1_Intron|CAST_uc003kmi.2_Intron|CAST_uc003kmj.2_Intron|CAST_uc003kmk.2_Intron	NM_016442	NP_057526	Q9NZ08	ERAP1_HUMAN	type 1 tumor necrosis factor receptor shedding						angiogenesis|antigen processing and presentation of endogenous peptide antigen via MHC class I|fat cell differentiation|membrane protein ectodomain proteolysis|regulation of blood pressure|regulation of innate immune response|response to bacterium	cytosol|endoplasmic reticulum lumen|endoplasmic reticulum membrane|extracellular region|integral to membrane	aminopeptidase activity|interleukin-1, Type II receptor binding|interleukin-6 receptor binding|metalloexopeptidase activity|zinc ion binding			ovary(1)|pancreas(1)	2		all_cancers(142;1.75e-06)|all_epithelial(76;3.08e-09)|all_lung(232;0.000435)|Lung NSC(167;0.000601)|Ovarian(225;0.024)|Colorectal(57;0.0432)|Breast(839;0.244)		all cancers(79;7.26e-15)|COAD - Colon adenocarcinoma(37;0.071)		TGCCGCTCTTCTCCTGATCTTCC	0.552													9	8	---	---	---	---	
ERAP2	64167	broad.mit.edu	37	5	96251189	96251190	+	Intron	DEL	TT	-	-	rs35533963		TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96251189_96251190delTT	uc003kmq.2	+						uc003kmo.1_Intron|ERAP2_uc003kmt.2_Intron|ERAP2_uc003kmr.2_Intron|ERAP2_uc003kms.2_Intron|ERAP2_uc003kmu.2_Intron	NM_022350	NP_071745	Q6P179	ERAP2_HUMAN	endoplasmic reticulum aminopeptidase 2						antigen processing and presentation of endogenous peptide antigen via MHC class I|proteolysis|regulation of blood pressure	endoplasmic reticulum lumen|endoplasmic reticulum membrane|integral to membrane	aminopeptidase activity|metallopeptidase activity|zinc ion binding				0		all_cancers(142;0.000311)|all_epithelial(76;1.54e-06)|all_lung(232;0.0131)|Lung NSC(167;0.0161)|Colorectal(57;0.0596)|Ovarian(225;0.105)		COAD - Colon adenocarcinoma(37;0.0703)		TGTATCTACATTTTCATTTTAT	0.238													14	15	---	---	---	---	
STARD4	134429	broad.mit.edu	37	5	110835388	110835388	+	3'UTR	DEL	A	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:110835388delA	uc003kph.1	-	6					STARD4_uc010jbw.1_3'UTR|STARD4_uc010jbx.1_3'UTR|STARD4_uc003kpi.1_RNA	NM_139164	NP_631903	Q96DR4	STAR4_HUMAN	StAR-related lipid transfer (START) domain						lipid transport		lipid binding			ovary(1)	1		all_cancers(142;0.00259)|all_epithelial(76;8.32e-05)|Prostate(80;0.0115)|Colorectal(10;0.0959)|Ovarian(225;0.156)|all_lung(232;0.18)|Lung NSC(167;0.248)		OV - Ovarian serous cystadenocarcinoma(64;4.91e-09)|Epithelial(69;1.39e-08)|all cancers(49;2.34e-06)|COAD - Colon adenocarcinoma(37;0.049)|Colorectal(14;0.138)		ctcaaaatttaaaaaaaaaaa	0.129													15	7	---	---	---	---	
NDST1	3340	broad.mit.edu	37	5	149918331	149918332	+	Intron	DEL	AC	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149918331_149918332delAC	uc003lsk.3	+						NDST1_uc011dcj.1_Intron|NDST1_uc003lsl.2_Intron	NM_001543	NP_001534	P52848	NDST1_HUMAN	N-deacetylase/N-sulfotransferase (heparan						heparan sulfate proteoglycan biosynthetic process|inflammatory response	Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine N-sulfotransferase activity|hydrolase activity			breast(1)|skin(1)	2		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			tgaggtggtgacaaggcaggcc	0.282													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	172816631	172816631	+	IGR	DEL	T	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172816631delT								STC2 (60125 upstream) : LOC285593 (190015 downstream)																							gtcctcatcattttttttttg	0.000													4	2	---	---	---	---	
CPLX2	10814	broad.mit.edu	37	5	175294808	175294808	+	Intron	DEL	G	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175294808delG	uc003mde.1	+							NM_006650	NP_006641	Q6PUV4	CPLX2_HUMAN	complexin 2						mast cell degranulation|positive regulation of synaptic plasticity|vesicle docking involved in exocytosis	cytosol				ovary(1)	1	all_cancers(89;0.004)|Renal(175;0.000269)|Lung NSC(126;0.00441)|all_lung(126;0.00747)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			CCACACTGCTGGGCACTCAAA	0.572													4	2	---	---	---	---	
RNF130	55819	broad.mit.edu	37	5	179390938	179390939	+	Intron	DEL	TC	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179390938_179390939delTC	uc003mll.1	-						RNF130_uc003mlm.1_Intron	NM_018434	NP_060904	Q86XS8	GOLI_HUMAN	ring finger protein 130 precursor						apoptosis	cytoplasm|integral to membrane|nucleus	ubiquitin-protein ligase activity|zinc ion binding			lung(2)|ovary(1)	3	all_cancers(89;5.49e-05)|all_epithelial(37;1.94e-05)|Renal(175;0.000159)|Lung NSC(126;0.00118)|all_lung(126;0.00212)	all_cancers(40;0.0294)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TTTATAACCTTCTTTCCTTCTT	0.401													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	17025760	17025760	+	IGR	DEL	T	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17025760delT								ATXN1 (264039 upstream) : RBM24 (256049 downstream)																							gccgcaggggtggaacactcg	0.000													4	2	---	---	---	---	
FAM65B	9750	broad.mit.edu	37	6	24850326	24850326	+	Intron	DEL	T	-	-	rs144920885		TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24850326delT	uc003neo.1	-						FAM65B_uc011djs.1_Intron|FAM65B_uc011dju.1_Intron|FAM65B_uc003nep.2_Intron|FAM65B_uc011djt.1_Intron	NM_014722	NP_055537	Q9Y4F9	FA65B_HUMAN	hypothetical protein LOC9750 isoform 1						cell differentiation|muscle organ development	cytoskeleton|filopodium|mitochondrion	binding			ovary(1)	1						tttctttttcttttttttttt	0.144													10	6	---	---	---	---	
LOC285830	285830	broad.mit.edu	37	6	29712722	29712722	+	Intron	DEL	A	-	-	rs11315966		TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29712722delA	uc003nnp.2	-						LOC285830_uc011dlz.1_Intron|LOC285830_uc003rsi.3_Intron	NR_026972				Homo sapiens cDNA FLJ35429 fis, clone SMINT2002126.												0						CTACTTTCACAGTACCTGTTT	0.517													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	32428097	32428098	+	IGR	INS	-	G	G	rs147642819	by1000genomes	TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32428097_32428098insG								HLA-DRA (15276 upstream) : HLA-DRB1 (57065 downstream)																							GACGCCTCTTTGCAAGGCTCTG	0.579													4	3	---	---	---	---	
LOC100132354	100132354	broad.mit.edu	37	6	43895075	43895076	+	Intron	DEL	TC	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43895075_43895076delTC	uc011dvm.1	+							NR_024478				Homo sapiens cDNA FLJ38229 fis, clone FCBBF2004256.												0						ACTGATAAGATCTAAAAGGGTT	0.554													4	2	---	---	---	---	
CDC5L	988	broad.mit.edu	37	6	44397842	44397842	+	Intron	DEL	T	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-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	---	---	---	---	
GPR111	222611	broad.mit.edu	37	6	47647594	47647594	+	Intron	DEL	A	-	-	rs58870329		TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:47647594delA	uc010jzj.1	+						GPR111_uc010jzk.1_Intron|GPR111_uc003oyy.2_Intron	NM_153839	NP_722581	Q8IZF7	GP111_HUMAN	G-protein coupled receptor 111						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			skin(1)	1						ATTCGGAGAGAGGGGAGTTAA	0.353													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	77384399	77384400	+	IGR	DEL	AC	-	-	rs6919605	by1000genomes	TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:77384399_77384400delAC								IMPG1 (602064 upstream) : HTR1B (787548 downstream)																							aaaaaaaaaaaccaaaacaaaa	0.228													4	2	---	---	---	---	
C6orf203	51250	broad.mit.edu	37	6	107348342	107348343	+	5'Flank	INS	-	GGAT	GGAT			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107348342_107348343insGGAT	uc003prq.2	+						C6orf203_uc011eaj.1_5'Flank|C6orf203_uc010kde.2_5'Flank	NM_016487	NP_057571	Q9P0P8	CF203_HUMAN	hypothetical protein LOC51250 isoform a												0	Breast(9;0.00124)|all_epithelial(6;0.0729)	all_cancers(87;0.00461)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|Colorectal(196;0.171)|all_epithelial(87;0.23)	BRCA - Breast invasive adenocarcinoma(8;0.000395)|all cancers(7;0.00065)|Epithelial(6;0.000834)|OV - Ovarian serous cystadenocarcinoma(5;0.244)	BRCA - Breast invasive adenocarcinoma(108;0.117)		taatgagagagggatggatgga	0.035													6	3	---	---	---	---	
HIVEP2	3097	broad.mit.edu	37	6	143236902	143236902	+	Intron	DEL	A	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:143236902delA	uc003qjd.2	-							NM_006734	NP_006725	P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)|skin(2)|central_nervous_system(1)	6				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		acaccctctcatccactacaa	0.000													4	2	---	---	---	---	
PCMT1	5110	broad.mit.edu	37	6	150092137	150092137	+	Intron	DEL	A	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150092137delA	uc003qne.2	+						PCMT1_uc003qna.2_Intron|PCMT1_uc003qnb.2_Intron|PCMT1_uc011eeg.1_Intron|PCMT1_uc003qnc.2_Intron|PCMT1_uc003qnd.2_Intron|PCMT1_uc003qnf.2_Intron	NM_005389	NP_005380			protein-L-isoaspartate (D-aspartate)											ovary(1)	1		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.221)	OV - Ovarian serous cystadenocarcinoma(155;5.63e-13)|GBM - Glioblastoma multiforme(68;0.207)		tctgtctcagaaaaaaaaaaa	0.000													4	5	---	---	---	---	
MICALL2	79778	broad.mit.edu	37	7	1477280	1477280	+	Intron	DEL	C	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1477280delC	uc003skj.3	-						MICALL2_uc003skh.3_Intron|MICALL2_uc003ski.3_Intron	NM_182924	NP_891554	Q8IY33	MILK2_HUMAN	MICAL-like 2 isoform 1							cytoplasm|cytoskeleton	zinc ion binding			central_nervous_system(1)	1		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;6.01e-15)		CCTGACTCTGCCGCCCTGTCC	0.716													1	5	---	---	---	---	
NXPH1	30010	broad.mit.edu	37	7	8543505	8543505	+	Intron	DEL	T	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:8543505delT	uc003srv.2	+						NXPH1_uc011jxh.1_Intron	NM_152745	NP_689958	P58417	NXPH1_HUMAN	neurexophilin 1 precursor							extracellular region				ovary(1)|central_nervous_system(1)	2		Ovarian(82;0.0628)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)		CTCAGTAATCTCCAATGCTTC	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	16623495	16623495	+	IGR	DEL	G	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:16623495delG								SOSTDC1 (53290 upstream) : ANKMY2 (15918 downstream)																							TGCACTTTGCGGGGGGGTGCC	0.632													6	3	---	---	---	---	
HOXA10	3206	broad.mit.edu	37	7	27211532	27211533	+	Frame_Shift_Del	DEL	AG	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27211532_27211533delAG	uc011jzm.1	-	2	1248_1249	c.1218_1219delCT	c.(1216-1221)AACTTTfs	p.N406fs	MIR196B_hsa-mir-196b|MI0001150_5'Flank|HOXA10_uc003syw.3_Frame_Shift_Del_p.N90fs	NM_018951	NP_061824	P31260	HXA10_HUMAN	homeobox A10 isoform a	406_407					spermatogenesis		protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						GAAAAATTAAAGTTGGCTGTGA	0.515													123	56	---	---	---	---	
FAM188B	84182	broad.mit.edu	37	7	30924272	30924272	+	Intron	DEL	G	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30924272delG	uc003tbt.2	+						FAM188B_uc010kwe.2_Intron|AQP1_uc011kac.1_Intron|FAM188B_uc003tbu.2_Intron	NM_032222	NP_115598	Q4G0A6	F188B_HUMAN	hypothetical protein LOC84182												0						ACCCCTCCCAGGGGGTGGCCC	0.582													4	2	---	---	---	---	
AUTS2	26053	broad.mit.edu	37	7	69371371	69371371	+	Intron	DEL	G	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:69371371delG	uc003tvw.3	+						AUTS2_uc003tvv.3_Intron|AUTS2_uc003tvx.3_Intron	NM_015570	NP_056385	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2 isoform 1											ovary(2)|central_nervous_system(1)	3		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		GGTAATGAGTGGGAAGTGGGA	0.478													4	2	---	---	---	---	
TYW1B	441250	broad.mit.edu	37	7	72298301	72298302	+	Intron	INS	-	T	T			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72298301_72298302insT	uc011kej.1	-						TYW1B_uc011keh.1_Intron|TYW1B_uc011kek.1_Intron|SBDSP1_uc003twf.2_5'Flank|SBDSP1_uc011kel.1_5'Flank|SBDSP1_uc003twg.2_5'Flank|SBDSP1_uc003twh.2_5'Flank|SBDSP1_uc003twe.2_5'Flank	NM_001145440	NP_001138912	Q6NUM6	TYW1B_HUMAN	tRNA-yW synthesizing protein 1 homolog B isoform						tRNA processing		4 iron, 4 sulfur cluster binding|FMN binding|iron ion binding|oxidoreductase activity				0						CTTACGTCTCATTTTTTTTTTT	0.351													4	2	---	---	---	---	
CLIP2	7461	broad.mit.edu	37	7	73787154	73787155	+	Intron	DEL	CT	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73787154_73787155delCT	uc003uam.2	+						CLIP2_uc003uan.2_Intron	NM_003388	NP_003379	Q9UDT6	CLIP2_HUMAN	CAP-GLY domain containing linker protein 2							microtubule associated complex				skin(3)	3						ATGACGCCTCctctctctctct	0.550													4	2	---	---	---	---	
GATSL1	389523	broad.mit.edu	37	7	74395334	74395334	+	Intron	DEL	T	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74395334delT	uc003ubo.2	+							NM_001145063	NP_001138535	A6NNH0	GATL1_HUMAN	GATS-like protein 1												0						cctctttttctttttttttga	0.284													4	3	---	---	---	---	
SERPINE1	5054	broad.mit.edu	37	7	100769706	100769707	+	5'Flank	INS	-	G	G	rs139304273	by1000genomes	TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100769706_100769707insG	uc003uxt.2	+						SERPINE1_uc011kkj.1_5'Flank|SERPINE1_uc003uxs.2_5'Flank	NM_000602	NP_000593	P05121	PAI1_HUMAN	plasminogen activator inhibitor-1 isoform 1						angiogenesis|cellular response to chemical stimulus|cellular response to lipopolysaccharide|chronological cell aging|defense response to Gram-negative bacterium|fibrinolysis|negative regulation of apoptosis|negative regulation of cell adhesion mediated by integrin|negative regulation of fibrinolysis|negative regulation of plasminogen activation|negative regulation of smooth muscle cell migration|negative regulation of smooth muscle cell-matrix adhesion|negative regulation of vascular wound healing|platelet activation|platelet degranulation|positive regulation of angiogenesis|positive regulation of interleukin-8 production|positive regulation of leukotriene production involved in inflammatory response|positive regulation of monocyte chemotaxis|positive regulation of receptor-mediated endocytosis|regulation of receptor activity	extracellular matrix|extracellular space|plasma membrane|platelet alpha granule lumen	protease binding|serine-type endopeptidase inhibitor activity			ovary(1)|lung(1)|central_nervous_system(1)	3	Lung NSC(181;0.136)|all_lung(186;0.182)				Atorvastatin(DB01076)|Dimethyl sulfoxide(DB01093)|Drotrecogin alfa(DB00055)|Simvastatin(DB00641)|Tenecteplase(DB00031)|Troglitazone(DB00197)|Urokinase(DB00013)	TCTGGACACGTGGGGAGTCAGC	0.594													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	157279098	157279098	+	IGR	DEL	T	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157279098delT								DNAJB6 (68966 upstream) : PTPRN2 (52653 downstream)																							CCCCATAAGATTTTTTTGAGA	0.403													4	2	---	---	---	---	
DDHD2	23259	broad.mit.edu	37	8	38099572	38099572	+	Intron	DEL	A	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38099572delA	uc003xlb.2	+						DDHD2_uc003xlc.2_Intron|DDHD2_uc011lbl.1_Intron	NM_015214	NP_056029	O94830	DDHD2_HUMAN	DDHD domain containing 2 isoform 1						lipid catabolic process	centrosome	hydrolase activity|metal ion binding			large_intestine(1)|ovary(1)	2	Colorectal(12;0.000442)	all_lung(54;0.0657)|Lung NSC(58;0.175)	BRCA - Breast invasive adenocarcinoma(5;3.76e-25)|COAD - Colon adenocarcinoma(9;0.0977)			actccatctcaaaaaaaaaaa	0.139													7	4	---	---	---	---	
PRKDC	5591	broad.mit.edu	37	8	48799931	48799931	+	Intron	DEL	T	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48799931delT	uc003xqi.2	-						PRKDC_uc003xqj.2_Intron|PRKDC_uc011ldh.1_Intron	NM_006904	NP_008835	P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic						cellular response to insulin stimulus|double-strand break repair via nonhomologous end joining|peptidyl-serine phosphorylation|positive regulation of transcription from RNA polymerase II promoter	DNA-dependent protein kinase-DNA ligase 4 complex|transcription factor complex	ATP binding|DNA binding|DNA-dependent protein kinase activity|transcription factor binding			lung(12)|central_nervous_system(9)|ovary(6)|skin(4)|large_intestine(3)	34		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)				TATTCCGTTCTTTTTTTTTTT	0.323								NHEJ					5	3	---	---	---	---	
PRKDC	5591	broad.mit.edu	37	8	48870182	48870183	+	Intron	DEL	TA	-	-	rs35930434		TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48870182_48870183delTA	uc003xqi.2	-						PRKDC_uc003xqj.2_Intron|PRKDC_uc011ldh.1_Intron	NM_006904	NP_008835	P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic						cellular response to insulin stimulus|double-strand break repair via nonhomologous end joining|peptidyl-serine phosphorylation|positive regulation of transcription from RNA polymerase II promoter	DNA-dependent protein kinase-DNA ligase 4 complex|transcription factor complex	ATP binding|DNA binding|DNA-dependent protein kinase activity|transcription factor binding			lung(12)|central_nervous_system(9)|ovary(6)|skin(4)|large_intestine(3)	34		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)				gccattctcctatctcagcctc	0.000								NHEJ					6	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	55088452	55088452	+	IGR	DEL	A	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55088452delA								MRPL15 (27378 upstream) : SOX17 (282043 downstream)																							GGAGGCAGTGAAAGCGACCGT	0.562													4	2	---	---	---	---	
STK3	6788	broad.mit.edu	37	8	99874926	99874926	+	Intron	DEL	A	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99874926delA	uc003yio.2	-							NM_006281	NP_006272	Q13188	STK3_HUMAN	serine/threonine kinase 3						apoptosis|hippo signaling cascade|intracellular protein kinase cascade|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of apoptosis	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein dimerization activity|protein serine/threonine kinase activator activity|protein serine/threonine kinase activity			lung(3)|ovary(1)	4	Breast(36;2.4e-06)	Breast(495;0.106)	OV - Ovarian serous cystadenocarcinoma(57;0.0382)	KIRC - Kidney renal clear cell carcinoma(542;9.44e-06)		CAATCATTTGAAGAACTGAGA	0.423													4	2	---	---	---	---	
UHRF2	115426	broad.mit.edu	37	9	6482599	6482599	+	Intron	DEL	T	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6482599delT	uc003zjy.2	+						UHRF2_uc003zjz.2_Intron|UHRF2_uc003zka.1_Intron	NM_152896	NP_690856	Q96PU4	UHRF2_HUMAN	ubiquitin-like with PHD and ring finger domains						cell cycle|cell differentiation|cell proliferation|protein autoubiquitination|regulation of cell cycle|ubiquitin-dependent protein catabolic process	nucleus	DNA binding|histone binding|ubiquitin-protein ligase activity|zinc ion binding			large_intestine(2)|ovary(1)	3		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.0392)|Lung(218;0.129)		AAGAGGGGCCttttttttttt	0.199													7	4	---	---	---	---	
GKAP1	80318	broad.mit.edu	37	9	86367975	86367976	+	Intron	INS	-	AAC	AAC			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86367975_86367976insAAC	uc004amy.2	-						GKAP1_uc004amz.2_Intron	NM_025211	NP_079487	Q5VSY0	GKAP1_HUMAN	G kinase anchoring protein 1 isoform a						signal transduction	Golgi apparatus					0						actccatctcaaacaacaacaa	0.084													8	4	---	---	---	---	
SEMA4D	10507	broad.mit.edu	37	9	92007622	92007625	+	Intron	DEL	TTCT	-	-	rs67832119		TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:92007622_92007625delTTCT	uc004aqo.1	-						SEMA4D_uc011ltm.1_Intron|SEMA4D_uc011ltn.1_Intron|SEMA4D_uc011lto.1_Intron|SEMA4D_uc004aqp.1_Intron	NM_006378	NP_006369	Q92854	SEM4D_HUMAN	semaphorin 4D isoform 1						anti-apoptosis|axon guidance|cell adhesion|immune response	integral to membrane|plasma membrane	receptor activity|receptor binding			ovary(1)|pancreas(1)	2						TGTCTTCTAGTTCTTTCTTTTTCG	0.265													5	3	---	---	---	---	
NOL8	55035	broad.mit.edu	37	9	95069664	95069665	+	Intron	DEL	AT	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95069664_95069665delAT	uc004arv.2	-						NOL8_uc010mqw.2_Intron|NOL8_uc004arw.2_Intron|NOL8_uc011ltw.1_Intron	NM_017948	NP_060418	Q76FK4	NOL8_HUMAN	nucleolar protein 8						DNA replication|positive regulation of cell growth	nucleolus	nucleotide binding|protein binding|RNA binding			ovary(1)	1						CATTCTAAACATAATCTAAATT	0.252													25	11	---	---	---	---	
PPP6C	5537	broad.mit.edu	37	9	127913971	127913972	+	Intron	DEL	GT	-	-	rs73668905	by1000genomes	TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127913971_127913972delGT	uc004bpg.3	-						PPP6C_uc010mwv.2_Intron|PPP6C_uc010mww.2_Intron|PPP6C_uc011lzr.1_Intron	NM_002721	NP_002712	O00743	PPP6_HUMAN	protein phosphatase 6, catalytic subunit isoform						G1/S transition of mitotic cell cycle|protein dephosphorylation	cytosol	metal ion binding|protein binding|protein serine/threonine phosphatase activity			ovary(1)|skin(1)	2						GCTTGCTCCAGTGTAGCTTTCT	0.416													6	3	---	---	---	---	
DIP2C	22982	broad.mit.edu	37	10	371306	371306	+	Intron	DEL	T	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:371306delT	uc001ifp.2	-							NM_014974	NP_055789	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C							nucleus	catalytic activity|transcription factor binding			breast(4)|ovary(2)|large_intestine(1)	7		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		AAGAGGCCAATTTTACACCAC	0.398													4	2	---	---	---	---	
SFMBT2	57713	broad.mit.edu	37	10	7217721	7217722	+	Intron	INS	-	A	A	rs140257360	by1000genomes	TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7217721_7217722insA	uc009xio.1	-						SFMBT2_uc001ijn.1_Intron|SFMBT2_uc010qay.1_Intron	NM_001029880	NP_001025051	Q5VUG0	SMBT2_HUMAN	Scm-like with four mbt domains 2						regulation of transcription, DNA-dependent	nucleus				ovary(4)|upper_aerodigestive_tract(2)|large_intestine(1)|central_nervous_system(1)	8						TTCCAAGGCCTACCAATGAAAA	0.401													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	49327101	49327101	+	Intron	DEL	A	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:49327101delA	uc009xny.1	-											Homo sapiens cDNA, FLJ99963.																		tataatcaggaaaaaaaaATG	0.104													11	5	---	---	---	---	
FAM13C	220965	broad.mit.edu	37	10	61027987	61027992	+	Intron	DEL	AAGAAG	-	-	rs112609095		TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61027987_61027992delAAGAAG	uc001jkn.2	-						FAM13C_uc001jko.2_Intron|FAM13C_uc010qid.1_Intron|FAM13C_uc010qie.1_Intron|FAM13C_uc010qif.1_Intron|FAM13C_uc001jkp.2_Intron	NM_198215	NP_937858	Q8NE31	FA13C_HUMAN	hypothetical protein LOC220965 isoform 1											ovary(2)	2						aaaaaagaaaaagaagaagaagaaga	0.243													4	2	---	---	---	---	
ZNF365	22891	broad.mit.edu	37	10	64382623	64382623	+	Intron	DEL	G	-	-	rs75156012		TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64382623delG	uc001jmd.1	+						ZNF365_uc001jmc.2_Intron	NM_199452	NP_955524	Q70YC4	TALAN_HUMAN	zinc finger protein 365 isoform D											ovary(1)|skin(1)	2	Prostate(12;0.0297)|all_hematologic(501;0.228)					TCCTTTTTTTGGGGGGGGGGG	0.388													5	3	---	---	---	---	
C10orf131	100127889	broad.mit.edu	37	10	97684286	97684287	+	Intron	INS	-	TA	TA	rs10882689		TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97684286_97684287insTA	uc010qoo.1	+						uc001klg.1_Intron|uc001klj.1_Intron	NM_001130446	NP_001123918	B4DG41	B4DG41_HUMAN	hypothetical protein LOC100127889												0						CTCTCTCTCTCTATATATATAT	0.302													21	10	---	---	---	---	
SLK	9748	broad.mit.edu	37	10	105752775	105752775	+	Frame_Shift_Del	DEL	A	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105752775delA	uc001kxo.1	+	4	432	c.398delA	c.(397-399)CAAfs	p.Q133fs	SLK_uc001kxp.1_Frame_Shift_Del_p.Q133fs	NM_014720	NP_055535	Q9H2G2	SLK_HUMAN	serine/threonine kinase 2	133	Protein kinase.				apoptosis|nucleotide-excision repair	cytoplasm|plasma membrane	ATP binding|DNA binding|nuclease activity|protein serine/threonine kinase activity			ovary(2)|stomach(2)|skin(2)|lung(1)|kidney(1)	8		Colorectal(252;0.178)		Epithelial(162;5.81e-10)|all cancers(201;2.35e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		TCCCAAATACAAGTAGTTTGC	0.333													238	111	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	131990054	131990054	+	IGR	DEL	T	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:131990054delT								GLRX3 (7270 upstream) : TCERG1L (900602 downstream)																							cttttctccatttttttttct	0.000													4	2	---	---	---	---	
NUP98	4928	broad.mit.edu	37	11	3723540	3723569	+	Intron	DEL	CACACTCTCTCTCTCTCTCTCTCTCTCTCT	-	-	rs113723777	by1000genomes	TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3723540_3723569delCACACTCTCTCTCTCTCTCTCTCTCTCTCT	uc001lyh.2	-						NUP98_uc001lyi.2_Intron|NUP98_uc001lyg.2_Intron	NM_016320	NP_057404	P52948	NUP98_HUMAN	nucleoporin 98kD isoform 1						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)		cacacacacacacactctctctctctctctctctctctctctctctctct	0.209			T	HOXA9|NSD1|WHSC1L1|DDX10|TOP1|HOXD13|PMX1|HOXA13|HOXD11|HOXA11|RAP1GDS1|HOXC11	AML								4	3	---	---	---	---	
C11orf49	79096	broad.mit.edu	37	11	47009041	47009042	+	Intron	INS	-	T	T	rs139839679	by1000genomes	TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47009041_47009042insT	uc001ndp.2	+						C11orf49_uc001nds.2_Intron|C11orf49_uc001ndq.2_Intron|C11orf49_uc001ndr.2_Intron|C11orf49_uc010rgx.1_Intron|C11orf49_uc010rgy.1_Intron|C11orf49_uc010rgz.1_Intron	NM_024113	NP_077018	Q9H6J7	CK049_HUMAN	hypothetical protein LOC79096 isoform 3												0						GGTGCAGCTAGTTTGTCCAGTG	0.401													4	10	---	---	---	---	
CELF1	10658	broad.mit.edu	37	11	47500678	47500678	+	Intron	DEL	A	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47500678delA	uc001nfl.2	-						CELF1_uc001nfm.2_Intron|CELF1_uc001nfn.2_Intron|CELF1_uc001nfo.1_Intron|CELF1_uc010rhm.1_Intron|CELF1_uc001nfp.2_Intron|CELF1_uc001nfq.1_Intron|CELF1_uc001nfr.1_Intron	NM_001025596	NP_001020767	Q92879	CELF1_HUMAN	CUG triplet repeat, RNA-binding protein 1						embryo development|mRNA splice site selection|regulation of RNA splicing|RNA interference	cytoplasm|nucleus|ribonucleoprotein complex	BRE binding|mRNA binding|nucleotide binding|translation repressor activity, nucleic acid binding			central_nervous_system(2)|ovary(1)	3						AGCACAGGACAAAAAAAAAAC	0.473													9	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	47902673	47902673	+	IGR	DEL	A	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47902673delA								NUP160 (32616 upstream) : PTPRJ (99437 downstream)																							agaaggaaagaaaaaaaaaag	0.323													3	4	---	---	---	---	
INTS5	80789	broad.mit.edu	37	11	62414350	62414351	+	3'UTR	INS	-	A	A			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62414350_62414351insA	uc001nud.2	-	2					GANAB_uc001nua.2_5'Flank|GANAB_uc001nub.2_5'Flank|GANAB_uc001nuc.2_5'Flank|GANAB_uc010rma.1_5'Flank|GANAB_uc010rmb.1_5'Flank	NM_030628	NP_085131	Q6P9B9	INT5_HUMAN	integrator complex subunit 5						snRNA processing	integral to membrane|integrator complex	protein binding			ovary(2)	2						ATTTTATTTAGAAAAAAAAAAG	0.490													4	2	---	---	---	---	
MRPL49	740	broad.mit.edu	37	11	64892402	64892402	+	Intron	DEL	C	-	-	rs73477209	by1000genomes	TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64892402delC	uc001oda.1	+						FAU_uc001ocx.2_5'Flank|MRPL49_uc001ocz.1_Intron	NM_004927	NP_004918	Q13405	RM49_HUMAN	mitochondrial ribosomal protein L49						translation	mitochondrial ribosome	protein binding|structural constituent of ribosome				0						GACCTTCTTTCCCCCCAGCag	0.264													4	2	---	---	---	---	
SHANK2	22941	broad.mit.edu	37	11	70463733	70463733	+	Intron	DEL	T	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70463733delT	uc001oqc.2	-						SHANK2_uc010rqn.1_Intron|SHANK2_uc001opz.2_Intron|uc009ysn.1_Intron|SHANK2_uc010rqp.1_Intron	NM_012309	NP_036441	Q9UPX8	SHAN2_HUMAN	SH3 and multiple ankyrin repeat domains 2						intracellular signal transduction	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	GKAP/Homer scaffold activity|ionotropic glutamate receptor binding|SH3 domain binding			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5			LUSC - Lung squamous cell carcinoma(11;4.72e-09)|STAD - Stomach adenocarcinoma(18;0.071)			CAAGCTCGAGTTCAGAGTTAA	0.537													4	2	---	---	---	---	
DLG2	1740	broad.mit.edu	37	11	83545042	83545042	+	Intron	DEL	A	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:83545042delA	uc001paj.2	-						DLG2_uc001pai.2_Intron|DLG2_uc010rsy.1_Intron|DLG2_uc010rsz.1_Intron|DLG2_uc010rta.1_Intron|DLG2_uc001pak.2_Intron|DLG2_uc010rtb.1_Intron|DLG2_uc001pal.1_Intron|DLG2_uc001pam.1_Intron	NM_001364	NP_001355	Q15700	DLG2_HUMAN	chapsyn-110 isoform 2							cell junction|postsynaptic density|postsynaptic membrane	guanylate kinase activity|protein binding|protein binding			ovary(3)|pancreas(2)|skin(1)	6		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)				CCTTCATTCTAAAAAAATTTC	0.343													4	2	---	---	---	---	
HTR3B	9177	broad.mit.edu	37	11	113815065	113815065	+	Intron	DEL	A	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113815065delA	uc001pok.2	+						HTR3B_uc001pol.2_Intron	NM_006028	NP_006019	O95264	5HT3B_HUMAN	5-hydroxytryptamine (serotonin) receptor 3B						synaptic transmission	integral to plasma membrane|postsynaptic membrane	serotonin receptor activity|serotonin-activated cation-selective channel activity				0		all_cancers(61;6.81e-18)|all_epithelial(67;6.67e-11)|all_hematologic(158;4.67e-05)|Melanoma(852;0.000316)|Acute lymphoblastic leukemia(157;0.000976)|Breast(348;0.0101)|Prostate(24;0.0154)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;3.04e-06)|Epithelial(105;1.98e-05)|all cancers(92;0.000201)|OV - Ovarian serous cystadenocarcinoma(223;0.151)		taccaaaaataaaaaaaaatt	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	119902454	119902454	+	IGR	DEL	G	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119902454delG								PVRL1 (303019 upstream) : TRIM29 (79541 downstream)																							ttctacttctgggctccctgc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	133696782	133696782	+	IGR	DEL	C	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133696782delC								OPCML (294379 upstream) : SPATA19 (13735 downstream)																							AACCTGGAATCCTAATCAGAG	0.488													4	2	---	---	---	---	
IGSF9B	22997	broad.mit.edu	37	11	133788723	133788724	+	Intron	INS	-	G	G	rs150958113		TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133788723_133788724insG	uc001qgx.3	-							NM_014987	NP_055802	Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B							integral to membrane|plasma membrane					0	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)		GAGAAGAGGGCGGGGGACGGGG	0.490													2	6	---	---	---	---	
DPY19L2	283417	broad.mit.edu	37	12	63991415	63991416	+	Intron	INS	-	T	T	rs138201669	by1000genomes	TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:63991415_63991416insT	uc001srp.1	-						DPY19L2_uc009zqk.1_Intron	NM_173812	NP_776173	Q6NUT2	D19L2_HUMAN	dpy-19-like 2						multicellular organismal development|spermatid development	integral to membrane				central_nervous_system(1)|skin(1)	2			GBM - Glioblastoma multiforme(1;2.77e-05)	GBM - Glioblastoma multiforme(28;0.044)		tagaggctatctttttttttta	0.050													8	4	---	---	---	---	
THAP2	83591	broad.mit.edu	37	12	72058496	72058497	+	Intron	DEL	TG	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72058496_72058497delTG	uc001swq.2	+						ZFC3H1_uc001swo.2_5'Flank|ZFC3H1_uc010sts.1_5'Flank|ZFC3H1_uc001swp.2_5'Flank	NM_031435	NP_113623	Q9H0W7	THAP2_HUMAN	THAP domain containing, apoptosis associated							nucleolus	DNA binding|metal ion binding			ovary(1)	1						GTATGTCCTTTGTGTTTCTCAA	0.416													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	82319500	82319500	+	IGR	DEL	T	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:82319500delT								PPFIA2 (166391 upstream) : CCDC59 (426590 downstream)																							gggctcgttcttTTTTTTTTC	0.010													8	4	---	---	---	---	
GLT8D2	83468	broad.mit.edu	37	12	104393544	104393544	+	Intron	DEL	C	-	-	rs145686804	by1000genomes	TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104393544delC	uc001tkh.1	-						GLT8D2_uc001tki.1_Intron	NM_031302	NP_112592	Q9H1C3	GL8D2_HUMAN	glycosyltransferase 8 domain containing 2							integral to membrane	transferase activity, transferring glycosyl groups			ovary(1)|skin(1)	2						CCAAATCTCTCCCCAGATCCA	0.388													4	2	---	---	---	---	
TCTN1	79600	broad.mit.edu	37	12	111079665	111079665	+	Intron	DEL	T	-	-	rs78912810		TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111079665delT	uc009zvs.2	+						TCTN1_uc001trp.3_Intron|TCTN1_uc001trn.3_Intron|TCTN1_uc001trk.3_Intron|HVCN1_uc001trq.1_Intron	NM_001082537	NP_001076006	Q2MV58	TECT1_HUMAN	tectonic family member 1 isoform 2						multicellular organismal development	extracellular region					0						AATGTCAGTGTTTTTTTTTTT	0.463													4	2	---	---	---	---	
ATP12A	479	broad.mit.edu	37	13	25256042	25256043	+	Intron	DEL	GT	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25256042_25256043delGT	uc001upp.2	+						ATP12A_uc010aaa.2_Intron	NM_001676	NP_001667	P54707	AT12A_HUMAN	hydrogen/potassium-exchanging ATPase 12A						ATP biosynthetic process	hydrogen:potassium-exchanging ATPase complex	ATP binding|hydrogen:potassium-exchanging ATPase activity|metal ion binding			ovary(2)|central_nervous_system(2)|large_intestine(1)|breast(1)	6		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)	Esomeprazole(DB00736)|Pantoprazole(DB00213)	tgtatgtgtggtgtgtgtgtat	0.079													4	2	---	---	---	---	
TPTE2P1	646405	broad.mit.edu	37	13	25527621	25527623	+	Intron	DEL	AAC	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25527621_25527623delAAC	uc010tdh.1	-						TPTE2P1_uc001upx.3_Intron	NR_026730				RecName: Full=C2 tensin-type domain-containing protein ENSP00000371290;												0						TGCAATCTATAACAATACACTCA	0.276													16	8	---	---	---	---	
CDADC1	81602	broad.mit.edu	37	13	49830213	49830214	+	Intron	INS	-	A	A	rs147882512	by1000genomes	TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49830213_49830214insA	uc001vcu.2	+						CDADC1_uc001vcs.1_Intron|CDADC1_uc001vct.1_Intron|CDADC1_uc010tgk.1_Intron|CDADC1_uc001vcv.2_Intron	NM_030911	NP_112173	Q9BWV3	CDAC1_HUMAN	cytidine and dCMP deaminase domain containing 1								hydrolase activity|zinc ion binding			upper_aerodigestive_tract(1)	1		Lung NSC(96;0.000705)|Breast(56;0.0011)|Prostate(109;0.00446)|Hepatocellular(98;0.0556)|Glioma(44;0.236)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;1.06e-08)|COAD - Colon adenocarcinoma(199;0.216)		CTCCTTTTTTTTAAAAAAAAAA	0.262													16	13	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	75493893	75493893	+	IGR	DEL	C	-	-	rs76273122		TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:75493893delC								KLF12 (785499 upstream) : LOC647288 (317997 downstream)																							TTGTTGTTTTCTTTTTTTTCA	0.363													6	3	---	---	---	---	
LRFN5	145581	broad.mit.edu	37	14	42364910	42364910	+	Intron	DEL	T	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:42364910delT	uc001wvm.2	+						LRFN5_uc010ana.2_Intron	NM_152447	NP_689660	Q96NI6	LRFN5_HUMAN	leucine rich repeat and fibronectin type III							integral to membrane				ovary(5)|pancreas(2)|central_nervous_system(1)	8			LUAD - Lung adenocarcinoma(50;0.0223)|Lung(238;0.0728)	GBM - Glioblastoma multiforme(112;0.00847)		TTATTTCCCCTTTTTTTTTTT	0.254										HNSCC(30;0.082)			6	3	---	---	---	---	
SDCCAG1	9147	broad.mit.edu	37	14	50094573	50094573	+	Intron	DEL	A	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50094573delA	uc010anj.1	-						C14orf104_uc001wws.3_Intron|C14orf104_uc001wwt.3_Intron	NM_004713	NP_004704	O60524	NEMF_HUMAN	serologically defined colon cancer antigen 1							cytoplasm|nucleus					0	all_epithelial(31;0.000822)|Breast(41;0.0117)	all_lung(585;1.02e-05)		OV - Ovarian serous cystadenocarcinoma(311;5.99e-34)		actccatctcaaaaaaaaaaa	0.104													16	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	55266705	55266706	+	IGR	DEL	CT	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55266705_55266706delCT								SAMD4A (6672 upstream) : GCH1 (42018 downstream)																							agttcacaagctcaagggtatg	0.030													4	2	---	---	---	---	
TIMM9	26520	broad.mit.edu	37	14	58878265	58878265	+	Intron	DEL	T	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58878265delT	uc010aph.2	-						TIMM9_uc001xds.2_Intron|TIMM9_uc010api.2_Intron	NM_012460	NP_036592	Q9Y5J7	TIM9_HUMAN	translocase of inner mitochondrial membrane 9						protein import into mitochondrial inner membrane|sensory perception of sound|transmembrane transport	mitochondrial inner membrane presequence translocase complex|mitochondrial intermembrane space protein transporter complex	zinc ion binding				0						ACTGACATGGttttttttttt	0.109													4	5	---	---	---	---	
POMT2	29954	broad.mit.edu	37	14	77747047	77747048	+	Intron	INS	-	GGAAAGA	GGAAAGA	rs140537636	by1000genomes	TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77747047_77747048insGGAAAGA	uc001xti.2	-						POMT2_uc001xth.1_Intron	NM_013382	NP_037514	Q9UKY4	POMT2_HUMAN	protein-O-mannosyltransferase 2						protein O-linked glycosylation	endoplasmic reticulum membrane|integral to membrane	dolichyl-phosphate-mannose-protein mannosyltransferase activity|metal ion binding			ovary(1)	1			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0292)		GGAAAAAGAAGGGAAAGAGGAA	0.475													8	4	---	---	---	---	
FBLN5	10516	broad.mit.edu	37	14	92347478	92347479	+	Intron	INS	-	AT	AT	rs77483000		TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92347478_92347479insAT	uc001xzx.3	-						FBLN5_uc010aud.2_Intron|FBLN5_uc010aue.2_Intron	NM_006329	NP_006320	Q9UBX5	FBLN5_HUMAN	fibulin 5 precursor						cell-matrix adhesion|elastic fiber assembly|protein localization at cell surface|regulation of removal of superoxide radicals	extracellular space|proteinaceous extracellular matrix|soluble fraction	calcium ion binding|integrin binding|protein C-terminus binding			ovary(3)|upper_aerodigestive_tract(1)|lung(1)|skin(1)	6		all_cancers(154;0.0722)				cacacacacacacacacacaca	0.233													6	3	---	---	---	---	
CCDC85C	317762	broad.mit.edu	37	14	100025552	100025553	+	Intron	INS	-	C	C	rs144311462	by1000genomes	TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100025552_100025553insC	uc010avr.2	-							NM_001144995	NP_001138467	A6NKD9	CC85C_HUMAN	coiled-coil domain containing 85C												0						aatacaggagtccccccgagag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	22482640	22482642	+	IGR	DEL	TGT	-	-	rs140253182		TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22482640_22482642delTGT								OR4N3P (68255 upstream) : MIR1268 (30587 downstream)																							ACAGAATAAATGTTGTATGAAAA	0.128													19	13	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	22488189	22488189	+	IGR	DEL	T	-	-	rs112177113		TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22488189delT								OR4N3P (73804 upstream) : MIR1268 (25040 downstream)																							TGTCTCCAGATAACAATAATG	0.433													4	2	---	---	---	---	
FAM189A1	23359	broad.mit.edu	37	15	29760165	29760165	+	Intron	DEL	G	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29760165delG	uc010azk.1	-							NM_015307	NP_056122	O60320	F1891_HUMAN	hypothetical protein LOC23359							integral to membrane					0						TCTTCTGATTGTTCCTGCCTC	0.552													4	2	---	---	---	---	
TMEM62	80021	broad.mit.edu	37	15	43433496	43433496	+	Intron	DEL	C	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43433496delC	uc001zqr.2	+						TMEM62_uc010bda.2_Intron|uc001zqs.1_5'Flank	NM_024956	NP_079232	Q0P6H9	TMM62_HUMAN	transmembrane protein 62							integral to membrane				ovary(1)|breast(1)	2		all_cancers(109;1.16e-10)|all_epithelial(112;2.01e-09)|Lung NSC(122;8.91e-07)|all_lung(180;8.8e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;4.23e-07)		ggagccaatgcccacttacca	0.189													4	2	---	---	---	---	
WDR72	256764	broad.mit.edu	37	15	54004802	54004803	+	Intron	INS	-	A	A	rs112182674		TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:54004802_54004803insA	uc002acj.2	-						WDR72_uc010bfi.1_Intron	NM_182758	NP_877435	Q3MJ13	WDR72_HUMAN	WD repeat domain 72											lung(1)|skin(1)	2				all cancers(107;0.0511)		ACCCCACCGCCAAAAAAAAAAA	0.188													9	9	---	---	---	---	
TRIP4	9325	broad.mit.edu	37	15	64717359	64717359	+	Intron	DEL	T	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64717359delT	uc002anm.2	+							NM_016213	NP_057297	Q15650	TRIP4_HUMAN	thyroid hormone receptor interactor 4						positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleus	ligand-dependent nuclear receptor binding|transcription coactivator activity|zinc ion binding			ovary(1)|kidney(1)|skin(1)	3						CATTTTGATGTTTTTTTTTTC	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	74015084	74015084	+	IGR	DEL	T	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74015084delT								CD276 (8225 upstream) : C15orf59 (17059 downstream)																							AAGGAGGTGATGAGCGCCATG	0.562													4	2	---	---	---	---	
RASGRF1	5923	broad.mit.edu	37	15	79324036	79324037	+	Intron	DEL	GA	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79324036_79324037delGA	uc002beq.2	-						RASGRF1_uc002bep.2_Intron|RASGRF1_uc010blm.1_Intron|RASGRF1_uc002ber.3_Intron	NM_002891	NP_002882	Q13972	RGRF1_HUMAN	Ras protein-specific guanine						activation of Rac GTPase activity|apoptosis|induction of apoptosis by extracellular signals|long-term memory|nerve growth factor receptor signaling pathway|neuron projection development|regulation of Rac protein signal transduction|small GTPase mediated signal transduction|synaptic transmission	cytosol|growth cone|plasma membrane|synaptosome	Rho guanyl-nucleotide exchange factor activity			skin(4)|ovary(1)|central_nervous_system(1)	6						gggaaagggggagagagagaga	0.262													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	95899807	95899808	+	IGR	INS	-	A	A	rs138965148	by1000genomes	TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:95899807_95899808insA								MCTP2 (872627 upstream) : LOC145820 (76514 downstream)																							ACCATCACATTAAAAAAAAACC	0.248													8	6	---	---	---	---	
PPL	5493	broad.mit.edu	37	16	4938632	4938632	+	Intron	DEL	T	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4938632delT	uc002cyd.1	-							NM_002705	NP_002696	O60437	PEPL_HUMAN	periplakin						keratinization	cytoskeleton|desmosome|mitochondrion|nucleus	protein binding|structural constituent of cytoskeleton			ovary(4)|central_nervous_system(1)|skin(1)	6						agctttccccttccactggac	0.134													4	2	---	---	---	---	
LPCAT2	54947	broad.mit.edu	37	16	55571300	55571300	+	Intron	DEL	C	-	-	rs111668979		TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55571300delC	uc002eie.3	+						LPCAT2_uc002eic.2_Intron	NM_017839	NP_060309	Q7L5N7	PCAT2_HUMAN	lysophosphatidylcholine acyltransferase 2						cellular membrane organization|platelet activating factor biosynthetic process	endoplasmic reticulum membrane|Golgi membrane|Golgi stack|integral to membrane	1-acylglycerophosphocholine O-acyltransferase activity|1-alkylglycerophosphocholine O-acetyltransferase activity|calcium ion binding				0						aagaccctgtccccaaaaaaa	0.144													23	11	---	---	---	---	
NDRG4	65009	broad.mit.edu	37	16	58540057	58540062	+	Intron	DEL	TGTGTC	-	-	rs145437540	by1000genomes	TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58540057_58540062delTGTGTC	uc002eno.2	+						NDRG4_uc002enk.2_Intron|NDRG4_uc002enm.2_Intron|NDRG4_uc010vif.1_Intron|NDRG4_uc010cdk.2_Intron|NDRG4_uc010vig.1_Intron|NDRG4_uc010vih.1_Intron|NDRG4_uc010vii.1_Intron|NDRG4_uc002enp.2_Intron|NDRG4_uc002enq.1_5'UTR	NM_022910	NP_075061	Q9ULP0	NDRG4_HUMAN	NDRG family member 4 isoform 1						cell differentiation|cell growth|multicellular organismal development|response to stress	cytoplasm				skin(1)	1						tgtgtgtgtgtgtgtctgtgtgtgtg	0.306													4	2	---	---	---	---	
KCTD19	146212	broad.mit.edu	37	16	67337448	67337448	+	Intron	DEL	T	-	-	rs11341413		TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67337448delT	uc002esu.2	-						KCTD19_uc002est.2_Intron|KCTD19_uc010vjj.1_Intron	NM_001100915	NP_001094385	Q17RG1	KCD19_HUMAN	potassium channel tetramerisation domain							voltage-gated potassium channel complex	voltage-gated potassium channel activity			skin(1)	1		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0311)|Epithelial(162;0.0906)		TGGAAGTCTAtttttttttct	0.244													5	3	---	---	---	---	
FUK	197258	broad.mit.edu	37	16	70508127	70508128	+	In_Frame_Ins	INS	-	CCA	CCA			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70508127_70508128insCCA	uc002eyy.2	+	16	1931_1932	c.1873_1874insCCA	c.(1873-1875)CGG>CCCAGG	p.624_625insP	FUK_uc010cft.2_In_Frame_Ins_p.656_657insP|FUK_uc002eyz.2_In_Frame_Ins_p.115_116insP	NM_145059	NP_659496	Q8N0W3	FUK_HUMAN	fucokinase	624_625						cytoplasm	ATP binding|fucokinase activity			ovary(1)	1		Ovarian(137;0.0694)				TGGGGGCTTGCGGAGCGGGCCA	0.698													4	2	---	---	---	---	
PLCG2	5336	broad.mit.edu	37	16	81914852	81914852	+	Intron	DEL	T	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81914852delT	uc002fgt.2	+						PLCG2_uc010chg.1_Intron	NM_002661	NP_002652	P16885	PLCG2_HUMAN	phospholipase C, gamma 2						intracellular signal transduction|phospholipid catabolic process|platelet activation	plasma membrane	phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity			large_intestine(4)|lung(2)|ovary(1)|skin(1)	8						AGGTTAATAGTTTTTTTTTTT	0.328													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	211145	211145	+	IGR	DEL	A	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:211145delA								RPH3AL (8569 upstream) : C17orf97 (48973 downstream)																							AATTGAAGGCAAAAAAAAGGA	0.338													4	2	---	---	---	---	
VPS53	55275	broad.mit.edu	37	17	564783	564783	+	Intron	DEL	A	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:564783delA	uc002frn.2	-						VPS53_uc002frk.2_Intron|VPS53_uc010cjo.1_Intron|VPS53_uc002frl.2_Intron|VPS53_uc002frm.2_Intron|VPS53_uc002fro.2_Intron|VPS53_uc010cjp.1_Intron	NM_018289	NP_060759	Q5VIR6	VPS53_HUMAN	vacuolar protein sorting 53 isoform 2						protein transport	endosome membrane|Golgi apparatus					0				UCEC - Uterine corpus endometrioid carcinoma (25;0.0265)		aaaaaTACCCAAaaaacaaaa	0.214													6	8	---	---	---	---	
SCARF1	8578	broad.mit.edu	37	17	1542804	1542804	+	Intron	DEL	A	-	-	rs71375519		TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1542804delA	uc002fsz.1	-						SCARF1_uc002fsy.1_Intron|SCARF1_uc002fta.1_Intron|SCARF1_uc010cjv.1_Intron	NM_003693	NP_003684	Q14162	SREC_HUMAN	scavenger receptor class F, member 1 isoform 1						cell adhesion|neuron remodeling|positive regulation of axon regeneration|receptor-mediated endocytosis	integral to membrane	low-density lipoprotein particle binding|scavenger receptor activity			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		gtcttaagggaaaaaaaaaaa	0.244													5	4	---	---	---	---	
SMYD4	114826	broad.mit.edu	37	17	1703754	1703754	+	Frame_Shift_Del	DEL	A	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1703754delA	uc002ftm.3	-	5	1102	c.934delT	c.(934-936)TGCfs	p.C312fs	SMYD4_uc002ftn.1_Frame_Shift_Del_p.C167fs	NM_052928	NP_443160	Q8IYR2	SMYD4_HUMAN	SET and MYND domain containing 4	312	MYND-type.						zinc ion binding			skin(3)|kidney(2)	5						GCATAACTGCATCCGTCACAC	0.547													73	34	---	---	---	---	
USP43	124739	broad.mit.edu	37	17	9583331	9583331	+	Intron	DEL	T	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9583331delT	uc010cod.2	+						USP43_uc002gma.3_Intron|USP43_uc010vva.1_Intron|USP43_uc010coe.2_Intron	NM_153210	NP_694942	Q70EL4	UBP43_HUMAN	ubiquitin specific protease 43						ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(2)|lung(1)|breast(1)|central_nervous_system(1)	5						AAAACTTAGATTTTTTTTTTT	0.303													7	8	---	---	---	---	
ZNF286A	57335	broad.mit.edu	37	17	15603253	15603253	+	Intron	DEL	G	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15603253delG	uc010cot.2	+						ZNF286A_uc002goz.3_Intron|ZNF286A_uc010vwa.1_Intron|ZNF286A_uc002gpa.2_5'Flank	NM_001130842	NP_001124314	Q9HBT8	Z286A_HUMAN	zinc finger protein 286						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(1115;0.0222)|BRCA - Breast invasive adenocarcinoma(8;0.0781)		TCCTCTCCTCGGGGGACGCGG	0.657													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	18334137	18334137	+	IGR	DEL	A	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18334137delA								LOC339240 (5491 upstream) : LGALS9C (45962 downstream)																							GCCTCTTGGCAGGGGTGGGGC	0.567													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21730445	21730446	+	Intron	DEL	GT	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21730445_21730446delGT	uc002gyy.3	+											SubName: Full=cDNA FLJ51326, highly similar to Homo sapiens ubiquitin B (UBB), mRNA;																		TCCAGAACAGGTAGTGGAGAAA	0.455													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	26796748	26796748	+	IGR	DEL	C	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26796748delC								SLC46A1 (63520 upstream) : SLC13A2 (3916 downstream)																							gaaaggtaaacaagactgaac	0.000													4	2	---	---	---	---	
SUZ12P	440423	broad.mit.edu	37	17	29062327	29062327	+	Intron	DEL	T	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29062327delT	uc002hfn.1	+						SUZ12P_uc002hfo.2_Intron|SUZ12P_uc002hfp.2_Intron|SUZ12P_uc002hfq.2_Intron					Homo sapiens cDNA clone IMAGE:5299523, containing frame-shift errors.												0						TGTTATTAGCTTTTTTTTTTT	0.199													8	4	---	---	---	---	
COX11	1353	broad.mit.edu	37	17	53041893	53041899	+	Intron	DEL	TTTAACT	-	-	rs72299663		TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53041893_53041899delTTTAACT	uc010wng.1	-						COX11_uc010wne.1_Intron|COX11_uc010wnf.1_Intron|COX11_uc002iue.2_Intron|COX11_uc010wnh.1_Intron	NM_004375	NP_004366	Q9Y6N1	COX11_HUMAN	COX11 homolog, cytochrome c oxidase assembly						respiratory chain complex IV assembly|respiratory gaseous exchange	integral to membrane|mitochondrial inner membrane	copper ion binding|cytochrome-c oxidase activity|electron carrier activity			ovary(1)	1						GAATTTATACTTTAACTTTTAAGTTAC	0.266													10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	54635249	54635250	+	IGR	DEL	AC	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54635249_54635250delAC								ANKFN1 (75242 upstream) : NOG (35810 downstream)																							TCCAGGGGGTACCTCCTGCCAA	0.609													4	2	---	---	---	---	
TBX4	9496	broad.mit.edu	37	17	59561081	59561081	+	3'UTR	DEL	A	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59561081delA	uc002izi.2	+	8					TBX4_uc010ddo.2_3'UTR|TBX4_uc010woy.1_3'UTR	NM_018488	NP_060958	P57082	TBX4_HUMAN	T-box 4						leg morphogenesis|skeletal system morphogenesis	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			skin(2)	2						CATGACAAGGAAAAAAAACAC	0.363													4	2	---	---	---	---	
TTYH2	94015	broad.mit.edu	37	17	72218928	72218928	+	Intron	DEL	T	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72218928delT	uc002jkc.2	+						TTYH2_uc010wqw.1_Intron	NM_032646	NP_116035	Q9BSA4	TTYH2_HUMAN	tweety 2 isoform 1							chloride channel complex|plasma membrane	chloride channel activity|protein binding			ovary(3)|large_intestine(1)	4						ATGTTGTCCCTTTTTTTTTTT	0.522													2	4	---	---	---	---	
RECQL5	9400	broad.mit.edu	37	17	73624087	73624087	+	Intron	DEL	A	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73624087delA	uc010dgl.2	-						RECQL5_uc010dgk.2_Intron|RECQL5_uc002jot.3_Intron	NM_004259	NP_004250	O94762	RECQ5_HUMAN	RecQ protein-like 5 isoform 1						DNA recombination|DNA repair	cytoplasm|nuclear membrane|nucleolus|nucleoplasm	ATP binding|ATP-dependent helicase activity|DNA helicase activity|nucleic acid binding			kidney(3)	3	all_cancers(13;2.73e-08)|Breast(9;6.04e-09)|all_epithelial(9;6.79e-09)		all cancers(21;1.15e-06)|Epithelial(20;2.19e-06)|Lung(188;0.101)|LUSC - Lung squamous cell carcinoma(166;0.112)			cgacagagataaaaaaaaaaa	0.294								Other_identified_genes_with_known_or_suspected_DNA_repair_function					3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	12931276	12931276	+	IGR	DEL	T	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12931276delT								PTPN2 (46942 upstream) : SEH1L (16707 downstream)																							tgcaacccccttacaaggact	0.045													4	2	---	---	---	---	
CABLES1	91768	broad.mit.edu	37	18	20794906	20794906	+	Intron	DEL	T	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:20794906delT	uc002kuc.2	+						C18orf45_uc010xaq.1_Intron|CABLES1_uc002kub.2_Intron|CABLES1_uc002kud.2_Intron	NM_001100619	NP_001094089	Q8TDN4	CABL1_HUMAN	Cdk5 and Abl enzyme substrate 1 isoform 2						blood coagulation|cell cycle|cell division|regulation of cell cycle|regulation of cell division	cytosol|nucleus	cyclin-dependent protein kinase regulator activity|protein binding			breast(1)	1	all_cancers(21;0.000102)|all_epithelial(16;2.48e-06)|Lung NSC(20;0.00696)|all_lung(20;0.0197)|Colorectal(14;0.0202)|Ovarian(20;0.127)					CTTTCCCCTGTAGATGTGCTA	0.507													4	2	---	---	---	---	
PSTPIP2	9050	broad.mit.edu	37	18	43578039	43578039	+	Intron	DEL	T	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43578039delT	uc002lbp.3	-						PSTPIP2_uc002lbq.3_Intron	NM_024430	NP_077748	Q9H939	PPIP2_HUMAN	proline-serine-threonine phosphatase interacting							membrane				ovary(1)	1						AGAAAGGTTCTAAGGAAGAAG	0.378													4	2	---	---	---	---	
MALT1	10892	broad.mit.edu	37	18	56358005	56358006	+	Intron	DEL	AC	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56358005_56358006delAC	uc002lhm.1	+						MALT1_uc002lhn.1_Intron	NM_006785	NP_006776	Q9UDY8	MALT1_HUMAN	mucosa associated lymphoid tissue lymphoma						activation of NF-kappaB-inducing kinase activity|anti-apoptosis|nuclear export|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-2 production|positive regulation of NF-kappaB transcription factor activity|positive regulation of phosphorylation|positive regulation of protein ubiquitination|positive regulation of T cell cytokine production|protein oligomerization|proteolysis|T cell receptor signaling pathway	CBM complex|cytosol|nucleus|perinuclear region of cytoplasm	cysteine-type endopeptidase activity|protein self-association|signal transducer activity|ubiquitin-protein ligase activity			ovary(2)|lung(1)|central_nervous_system(1)	4						CCTCTGGCTTACCGAGGCCAAG	0.495			T	BIRC3	MALT								4	2	---	---	---	---	
ATP5D	513	broad.mit.edu	37	19	1242447	1242447	+	Intron	DEL	G	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1242447delG	uc002lrn.2	+						ATP5D_uc002lro.2_Intron	NM_001001975	NP_001001975	P30049	ATPD_HUMAN	ATP synthase, H+ transporting, mitochondrial F1						mitochondrial ATP synthesis coupled proton transport|oxidative phosphorylation|respiratory electron transport chain|response to copper ion	mitochondrial matrix|mitochondrial proton-transporting ATP synthase complex, catalytic core F(1)	hydrogen ion transporting ATP synthase activity, rotational mechanism|proton-transporting ATPase activity, rotational mechanism				0		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|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)	Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	CCACGCTGTTGTCTGCAGGTG	0.687													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	11696740	11696740	+	IGR	DEL	T	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11696740delT								ACP5 (6939 upstream) : ZNF627 (11495 downstream)																							CGTGACAACGtttttttttgg	0.284													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	13977688	13977689	+	IGR	DEL	CA	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13977688_13977689delCA								MIR23A (30215 upstream) : MIR181C (7824 downstream)																							TCACCCCCACcacacacacaca	0.391													3	3	---	---	---	---	
CCNE1	898	broad.mit.edu	37	19	30311985	30311985	+	Intron	DEL	A	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30311985delA	uc002nsn.2	+						CCNE1_uc002nso.2_Intron|CCNE1_uc002nsp.2_5'Flank	NM_001238	NP_001229	P24864	CCNE1_HUMAN	cyclin E1 isoform 1						androgen receptor signaling pathway|cell division|positive regulation of transcription, DNA-dependent|regulation of cyclin-dependent protein kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle	cytosol|nucleoplasm	androgen receptor binding|protein kinase binding|transcription coactivator activity			lung(2)	2	all_cancers(1;2.19e-31)|all_epithelial(1;1.49e-30)|all_lung(1;1.37e-11)|Lung NSC(1;2.35e-11)|Ovarian(5;0.000902)|Breast(6;0.0203)|Esophageal squamous(110;0.195)		UCEC - Uterine corpus endometrioid carcinoma (4;2.65e-06)|Epithelial(1;6.85e-98)|all cancers(1;1.38e-94)|OV - Ovarian serous cystadenocarcinoma(1;1.38e-90)|STAD - Stomach adenocarcinoma(5;5.8e-07)|GBM - Glioblastoma multiforme(4;0.0394)|Lung(7;0.092)|LUAD - Lung adenocarcinoma(5;0.115)|BRCA - Breast invasive adenocarcinoma(6;0.183)|COAD - Colon adenocarcinoma(1;0.188)|Colorectal(1;0.202)			ACATTGAGCCAAAAAAAAAAA	0.249													4	6	---	---	---	---	
WDR88	126248	broad.mit.edu	37	19	33641675	33641675	+	Intron	DEL	C	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33641675delC	uc002nui.2	+							NM_173479	NP_775750	Q6ZMY6	WDR88_HUMAN	PQQ repeat and WD repeat domain containing											ovary(1)|breast(1)|central_nervous_system(1)	3	Esophageal squamous(110;0.137)					catgatccggcccaggccttt	0.095													4	2	---	---	---	---	
HPN	3249	broad.mit.edu	37	19	35533699	35533699	+	Intron	DEL	G	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35533699delG	uc002nxq.1	+						HPN_uc002nxr.1_Intron|HPN_uc002nxs.1_Intron	NM_002151	NP_002142	P05981	HEPS_HUMAN	hepsin						cell growth|proteolysis	cytoplasm|integral to plasma membrane	scavenger receptor activity|serine-type endopeptidase activity			ovary(1)|central_nervous_system(1)	2	all_lung(56;5.38e-08)|Lung NSC(56;8.61e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)		Coagulation factor VIIa(DB00036)	AGCTAACTCTGGACTTGTCCT	0.373													4	2	---	---	---	---	
RBM42	79171	broad.mit.edu	37	19	36122478	36122479	+	Intron	DEL	TT	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36122478_36122479delTT	uc002oan.2	+						RBM42_uc010xsx.1_3'UTR|RBM42_uc010eef.2_Intron|RBM42_uc002oao.2_Intron|RBM42_uc002oap.2_Intron|RBM42_uc002oaq.2_Intron|RBM42_uc010eeg.2_Intron	NM_024321	NP_077297	Q9BTD8	RBM42_HUMAN	RNA binding motif protein 42							cytoplasm|nucleus	nucleotide binding|RNA binding				0	all_lung(56;1.58e-07)|Lung NSC(56;2.43e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			GTCAATTTTGTTTTAACCTGAT	0.312													4	2	---	---	---	---	
AXL	558	broad.mit.edu	37	19	41758082	41758083	+	Intron	DEL	AC	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41758082_41758083delAC	uc010ehj.2	+						CYP2F1_uc010xvw.1_Intron|AXL_uc010ehk.2_Intron	NM_021913	NP_068713	P30530	UFO_HUMAN	AXL receptor tyrosine kinase isoform 1							integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(4)|stomach(3)|ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)	13						acacacacagacacacacacat	0.010													4	2	---	---	---	---	
NPAS1	4861	broad.mit.edu	37	19	47548359	47548359	+	Intron	DEL	G	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47548359delG	uc002pfw.2	+						NPAS1_uc002pfx.2_Intron|NPAS1_uc002pfy.2_Intron|NPAS1_uc010xyj.1_Intron	NM_002517	NP_002508	Q99742	NPAS1_HUMAN	neuronal PAS domain protein 1						central nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity				0		all_cancers(25;4.31e-08)|all_epithelial(76;2.96e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.102)		all cancers(93;6.02e-05)|OV - Ovarian serous cystadenocarcinoma(262;7.35e-05)|Epithelial(262;0.00389)|GBM - Glioblastoma multiforme(486;0.0252)		GAGAACTACAGGTCTGGCCCA	0.383													4	2	---	---	---	---	
ADAM33	80332	broad.mit.edu	37	20	3652979	3652983	+	Intron	DEL	GCGCA	-	-	rs56355127		TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3652979_3652983delGCGCA	uc002wit.2	-						ADAM33_uc002wiq.1_5'Flank|ADAM33_uc002wir.1_Intron|ADAM33_uc002wis.2_Intron|ADAM33_uc002wiu.2_Intron|uc002wiv.1_5'Flank|ADAM33_uc002wiw.1_Intron|ADAM33_uc010gba.1_Intron|ADAM33_uc010gbb.1_Intron	NM_025220	NP_079496	Q9BZ11	ADA33_HUMAN	ADAM metallopeptidase domain 33 isoform alpha						proteolysis	integral to membrane	metalloendopeptidase activity|zinc ion binding			large_intestine(2)|ovary(1)|skin(1)	4						GGCTTCAGCTGCGCAGGTGACGGGT	0.673													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	22452531	22452532	+	IGR	INS	-	C	C			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:22452531_22452532insC								LOC284788 (51250 upstream) : C20orf56 (88662 downstream)																							gatacacaccacacacacacat	0.223													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29597565	29597566	+	IGR	DEL	TT	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29597565_29597566delTT								None (None upstream) : FRG1B (14313 downstream)																							ttttataaacttgttctaaaaa	0.129													4	2	---	---	---	---	
TSHZ2	128553	broad.mit.edu	37	20	51949524	51949525	+	Intron	DEL	GT	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51949524_51949525delGT	uc002xwo.2	+							NM_173485	NP_775756	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2						multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|haematopoietic_and_lymphoid_tissue(1)	6			STAD - Stomach adenocarcinoma(23;0.1)			AACTACACTGGTGTGTGTGATT	0.441													4	2	---	---	---	---	
TFAP2C	7022	broad.mit.edu	37	20	55208252	55208252	+	Intron	DEL	A	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55208252delA	uc002xya.2	+						TFAP2C_uc010zzi.1_Intron	NM_003222	NP_003213	Q92754	AP2C_HUMAN	transcription factor AP-2 gamma						cell-cell signaling|male gonad development|regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein dimerization activity|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)	1			Colorectal(105;0.229)			gactcttattatttttttttt	0.174													5	3	---	---	---	---	
CDH4	1002	broad.mit.edu	37	20	60500507	60500508	+	Intron	DEL	TC	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60500507_60500508delTC	uc002ybn.1	+						CDH4_uc002ybp.1_Intron	NM_001794	NP_001785	P55283	CADH4_HUMAN	cadherin 4, type 1 preproprotein						adherens junction organization|cell junction assembly		calcium ion binding			lung(3)|ovary(2)|skin(1)	6			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			cccctgagaatcaaacgagtcg	0.163													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	62028685	62028686	+	5'Flank	DEL	GT	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62028685_62028686delGT	uc002yew.1	-											Homo sapiens cDNA FLJ31705 fis, clone NT2RI2006183, weakly similar to Proline-rich protein M14 precursor.																		tctgcctctcgtgaatgacgct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10208194	10208194	+	IGR	DEL	T	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10208194delT								None (None upstream) : TPTE (698549 downstream)																							GTTCTTTACCTAAAACACTTC	0.328													4	2	---	---	---	---	
PDE9A	5152	broad.mit.edu	37	21	44138580	44138580	+	Intron	DEL	T	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44138580delT	uc002zbm.2	+						PDE9A_uc002zbn.2_Intron|PDE9A_uc002zbo.2_Intron|PDE9A_uc002zbp.2_Intron|PDE9A_uc002zbq.2_Intron|PDE9A_uc002zbs.2_Intron|PDE9A_uc002zbr.2_Intron|PDE9A_uc002zbt.2_Intron|PDE9A_uc002zbu.2_Intron|PDE9A_uc002zbv.2_Intron|PDE9A_uc002zbw.2_Intron|PDE9A_uc002zbx.2_Intron|PDE9A_uc002zby.2_Intron|PDE9A_uc002zbz.2_Intron|PDE9A_uc002zca.2_Intron|PDE9A_uc002zcb.2_Intron|PDE9A_uc002zcc.2_Intron|PDE9A_uc002zcd.2_Intron|PDE9A_uc002zce.2_Intron|PDE9A_uc002zcf.2_Intron|PDE9A_uc002zcg.2_Intron	NM_002606	NP_002597	O76083	PDE9A_HUMAN	phosphodiesterase 9A isoform a						platelet activation|signal transduction	cytosol|endoplasmic reticulum|Golgi apparatus|perinuclear region of cytoplasm|ruffle membrane	3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding|protein binding			ovary(1)|skin(1)	2						ttttataatcttttttttctt	0.000													3	3	---	---	---	---	
PCNT	5116	broad.mit.edu	37	21	47768704	47768704	+	Intron	DEL	T	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47768704delT	uc002zji.3	+						PCNT_uc002zjj.2_Intron|PCNT_uc010gqk.1_Intron	NM_006031	NP_006022	O95613	PCNT_HUMAN	pericentrin						cilium assembly|G2/M transition of mitotic cell cycle	cytosol|microtubule	calmodulin binding			ovary(4)|breast(2)|pancreas(2)	8	Breast(49;0.112)					aatttttgtattttttttttt	0.000													4	2	---	---	---	---	
MICAL3	57553	broad.mit.edu	37	22	18310261	18310261	+	Intron	DEL	C	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18310261delC	uc002zng.3	-						MICAL3_uc011agl.1_Intron	NM_015241	NP_056056	Q7RTP6	MICA3_HUMAN	microtubule associated monoxygenase, calponin							cytoplasm|cytoskeleton	monooxygenase activity|zinc ion binding				0		all_epithelial(15;0.198)		Lung(27;0.0427)		ACAGGTGTCACAACTGACAGC	0.517													6	6	---	---	---	---	
EP300	2033	broad.mit.edu	37	22	41556423	41556424	+	Intron	INS	-	A	A	rs35492332		TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41556423_41556424insA	uc003azl.3	+							NM_001429	NP_001420	Q09472	EP300_HUMAN	E1A binding protein p300						apoptosis|cell cycle|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|histone H4 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of androgen receptor signaling pathway|response to estrogen stimulus|response to hypoxia	centrosome|histone acetyltransferase complex	androgen receptor binding|beta-catenin binding|DNA binding|histone acetyltransferase activity|RNA polymerase II activating transcription factor binding|transcription coactivator activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(22)|large_intestine(13)|breast(9)|central_nervous_system(5)|upper_aerodigestive_tract(4)|pancreas(4)|lung(3)|ovary(2)|stomach(1)|skin(1)	64						GCTTTGATTGcaaaaaaaaaaa	0.238			T| N|F|Mis|O	MLL|RUNXBP2	colorectal|breast|pancreatic|AML|ALL|DLBCL				Rubinstein-Taybi_syndrome				7	6	---	---	---	---	
TTLL12	23170	broad.mit.edu	37	22	43575350	43575350	+	Intron	DEL	C	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43575350delC	uc003bdq.2	-						TTLL12_uc003bdr.1_Intron	NM_015140	NP_055955	Q14166	TTL12_HUMAN	tubulin tyrosine ligase-like family, member 12						protein modification process		tubulin-tyrosine ligase activity			central_nervous_system(1)	1		Ovarian(80;0.221)|Glioma(61;0.222)				AACTGCACAGCCCCCTCCTTC	0.652													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	49782342	49782342	+	IGR	DEL	T	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49782342delT								FAM19A5 (634600 upstream) : C22orf34 (25834 downstream)																							tagctgtaagtttttcataaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	50238933	50238933	+	IGR	DEL	A	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50238933delA								BRD1 (17753 upstream) : ZBED4 (8564 downstream)																							tgtttattataaaagatacga	0.000													4	2	---	---	---	---	
BMX	660	broad.mit.edu	37	X	15554697	15554697	+	Intron	DEL	A	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:15554697delA	uc004cww.2	+						BMX_uc004cwx.3_Intron|BMX_uc004cwy.3_Intron	NM_203281	NP_975010	P51813	BMX_HUMAN	BMX non-receptor tyrosine kinase						cellular component disassembly involved in apoptosis|intracellular signal transduction|mesoderm development	cytosol	ATP binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding|signal transducer activity			lung(3)|ovary(2)	5	Hepatocellular(33;0.183)					GATTTTCTTTAAAAAAAAAAA	0.313													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	106846640	106846640	+	IGR	DEL	G	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:106846640delG								CXorf41 (359168 upstream) : PRPS1 (25014 downstream)																							CCCCAACCATGGCCCCAGGTT	0.557													4	2	---	---	---	---	
PRPS1	5631	broad.mit.edu	37	X	106893109	106893109	+	Intron	DEL	A	-	-			TCGA-B2-4099-01A-02D-1251-10	TCGA-B2-4099-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:106893109delA	uc004ene.3	+						PRPS1_uc010npg.2_Intron|PRPS1_uc011msj.1_Intron	NM_002764	NP_002755	P60891	PRPS1_HUMAN	phosphoribosyl pyrophosphate synthetase 1						5-phosphoribose 1-diphosphate biosynthetic process|hypoxanthine biosynthetic process|nervous system development|nucleoside metabolic process|purine nucleotide biosynthetic process|pyrimidine nucleotide biosynthetic process|ribonucleoside monophosphate biosynthetic process|urate biosynthetic process	cytosol	ATP binding|kinase activity|magnesium ion binding|protein homodimerization activity|ribose phosphate diphosphokinase activity			breast(3)|large_intestine(1)	4						CAGTGTCTGCAAATTGGCCAG	0.458													20	32	---	---	---	---	
ESPNP	284729	broad.mit.edu	37	1	17034125	17034126	+	Frame_Shift_Ins	INS	-	AGCT	AGCT	rs141324796	by1000genomes	TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17034125_17034126insAGCT	uc001azn.1	-	3	478_479	c.364_365insAGCT	c.(364-366)TGGfs	p.W122fs	ESPNP_uc010ocj.1_Frame_Shift_Ins_p.W52fs	NR_026567				RecName: Full=Espin; AltName: Full=Ectoplasmic specialization protein; AltName: Full=Autosomal recessive deafness type 36 protein;												0						CAGCAGCAGCCAGCTGAGCACC	0.663													4	3	---	---	---	---	
DNAJC6	9829	broad.mit.edu	37	1	65874626	65874627	+	Intron	INS	-	T	T	rs140651200	by1000genomes	TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65874626_65874627insT	uc001dcd.1	+						DNAJC6_uc010opc.1_Intron|DNAJC6_uc001dce.1_Intron	NM_014787	NP_055602	O75061	AUXI_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 6						cellular membrane organization|post-Golgi vesicle-mediated transport	cytosol	heat shock protein binding|protein tyrosine phosphatase activity|SH3 domain binding			large_intestine(1)|lung(1)|ovary(1)	3						aaacaacaggattttttttttc	0.079													4	3	---	---	---	---	
CSDE1	7812	broad.mit.edu	37	1	115266236	115266238	+	Intron	DEL	TTG	-	-	rs144694123		TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115266236_115266238delTTG	uc001efk.2	-						CSDE1_uc001efi.2_Intron|CSDE1_uc001efj.2_Intron|CSDE1_uc001efl.2_Intron|CSDE1_uc001efm.2_Intron|CSDE1_uc009wgv.2_Intron|CSDE1_uc001efn.2_Intron	NM_001007553	NP_001007554	O75534	CSDE1_HUMAN	upstream of NRAS isoform 1						male gonad development|regulation of transcription, DNA-dependent	cytoplasm	DNA binding|protein binding|RNA binding			ovary(1)	1	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;2.21e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		TTATCAGAGTTTGTTGTTAAGTC	0.330													4	3	---	---	---	---	
FAM46C	54855	broad.mit.edu	37	1	118166786	118166787	+	3'UTR	INS	-	T	T	rs75632243		TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118166786_118166787insT	uc001ehe.2	+	2						NM_017709	NP_060179	Q5VWP2	FA46C_HUMAN	hypothetical protein LOC54855												0	Lung SC(450;0.225)	all_cancers(81;0.000101)|all_lung(203;3.4e-06)|all_epithelial(167;4.98e-06)|Lung NSC(69;2.33e-05)		Lung(183;0.0576)|LUSC - Lung squamous cell carcinoma(189;0.192)|Colorectal(144;0.247)		TCTGATTCTGCTTTTTTTTTTT	0.470										Multiple Myeloma(3;1.13e-06)			5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	121354362	121354362	+	IGR	DEL	A	-	-			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:121354362delA								LOC647121 (40676 upstream) : None (None downstream)																							atgagaagatatttccttttc	0.000													4	2	---	---	---	---	
NUP210L	91181	broad.mit.edu	37	1	153968474	153968474	+	Intron	DEL	A	-	-			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153968474delA	uc001fdw.2	-						NUP210L_uc009woq.2_Intron|NUP210L_uc010peh.1_Intron	NM_207308	NP_997191	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like isoform 1							integral to membrane				skin(5)|ovary(4)|large_intestine(1)|central_nervous_system(1)	11	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)			GAGGAGACTTAAAAAAAAAAT	0.184													3	3	---	---	---	---	
NCSTN	23385	broad.mit.edu	37	1	160320244	160320244	+	Intron	DEL	A	-	-	rs5778159		TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160320244delA	uc001fvx.2	+						NCSTN_uc001fvy.2_Intron|NCSTN_uc010pjf.1_Intron|NCSTN_uc001fvz.2_Intron|NCSTN_uc010pjg.1_Intron	NM_015331	NP_056146	Q92542	NICA_HUMAN	nicastrin precursor						amyloid precursor protein catabolic process|apoptosis|induction of apoptosis by extracellular signals|membrane protein ectodomain proteolysis|membrane protein intracellular domain proteolysis|nerve growth factor receptor signaling pathway|Notch receptor processing|Notch signaling pathway|positive regulation of catalytic activity|protein processing	endoplasmic reticulum|Golgi apparatus|integral to plasma membrane|melanosome	protein binding			ovary(1)|lung(1)	2	all_cancers(52;8.15e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			cctgtgtcacaaaaaaaaaaa	0.179													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	207273434	207273439	+	IGR	DEL	TGTGTA	-	-	rs35665980		TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207273434_207273439delTGTGTA								C4BPB (99 upstream) : C4BPA (4072 downstream)																							tgtgtgtgtgtgtgtatgtgtgtgtg	0.257													8	5	---	---	---	---	
CNST	163882	broad.mit.edu	37	1	246810555	246810555	+	Frame_Shift_Del	DEL	T	-	-			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246810555delT	uc001ibp.2	+	9	1430	c.1052delT	c.(1051-1053)CTTfs	p.L351fs	CNST_uc001ibo.3_Frame_Shift_Del_p.L351fs	NM_152609	NP_689822	Q6PJW8	CNST_HUMAN	hypothetical protein LOC163882 isoform 1	351					positive regulation of Golgi to plasma membrane protein transport	integral to membrane|plasma membrane|protein complex|trans-Golgi network|transport vesicle	connexin binding				0						TCCCCAAGCCTTTCGGTAACT	0.582											OREG0014367	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	150	88	---	---	---	---	
OR2L13	284521	broad.mit.edu	37	1	248166156	248166157	+	Intron	INS	-	A	A			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248166156_248166157insA	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)			gactccagctcaaaaaaaaaaa	0.000													3	3	---	---	---	---	
PUM2	23369	broad.mit.edu	37	2	20453929	20453929	+	Intron	DEL	T	-	-	rs149877577		TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20453929delT	uc002rds.1	-						PUM2_uc002rdq.1_Intron|PUM2_uc002rdt.1_Intron|PUM2_uc002rdr.2_Intron|PUM2_uc010yjy.1_Intron|PUM2_uc002rdu.1_Intron|PUM2_uc010yjz.1_Intron	NM_015317	NP_056132	Q8TB72	PUM2_HUMAN	pumilio homolog 2						regulation of translation	perinuclear region of cytoplasm|stress granule	protein binding|RNA binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					tattttgttcttttttttttt	0.134													6	4	---	---	---	---	
NRBP1	29959	broad.mit.edu	37	2	27660289	27660289	+	Intron	DEL	C	-	-			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27660289delC	uc002rko.2	+						NRBP1_uc002rkq.2_Intron|NRBP1_uc002rkp.2_Intron|NRBP1_uc002rkr.2_Intron	NM_013392	NP_037524	Q9UHY1	NRBP_HUMAN	nuclear receptor binding protein						ER to Golgi vesicle-mediated transport|gene expression|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	cell cortex|endomembrane system|lamellipodium|membrane|nucleoplasm	ATP binding|protein homodimerization activity|protein kinase activity			ovary(2)|lung(1)	3	Acute lymphoblastic leukemia(172;0.155)					GGTTTTTCTTCCTTTGTACCC	0.433													21	10	---	---	---	---	
SPAST	6683	broad.mit.edu	37	2	32362049	32362049	+	Intron	DEL	T	-	-			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32362049delT	uc002roc.2	+						SPAST_uc002rod.2_Intron	NM_014946	NP_055761	Q9UBP0	SPAST_HUMAN	spastin isoform 1						cell cycle|cell death|cell differentiation|cytokinesis, completion of separation|ER to Golgi vesicle-mediated transport|microtubule bundle formation|microtubule severing|nervous system development|protein hexamerization|protein homooligomerization	endoplasmic reticulum|endosome|integral to membrane|microtubule|microtubule organizing center|nucleus|perinuclear region of cytoplasm|spindle	alpha-tubulin binding|ATP binding|beta-tubulin binding|microtubule binding|microtubule-severing ATPase activity			breast(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					TAAGTGTTGATTATGATATTT	0.294													40	19	---	---	---	---	
CCDC142	84865	broad.mit.edu	37	2	74707717	74707718	+	Intron	INS	-	AAA	AAA			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74707717_74707718insAAA	uc002slr.2	-						TTC31_uc002sls.2_5'Flank|TTC31_uc010yrv.1_5'Flank|TTC31_uc002slt.2_5'Flank|TTC31_uc002slu.2_5'Flank|CCDC142_uc002slo.2_Intron|CCDC142_uc002slq.2_Intron|CCDC142_uc002slp.2_Intron	NM_032779	NP_116168	Q17RM4	CC142_HUMAN	coiled-coil domain containing 142											central_nervous_system(1)	1						gaccctgtctcaaaaaaaaaaa	0.139													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	92121302	92121303	+	IGR	DEL	AT	-	-			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92121302_92121303delAT								GGT8P (151149 upstream) : FKSG73 (7856 downstream)																							aggcaaagccatacacacacac	0.015													4	2	---	---	---	---	
PTPN18	26469	broad.mit.edu	37	2	131129929	131129934	+	In_Frame_Del	DEL	GACGGG	-	-	rs112040677		TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131129929_131129934delGACGGG	uc002trc.2	+	13	1214_1219	c.1113_1118delGACGGG	c.(1111-1119)CAGACGGGG>CAG	p.TG378del	PTPN18_uc002trd.2_In_Frame_Del_p.TG357del|PTPN18_uc002trb.2_In_Frame_Del_p.TG271del|PTPN18_uc002tre.2_In_Frame_Del_p.TG29del	NM_014369	NP_055184	Q99952	PTN18_HUMAN	protein tyrosine phosphatase, non-receptor type	378_379				Missing (in Ref. 1; CAA56105).		cytoplasm|nucleus	non-membrane spanning protein tyrosine phosphatase activity			ovary(3)|kidney(1)	4	Colorectal(110;0.1)					gtgggacgcagacggggacggggacg	0.568													8	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	131378845	131378846	+	IGR	INS	-	T	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131378845_131378846insT								LOC150527 (71374 upstream) : C2orf14 (58777 downstream)																							AGATAAGAGGGTTTTTTTTGGT	0.371													7	4	---	---	---	---	
LY75	4065	broad.mit.edu	37	2	160634565	160634566	+	Intron	DEL	CC	-	-	rs35013477		TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160634565_160634566delCC	uc002ubb.3	-						LY75_uc010fos.2_Intron|CD302_uc002uba.2_Intron|CD302_uc010zco.1_Intron	NM_002349	NP_002340	O60449	LY75_HUMAN	lymphocyte antigen 75 precursor						endocytosis|immune response|inflammatory response	integral to plasma membrane	receptor activity|sugar binding				0				COAD - Colon adenocarcinoma(177;0.132)		TAAAAATAAACCCTTTTATTAG	0.233													6	3	---	---	---	---	
NOSTRIN	115677	broad.mit.edu	37	2	169712115	169712116	+	Intron	INS	-	A	A	rs74552507		TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:169712115_169712116insA	uc002ueg.2	+						NOSTRIN_uc002uef.2_Intron|NOSTRIN_uc002uei.2_Intron|NOSTRIN_uc010fpu.2_Intron|NOSTRIN_uc002ueh.2_Intron|NOSTRIN_uc002uej.2_Intron|NOSTRIN_uc002uek.2_5'Flank	NM_001039724	NP_001034813	Q8IVI9	NOSTN_HUMAN	nitric oxide synthase trafficker isoform 2						endocytosis|nitric oxide metabolic process|regulation of nitric-oxide synthase activity	cytoplasmic membrane-bounded vesicle|cytoskeleton|plasma membrane	protein binding				0						GTTGTGTGAACaaaaaaaaaaa	0.248													6	4	---	---	---	---	
VHL	7428	broad.mit.edu	37	3	10191649	10191650	+	3'UTR	DEL	AA	-	-			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10191649_10191650delAA	uc003bvc.2	+	3					VHL_uc003bvd.2_3'UTR	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1						anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.?(1)|p.*214C(1)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		TGGGAGATTGAAGATTTCTGTT	0.455		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				8	16	---	---	---	---	
WDR48	57599	broad.mit.edu	37	3	39107048	39107048	+	Intron	DEL	A	-	-	rs34404622		TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39107048delA	uc003cit.2	+						WDR48_uc011ayt.1_Intron|WDR48_uc011ayu.1_Intron|WDR48_uc011ayv.1_Intron|WDR48_uc003ciu.2_Intron	NM_020839	NP_065890	Q8TAF3	WDR48_HUMAN	WD repeat domain 48						interspecies interaction between organisms|protein deubiquitination	lysosome|nucleus	protein binding			ovary(1)|breast(1)	2				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		TTAACAAGGCAAAAAAAAAAA	0.363													2	4	---	---	---	---	
PBRM1	55193	broad.mit.edu	37	3	52620529	52620550	+	Frame_Shift_Del	DEL	ACAGAGGCCACGCGAACCACAG	-	-	rs143085435		TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52620529_52620550delACAGAGGCCACGCGAACCACAG	uc003des.2	-	20	3290_3311	c.3278_3299delCTGTGGTTCGCGTGGCCTCTGT	c.(3277-3300)CCTGTGGTTCGCGTGGCCTCTGTAfs	p.P1093fs	PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Frame_Shift_Del_p.P1093fs|PBRM1_uc003der.2_Frame_Shift_Del_p.P1061fs|PBRM1_uc003det.2_Frame_Shift_Del_p.P1108fs|PBRM1_uc003deu.2_Frame_Shift_Del_p.P1108fs|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Frame_Shift_Del_p.P1093fs|PBRM1_uc010hmk.1_Frame_Shift_Del_p.P1068fs|PBRM1_uc003dey.2_Frame_Shift_Del_p.P1068fs|PBRM1_uc003dez.1_Frame_Shift_Del_p.P1092fs|PBRM1_uc003dfb.1_Frame_Shift_Del_p.P1005fs|PBRM1_uc003dfa.1_Frame_Shift_Del_p.P439fs	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	1093_1100					chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		ATTTGCAAATACAGAGGCCACGCGAACCACAGGCAGAGGCAC	0.437			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								121	72	---	---	---	---	
MUC13	56667	broad.mit.edu	37	3	124626850	124626851	+	Intron	DEL	TC	-	-			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124626850_124626851delTC	uc003ehq.1	-							NM_033049	NP_149038	Q9H3R2	MUC13_HUMAN	mucin 13, epithelial transmembrane							extracellular region|integral to membrane|plasma membrane					0						TCCTTTTTGATCTCTCTCTCTC	0.322													4	2	---	---	---	---	
USP13	8975	broad.mit.edu	37	3	179368059	179368060	+	5'Flank	DEL	GA	-	-			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179368059_179368060delGA	uc003fkh.2	+						USP13_uc003fkf.2_5'Flank	NM_003940	NP_003931	Q92995	UBP13_HUMAN	ubiquitin thiolesterase 13						ubiquitin-dependent protein catabolic process		cysteine-type endopeptidase activity|omega peptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			ovary(1)	1	all_cancers(143;7.79e-15)|Ovarian(172;0.0338)|Breast(254;0.148)		OV - Ovarian serous cystadenocarcinoma(80;1e-25)|GBM - Glioblastoma multiforme(14;0.0169)			GCTGGTGTTGGAGAGCGATGGC	0.351													4	2	---	---	---	---	
ZNF876P	642280	broad.mit.edu	37	4	247254	247255	+	Intron	DEL	TA	-	-	rs34738994		TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:247254_247255delTA	uc010iba.2	+							NR_027481				Homo sapiens cDNA clone IMAGE:4828836.												0						TTTGTATAAGTATATATATATT	0.134													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	20620789	20620790	+	IGR	INS	-	A	A	rs75247881		TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20620789_20620790insA								SLIT2 (1 upstream) : PACRGL (77115 downstream)																							TCTGCATTTGGAAAAAAAAAAA	0.307													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	70422906	70422906	+	Intron	DEL	T	-	-			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:70422906delT	uc010iyn.2	-											Homo sapiens cDNA FLJ78390 complete cds.																		ATTATCTGACttttttttttt	0.189													4	2	---	---	---	---	
DOCK2	1794	broad.mit.edu	37	5	169435220	169435229	+	Intron	DEL	CAACAACAAC	-	-	rs67671523		TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169435220_169435229delCAACAACAAC	uc003maf.2	+						DOCK2_uc011der.1_Intron|DOCK2_uc010jjm.2_Intron	NM_004946	NP_004937	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2						actin cytoskeleton organization|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|endomembrane system|membrane	electron carrier activity|GTP binding|GTPase binding|heme binding|Rac guanyl-nucleotide exchange factor activity|T cell receptor binding			ovary(5)|pancreas(2)	7	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			acaacaacaacaacaacaacaaAAAAAAAA	0.362													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	170261080	170261082	+	IGR	DEL	CAT	-	-	rs111380690		TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170261080_170261082delCAT								GABRP (20032 upstream) : RANBP17 (27940 downstream)																							ccaccatcaccatcaccaccacc	0.118													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	3615281	3615281	+	IGR	DEL	A	-	-			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3615281delA								SLC22A23 (158488 upstream) : C6orf145 (107555 downstream)																							ggaaggaaggaaaggagggga	0.045													4	2	---	---	---	---	
F13A1	2162	broad.mit.edu	37	6	6266630	6266630	+	Intron	DEL	A	-	-			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6266630delA	uc003mwv.2	-						F13A1_uc011dib.1_Intron	NM_000129	NP_000120	P00488	F13A_HUMAN	coagulation factor XIII A1 subunit precursor						peptide cross-linking|platelet activation|platelet degranulation	extracellular region|platelet alpha granule lumen	acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|pancreas(1)|skin(1)	6	Ovarian(93;0.0816)	all_hematologic(90;0.152)			L-Glutamine(DB00130)	acacccatctaatttttaatt	0.000													13	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	32441392	32441393	+	IGR	INS	-	T	T	rs71556927		TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32441392_32441393insT								HLA-DRA (28571 upstream) : HLA-DRB1 (43770 downstream)																							AATTATGGGGAGGAGGTTACTG	0.505													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	34158925	34158925	+	IGR	DEL	A	-	-			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34158925delA								GRM4 (45056 upstream) : HMGA1 (45652 downstream)																							GTCATTGTGGaaaaaaaaaaa	0.294													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	159946964	159946964	+	IGR	DEL	T	-	-			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:159946964delT								FNDC1 (253825 upstream) : SOD2 (153187 downstream)																							ccaatcagggttttttttttt	0.085													4	4	---	---	---	---	
HOXA10	3206	broad.mit.edu	37	7	27211532	27211533	+	Frame_Shift_Del	DEL	AG	-	-			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27211532_27211533delAG	uc011jzm.1	-	2	1248_1249	c.1218_1219delCT	c.(1216-1221)AACTTTfs	p.N406fs	MIR196B_hsa-mir-196b|MI0001150_5'Flank|HOXA10_uc003syw.3_Frame_Shift_Del_p.N90fs	NM_018951	NP_061824	P31260	HXA10_HUMAN	homeobox A10 isoform a	406_407					spermatogenesis		protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						GAAAAATTAAAGTTGGCTGTGA	0.515													126	72	---	---	---	---	
PMS2L11	441263	broad.mit.edu	37	7	76634275	76634280	+	Intron	DEL	TGCTGT	-	-	rs67390349		TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76634275_76634280delTGCTGT	uc003ufw.3	+						PMS2L11_uc011kgn.1_Intron	NR_023383				Homo sapiens cDNA FLJ59034 complete cds, moderately similar to Protein deltex-2.												0						GTGCGGGGACTGCTGTGGGGCCTGGG	0.660													6	4	---	---	---	---	
LOC100132832	100132832	broad.mit.edu	37	7	76669648	76669649	+	Intron	INS	-	ATCTC	ATCTC			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76669648_76669649insATCTC	uc003ufy.2	+						PMS2L11_uc011kgn.1_Intron	NR_028058				Homo sapiens cDNA FLJ59034 complete cds, moderately similar to Protein deltex-2.												0						TGCACAGAAATATTTAATTTGC	0.208													5	6	---	---	---	---	
FAM71F2	346653	broad.mit.edu	37	7	128312704	128312704	+	Intron	DEL	G	-	-	rs10265601		TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128312704delG	uc003vnk.3	+						FAM71F2_uc010llm.1_Intron|FAM71F2_uc003vnl.2_Intron|FAM71F2_uc010lln.1_Intron	NM_001012454	NP_001012457	Q6NXP2	F71F2_HUMAN	hypothetical protein LOC346653 isoform a												0						CCCTGGGGGAGGGGGGGGCGG	0.552											OREG0018296	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	5	---	---	---	---	
DEFB134	613211	broad.mit.edu	37	8	11853467	11853468	+	Intron	INS	-	A	A	rs34837269		TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11853467_11853468insA	uc011kxn.1	-							NM_001033019	NP_001028191	Q4QY38	DB134_HUMAN	beta-defensin 134 precursor						defense response to bacterium	extracellular region					0			STAD - Stomach adenocarcinoma(15;0.033)	COAD - Colon adenocarcinoma(149;0.159)		TCAGTTCAGCCAAAAAAAAAAa	0.059													7	5	---	---	---	---	
NKX6-3	157848	broad.mit.edu	37	8	41503854	41503857	+	3'UTR	DEL	AAAG	-	-	rs5891165		TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41503854_41503857delAAAG	uc003xoa.2	-	2					NKX6-3_uc010lxa.1_3'UTR	NM_152568	NP_689781	A6NJ46	NKX63_HUMAN	NK6 homeobox 3							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0	Ovarian(28;0.00541)|Colorectal(14;0.0202)|Lung SC(25;0.211)	all_lung(54;0.0131)|Lung NSC(58;0.0363)|Esophageal squamous(32;0.0844)|Hepatocellular(245;0.154)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)			CCCCTCATCCAAAGAAAGACTCAG	0.475													3	4	---	---	---	---	
GLDC	2731	broad.mit.edu	37	9	6639659	6639660	+	Intron	INS	-	AA	AA			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6639659_6639660insAA	uc003zkc.2	-							NM_000170	NP_000161	P23378	GCSP_HUMAN	glycine dehydrogenase (decarboxylating)						glycine catabolic process	mitochondrion	electron carrier activity|glycine dehydrogenase (decarboxylating) activity|lyase activity|pyridoxal phosphate binding			ovary(2)	2		Acute lymphoblastic leukemia(23;0.161)		GBM - Glioblastoma multiforme(50;0.0421)|Lung(218;0.134)	Glycine(DB00145)|Pyridoxal Phosphate(DB00114)	CTTTTCACCataaaaaaaaagt	0.223													12	7	---	---	---	---	
B4GALT1	2683	broad.mit.edu	37	9	33120193	33120193	+	Intron	DEL	A	-	-			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33120193delA	uc003zsg.2	-							NM_001497	NP_001488	P15291	B4GT1_HUMAN	UDP-Gal:betaGlcNAc beta 1,4-						oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	basolateral plasma membrane|brush border membrane|desmosome|external side of plasma membrane|extracellular region|glycocalyx|Golgi cisterna membrane|Golgi trans cisterna|integral to membrane	alpha-tubulin binding|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity|beta-tubulin binding|lactose synthase activity|metal ion binding|N-acetyllactosamine synthase activity|protein binding|protein homodimerization activity				0			LUSC - Lung squamous cell carcinoma(29;0.0084)	GBM - Glioblastoma multiforme(74;0.121)	N-Acetyl-D-glucosamine(DB00141)	aaaaacaaacaaaaaaaaaaa	0.189													4	2	---	---	---	---	
FRMPD1	22844	broad.mit.edu	37	9	37736856	37736857	+	Intron	DEL	GT	-	-			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37736856_37736857delGT	uc004aag.1	+						FRMPD1_uc004aah.1_Intron|FRMPD1_uc011lqm.1_Intron|FRMPD1_uc011lqn.1_Intron	NM_014907	NP_055722	Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1							cytoskeleton|cytosol|plasma membrane				ovary(4)|central_nervous_system(2)|skin(2)|breast(1)	9				GBM - Glioblastoma multiforme(29;0.00655)		gtgcgtgagagtgtgtgtgtgt	0.366													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68430364	68430365	+	IGR	INS	-	A	A	rs140332329		TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68430364_68430365insA								FAM27B (636175 upstream) : MIR1299 (571874 downstream)																							TTATGCAGAAGAAAAAATTAAC	0.322													8	4	---	---	---	---	
WDR34	89891	broad.mit.edu	37	9	131397627	131397627	+	Intron	DEL	A	-	-			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131397627delA	uc004bvq.1	-						WDR34_uc004bvs.1_Intron|WDR34_uc004bvr.1_Intron	NM_052844	NP_443076	Q96EX3	WDR34_HUMAN	WD repeat domain 34							cytoplasm				central_nervous_system(2)|skin(1)	3						CTCTTCCAGGAAAAAAAAAAA	0.622											OREG0019522	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	7	5	---	---	---	---	
PRKG1	5592	broad.mit.edu	37	10	53667021	53667022	+	Intron	INS	-	T	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:53667021_53667022insT	uc001jjm.2	+						PRKG1_uc001jjn.2_Intron|PRKG1_uc001jjo.2_Intron	NM_001098512	NP_001091982	Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I isoform						actin cytoskeleton organization|platelet activation|signal transduction	cytosol	ATP binding|cGMP binding|cGMP-dependent protein kinase activity			lung(2)|stomach(1)|ovary(1)|central_nervous_system(1)|skin(1)	6		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)		caaactccaagtttttttttca	0.109													4	2	---	---	---	---	
AGAP11	119385	broad.mit.edu	37	10	88767879	88767880	+	Intron	INS	-	T	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88767879_88767880insT	uc001kee.2	+						AGAP11_uc001kef.2_Intron	NM_133447	NP_597704	Q8TF27	AGA11_HUMAN	ankyrin repeat and GTPase domain Arf GTPase						regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding				0						ttttttctttcttttttttttt	0.000													5	4	---	---	---	---	
UBTD1	80019	broad.mit.edu	37	10	99329675	99329676	+	Intron	INS	-	A	A	rs79148719		TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99329675_99329676insA	uc001knv.1	+						ANKRD2_uc001knw.2_5'Flank|ANKRD2_uc009xvu.2_5'Flank	NM_024954	NP_079230	Q9HAC8	UBTD1_HUMAN	ubiquitin domain containing 1												0		Colorectal(252;0.162)		Epithelial(162;3.04e-10)|all cancers(201;2.86e-08)		tgtctcaaaagaaaaaaaaaaa	0.000													13	6	---	---	---	---	
SEC23IP	11196	broad.mit.edu	37	10	121691448	121691448	+	Intron	DEL	A	-	-	rs77894008		TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121691448delA	uc001leu.1	+						SEC23IP_uc010qtc.1_Intron|SEC23IP_uc009xzk.1_Intron	NM_007190	NP_009121	Q9Y6Y8	S23IP_HUMAN	Sec23-interacting protein p125						Golgi organization|intracellular protein transport	endoplasmic reticulum|ER to Golgi transport vesicle membrane|ER-Golgi intermediate compartment	metal ion binding			ovary(3)	3		Lung NSC(174;0.109)|all_lung(145;0.142)|all_neural(114;0.234)		all cancers(201;0.00515)		TTTAGTCATTAAAAAAAAAAG	0.303													5	3	---	---	---	---	
WDR11	55717	broad.mit.edu	37	10	122619467	122619468	+	Intron	DEL	AC	-	-	rs3217470		TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:122619467_122619468delAC	uc010qtf.1	+						WDR11_uc010qte.1_Intron|WDR11_uc001lfd.1_Intron	NM_018117	NP_060587	Q9BZH6	WDR11_HUMAN	bromodomain and WD repeat domain containing 2							integral to membrane					0						GAATATTGATacacacacacac	0.238													2	4	---	---	---	---	
IFITM2	10581	broad.mit.edu	37	11	308885	308886	+	Intron	INS	-	C	C	rs5789178		TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:308885_308886insC	uc001lox.3	+							NM_006435	NP_006426	Q01629	IFM2_HUMAN	interferon induced transmembrane protein 2						response to virus|type I interferon-mediated signaling pathway	integral to membrane|plasma membrane	protein binding				0		all_cancers(49;2e-09)|all_epithelial(84;3.36e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;5.73e-28)|Epithelial(43;3.42e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.14e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0328)|LUSC - Lung squamous cell carcinoma(625;0.122)		GAGAGTCTGAGCCGGGTGAGGA	0.639													11	6	---	---	---	---	
TSGA10IP	254187	broad.mit.edu	37	11	65715748	65715751	+	Intron	DEL	CATC	-	-	rs585897		TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65715748_65715751delCATC	uc001ogk.1	+						TSGA10IP_uc009yqw.1_Intron|TSGA10IP_uc009yqx.1_Intron	NM_152762	NP_689975	Q3SY00	T10IP_HUMAN	testis specific, 10 interacting protein												0						ACTTTTGGATcatccatccatcca	0.201													6	3	---	---	---	---	
PAAF1	80227	broad.mit.edu	37	11	73611047	73611047	+	Intron	DEL	T	-	-	rs34058264		TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73611047delT	uc001ouk.1	+						PAAF1_uc001oul.1_Intron|PAAF1_uc009ytx.1_Intron|PAAF1_uc001oum.1_Intron	NM_025155	NP_079431	Q9BRP4	PAAF1_HUMAN	proteasomal ATPase-associated factor 1						interspecies interaction between organisms	proteasome complex	protein binding			ovary(1)|skin(1)	2	Breast(11;7.42e-05)					CATGGAATTCTTTTTTTTTTT	0.378													4	2	---	---	---	---	
DSCAML1	57453	broad.mit.edu	37	11	117651018	117651019	+	Intron	DEL	AG	-	-	rs146014553		TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117651018_117651019delAG	uc001prh.1	-						DSCAML1_uc001pri.1_Intron	NM_020693	NP_065744	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1						axonogenesis|brain development|cell fate determination|dorsal/ventral pattern formation|embryonic skeletal system morphogenesis|homophilic cell adhesion	cell surface|integral to membrane|plasma membrane	protein homodimerization activity			ovary(3)|large_intestine(2)|skin(2)|upper_aerodigestive_tract(1)	8	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		aaagaaagaaagagagaaagga	0.158													6	6	---	---	---	---	
ARHGEF12	23365	broad.mit.edu	37	11	120352470	120352470	+	Intron	DEL	T	-	-			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120352470delT	uc001pxl.1	+						ARHGEF12_uc009zau.1_Intron	NM_015313	NP_056128	Q9NZN5	ARHGC_HUMAN	Rho guanine nucleotide exchange factor (GEF) 12						apoptosis|axon guidance|G-protein coupled receptor protein signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|membrane	G-protein-coupled receptor binding|GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(2)|breast(2)|skin(2)|ovary(1)	7		Breast(109;0.000813)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_hematologic(192;0.107)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.231)		tctttctttcttttttttttt	0.144			T	MLL	AML								4	3	---	---	---	---	
VWF	7450	broad.mit.edu	37	12	6092567	6092568	+	Intron	INS	-	GATAGATAGATA	GATAGATAGATA	rs138350612	by1000genomes	TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6092567_6092568insGATAGATAGATA	uc001qnn.1	-						VWF_uc010set.1_Intron	NM_000552	NP_000543	P04275	VWF_HUMAN	von Willebrand factor preproprotein						blood coagulation, intrinsic pathway|cell-substrate adhesion|platelet activation|platelet degranulation|protein homooligomerization	endoplasmic reticulum|platelet alpha granule lumen|proteinaceous extracellular matrix|Weibel-Palade body	chaperone binding|collagen binding|glycoprotein binding|immunoglobulin binding|integrin binding|protease binding|protein homodimerization activity|protein N-terminus binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|breast(1)	12					Antihemophilic Factor(DB00025)	ACATGGGTTAGgatagatagat	0.198													4	3	---	---	---	---	
CLEC4E	26253	broad.mit.edu	37	12	8691946	8691946	+	Intron	DEL	A	-	-			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8691946delA	uc001quo.1	-							NM_014358	NP_055173	Q9ULY5	CLC4E_HUMAN	C-type lectin domain family 4, member E							integral to membrane	sugar binding			central_nervous_system(1)	1	Lung SC(5;0.184)					TATTTCGGTTAAAAATGTCAG	0.323													80	47	---	---	---	---	
MFAP5	8076	broad.mit.edu	37	12	8808611	8808611	+	Intron	DEL	A	-	-			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8808611delA	uc001qut.1	-						MFAP5_uc001qus.2_Intron|MFAP5_uc009zge.1_Intron	NM_003480	NP_003471	Q13361	MFAP5_HUMAN	microfibrillar associated protein 5 precursor							microfibril	extracellular matrix structural constituent			breast(1)	1	Lung SC(5;0.184)					ATTTAAAATGAAATCGGATAT	0.244													18	13	---	---	---	---	
THAP2	83591	broad.mit.edu	37	12	72058496	72058497	+	Intron	DEL	TG	-	-			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72058496_72058497delTG	uc001swq.2	+						ZFC3H1_uc001swo.2_5'Flank|ZFC3H1_uc010sts.1_5'Flank|ZFC3H1_uc001swp.2_5'Flank	NM_031435	NP_113623	Q9H0W7	THAP2_HUMAN	THAP domain containing, apoptosis associated							nucleolus	DNA binding|metal ion binding			ovary(1)	1						GTATGTCCTTTGTGTTTCTCAA	0.416													13	6	---	---	---	---	
TPTE2P1	646405	broad.mit.edu	37	13	25511130	25511131	+	Intron	INS	-	CA	CA	rs145506456	by1000genomes	TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25511130_25511131insCA	uc010tdh.1	-						TPTE2P1_uc001upw.2_Intron|TPTE2P1_uc001upx.3_Intron	NR_026730				RecName: Full=C2 tensin-type domain-containing protein ENSP00000371290;												0						ACAAAATATTTGTTTTCTGTGT	0.149													3	4	---	---	---	---	
CDADC1	81602	broad.mit.edu	37	13	49830214	49830215	+	Intron	INS	-	A	A	rs35925057		TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49830214_49830215insA	uc001vcu.2	+						CDADC1_uc001vcs.1_Intron|CDADC1_uc001vct.1_Intron|CDADC1_uc010tgk.1_Intron|CDADC1_uc001vcv.2_Intron	NM_030911	NP_112173	Q9BWV3	CDAC1_HUMAN	cytidine and dCMP deaminase domain containing 1								hydrolase activity|zinc ion binding			upper_aerodigestive_tract(1)	1		Lung NSC(96;0.000705)|Breast(56;0.0011)|Prostate(109;0.00446)|Hepatocellular(98;0.0556)|Glioma(44;0.236)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;1.06e-08)|COAD - Colon adenocarcinoma(199;0.216)		TCCTTTTTTTTAAAAAAAAAAG	0.262													4	4	---	---	---	---	
RNF219	79596	broad.mit.edu	37	13	79216106	79216107	+	Intron	INS	-	A	A	rs141070590	by1000genomes	TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:79216106_79216107insA	uc001vkw.1	-						RNF219_uc010afb.1_Intron|RNF219_uc010afc.2_Intron	NM_024546	NP_078822	Q5W0B1	RN219_HUMAN	ring finger protein 219								zinc ion binding			large_intestine(2)	2		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.0848)		GBM - Glioblastoma multiforme(99;0.0414)		AAGGAAAAAAGAAAAAAGAATT	0.282													11	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	99439134	99439135	+	IGR	INS	-	TTTTTTTTTTTTTTTTT	TTTTTTTTTTTTTTTTT			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99439134_99439135insTTTTTTTTTTTTTTTTT								C14orf177 (255037 upstream) : BCL11B (196492 downstream)																							ctacacacttcttttttttttt	0.153													8	4	---	---	---	---	
CATSPER2	117155	broad.mit.edu	37	15	43931609	43931609	+	Intron	DEL	T	-	-			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43931609delT	uc001zsh.2	-						CATSPER2_uc010bdm.2_Intron|CATSPER2_uc001zsi.2_Intron|CATSPER2_uc001zsj.2_Intron	NM_172095	NP_742093	Q96P56	CTSR2_HUMAN	sperm-associated cation channel 2 isoform 2						cell differentiation|multicellular organismal development|spermatogenesis	cilium|flagellar membrane|integral to membrane	calcium channel activity|protein binding|voltage-gated ion channel activity			ovary(1)	1		all_cancers(109;3.26e-15)|all_epithelial(112;1.48e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.56e-07)		agcccggcaattttttttttt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	70823753	70823754	+	IGR	INS	-	A	A	rs75064920		TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70823753_70823754insA								TLE3 (433497 upstream) : UACA (123141 downstream)																							agggagggagggagggagggag	0.153													3	3	---	---	---	---	
ATP2C2	9914	broad.mit.edu	37	16	84459658	84459658	+	Intron	DEL	A	-	-	rs11286978		TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84459658delA	uc002fhx.2	+						ATP2C2_uc010chj.2_Intron|ATP2C2_uc002fhy.2_Intron|ATP2C2_uc002fhz.2_Intron	NM_014861	NP_055676	O75185	AT2C2_HUMAN	ATPase, Ca++ transporting, type 2C, member 2						ATP biosynthetic process	Golgi membrane|integral to membrane	ATP binding|calcium-transporting ATPase activity|metal ion binding|protein binding			breast(1)|central_nervous_system(1)	2						ttgcattgctaaaaaaaaaaa	0.189													6	4	---	---	---	---	
RPH3AL	9501	broad.mit.edu	37	17	165475	165475	+	Intron	DEL	A	-	-	rs67183030		TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:165475delA	uc002frd.1	-						RPH3AL_uc010vpy.1_Intron|RPH3AL_uc002fre.1_Intron|RPH3AL_uc002frf.1_Intron|RPH3AL_uc010cjl.1_Intron	NM_006987	NP_008918	Q9UNE2	RPH3L_HUMAN	rabphilin 3A-like (without C2 domains)						exocytosis|intracellular protein transport	transport vesicle membrane	cytoskeletal protein binding|Rab GTPase binding|zinc ion binding			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.023)|all cancers(1;4.96e-06)|Epithelial(1;2.86e-05)|BRCA - Breast invasive adenocarcinoma(1;0.00453)|OV - Ovarian serous cystadenocarcinoma(1;0.0716)|LUAD - Lung adenocarcinoma(1115;0.102)|COAD - Colon adenocarcinoma(4;0.107)		AGTCCCTGTGACCCCACCTCC	0.567													4	2	---	---	---	---	
SMYD4	114826	broad.mit.edu	37	17	1703754	1703754	+	Frame_Shift_Del	DEL	A	-	-			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1703754delA	uc002ftm.3	-	5	1102	c.934delT	c.(934-936)TGCfs	p.C312fs	SMYD4_uc002ftn.1_Frame_Shift_Del_p.C167fs	NM_052928	NP_443160	Q8IYR2	SMYD4_HUMAN	SET and MYND domain containing 4	312	MYND-type.						zinc ion binding			skin(3)|kidney(2)	5						GCATAACTGCATCCGTCACAC	0.547													143	71	---	---	---	---	
CRLF3	51379	broad.mit.edu	37	17	29112800	29112800	+	Intron	DEL	A	-	-			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29112800delA	uc002hfr.3	-						CRLF3_uc010wbr.1_Intron	NM_015986	NP_057070	Q8IUI8	CRLF3_HUMAN	cytokine receptor-like factor 3						negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|positive regulation of cell cycle arrest|positive regulation of JAK-STAT cascade|positive regulation of transcription from RNA polymerase II promoter	cytoplasm					0		all_hematologic(16;0.014)|Acute lymphoblastic leukemia(14;0.0236)|Myeloproliferative disorder(56;0.0255)				acttcataataaaaaaaaaaa	0.095													5	4	---	---	---	---	
CASC3	22794	broad.mit.edu	37	17	38325410	38325411	+	Intron	INS	-	T	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38325410_38325411insT	uc010cwt.1	+						CASC3_uc002hue.2_Intron	NM_007359	NP_031385	O15234	CASC3_HUMAN	metastatic lymph node 51						mRNA processing|mRNA transport|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of translation|response to stress|RNA splicing	exon-exon junction complex|nuclear speck|perinuclear region of cytoplasm	identical protein binding|RNA binding|ubiquitin protein ligase binding			ovary(1)	1						ATAATGAAGAATTAAGGCAAAA	0.327													40	21	---	---	---	---	
INTS2	57508	broad.mit.edu	37	17	59946936	59946936	+	Intron	DEL	A	-	-			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59946936delA	uc002izn.2	-						INTS2_uc002izm.2_Intron	NM_020748	NP_065799	Q9H0H0	INT2_HUMAN	integrator complex subunit 2						snRNA processing	integral to membrane|integrator complex|nuclear membrane	protein binding			ovary(1)|lung(1)|pancreas(1)	3						TCATTAGGTTAAAAAAAAAAA	0.328													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	76490463	76490463	+	5'Flank	DEL	C	-	-	rs34910684		TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76490463delC	uc002jvt.1	+											Homo sapiens cDNA FLJ45552 fis, clone BRTHA2038279.																		TTGCCTGAAGCCCCCCCAGCC	0.627													3	5	---	---	---	---	
MYOM1	8736	broad.mit.edu	37	18	3085192	3085192	+	Intron	DEL	T	-	-	rs148266515		TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3085192delT	uc002klp.2	-						MYOM1_uc002klq.2_Intron	NM_003803	NP_003794	P52179	MYOM1_HUMAN	myomesin 1 isoform a							striated muscle myosin thick filament	structural constituent of muscle			ovary(3)|central_nervous_system(1)|pancreas(1)	5						GTATCTGTGATTTTTTTTTTT	0.294													10	5	---	---	---	---	
C18orf1	753	broad.mit.edu	37	18	13612545	13612545	+	Intron	DEL	C	-	-	rs11311417		TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13612545delC	uc002ksa.2	+						C18orf1_uc002ksb.2_Intron|C18orf1_uc002kse.2_5'UTR|C18orf1_uc002ksf.2_5'UTR|C18orf1_uc002ksg.1_Intron	NM_181481	NP_852146	O15165	CR001_HUMAN	hypothetical protein LOC753 isoform alpha 1							integral to membrane|plasma membrane				ovary(2)|skin(1)	3				READ - Rectum adenocarcinoma(73;0.0642)		CAGAAACACACCCCCCCCCCC	0.597													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	46005696	46005697	+	IGR	INS	-	T	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46005696_46005697insT								ZBTB7C (70033 upstream) : KIAA0427 (59730 downstream)																							AAGTATTTTTGTTTTTTTTTTT	0.277													5	3	---	---	---	---	
DCC	1630	broad.mit.edu	37	18	50929445	50929452	+	Intron	DEL	CACACACA	-	-	rs74180421		TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50929445_50929452delCACACACA	uc002lfe.1	+						DCC_uc010xdr.1_Intron|DCC_uc010dpf.1_Intron	NM_005215	NP_005206	P43146	DCC_HUMAN	netrin receptor DCC precursor						apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane				skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	17		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		TCTAATGGTGcacacacacacacacaca	0.288													5	3	---	---	---	---	
DIRAS1	148252	broad.mit.edu	37	19	2717066	2717067	+	3'UTR	INS	-	C	C	rs150982606	by1000genomes	TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2717066_2717067insC	uc002lwf.3	-	2						NM_145173	NP_660156	O95057	DIRA1_HUMAN	DIRAS family, GTP-binding RAS-like 1						small GTPase mediated signal transduction	intracellular|plasma membrane	GTP binding|GTPase activity			ovary(1)	1				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)		GGCAGCGGAGGGGGGGGCGGTG	0.668													1	5	---	---	---	---	
FBN3	84467	broad.mit.edu	37	19	8150105	8150108	+	Intron	DEL	ACAC	-	-	rs151269046		TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8150105_8150108delACAC	uc002mjf.2	-						FBN3_uc002mje.2_Intron	NM_032447	NP_115823	Q75N90	FBN3_HUMAN	fibrillin 3 precursor							proteinaceous extracellular matrix	calcium ion binding|extracellular matrix structural constituent			ovary(6)|skin(3)|pancreas(1)|central_nervous_system(1)	11						TAGCACAAAGacacacacacacac	0.426													4	2	---	---	---	---	
GPATCH1	55094	broad.mit.edu	37	19	33617861	33617862	+	Intron	INS	-	AAAC	AAAC	rs141950830	by1000genomes	TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33617861_33617862insAAAC	uc002nug.1	+						GPATCH1_uc002nuh.1_Intron	NM_018025	NP_060495	Q9BRR8	GPTC1_HUMAN	G patch domain containing 1							catalytic step 2 spliceosome	nucleic acid binding			skin(1)	1	Esophageal squamous(110;0.137)					cagctctacaaaaacaaacaaa	0.000													5	3	---	---	---	---	
LYPD3	27076	broad.mit.edu	37	19	43966188	43966189	+	Intron	INS	-	A	A	rs35056869		TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43966188_43966189insA	uc002owl.1	-						LYPD3_uc002owm.2_3'UTR	NM_014400	NP_055215	O95274	LYPD3_HUMAN	GPI-anchored metastasis-associated protein							anchored to plasma membrane				pancreas(1)	1		Prostate(69;0.0153)				ctctgtcttgcaaaaaaaaaaa	0.203													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	44917435	44917436	+	IGR	INS	-	TCCG	TCCG			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44917435_44917436insTCCG								ZFP112 (11658 upstream) : ZNF229 (12990 downstream)																							TTCtccttccttctttccttcc	0.178													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	31551795	31551800	+	IGR	DEL	TTCTCC	-	-			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31551795_31551800delTTCTCC								MAPRE1 (113585 upstream) : SUN5 (19782 downstream)																							ccttcctcctttctccttctccttct	0.000													4	2	---	---	---	---	
KCNQ2	3785	broad.mit.edu	37	20	62074331	62074333	+	Intron	DEL	CAC	-	-			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62074331_62074333delCAC	uc002yey.1	-						KCNQ2_uc002yez.1_Intron|KCNQ2_uc002yfa.1_Intron|KCNQ2_uc002yfb.1_Intron|KCNQ2_uc011aax.1_Intron|KCNQ2_uc002yfc.1_Intron	NM_172107	NP_742105	O43526	KCNQ2_HUMAN	potassium voltage-gated channel KQT-like protein						axon guidance|synaptic transmission	voltage-gated potassium channel complex	voltage-gated potassium channel activity			upper_aerodigestive_tract(1)|ovary(1)	2	all_cancers(38;1.24e-11)		BRCA - Breast invasive adenocarcinoma(10;1.04e-05)		Amitriptyline(DB00321)	ccaccaccatcaccaccattacc	0.000													4	4	---	---	---	---	
LOC96610	96610	broad.mit.edu	37	22	22657416	22657419	+	Intron	DEL	ACTA	-	-	rs138873705		TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22657416_22657419delACTA	uc011aim.1	+						LOC96610_uc011aiq.1_Intron|LOC96610_uc011aip.1_Intron|LOC96610_uc010gto.2_Intron					Parts of antibodies, mostly variable regions.												0						ATGATGAAATACTAACTGTTTTAC	0.402													4	2	---	---	---	---	
C22orf13	83606	broad.mit.edu	37	22	24940236	24940237	+	Intron	DEL	GG	-	-			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24940236_24940237delGG	uc003aah.2	-						C22orf13_uc003aal.2_Intron|C22orf13_uc003aai.3_Intron|C22orf13_uc003aaj.3_Intron|C22orf13_uc003aak.3_Intron	NM_031444	NP_113632	Q96NT3	CV013_HUMAN	chromosome 22 open reading frame 13												0						GGAGACCGGTGGGGGGGGTGTG	0.589													5	4	---	---	---	---	
ZC3H7B	23264	broad.mit.edu	37	22	41735629	41735630	+	Intron	INS	-	A	A	rs77163674		TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41735629_41735630insA	uc003azw.2	+						ZC3H7B_uc010gyl.1_Intron	NM_017590	NP_060060	Q9UGR2	Z3H7B_HUMAN	zinc finger CCCH-type containing 7B						interspecies interaction between organisms	nucleus	nucleic acid binding|protein binding|zinc ion binding			central_nervous_system(1)	1						gactccgtctcaaaaaaaaaaa	0.248													4	4	---	---	---	---	
ZC3H7B	23264	broad.mit.edu	37	22	41747815	41747819	+	Intron	DEL	ATTTT	-	-	rs71803158		TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41747815_41747819delATTTT	uc003azw.2	+						ZC3H7B_uc010gyl.1_Intron	NM_017590	NP_060060	Q9UGR2	Z3H7B_HUMAN	zinc finger CCCH-type containing 7B						interspecies interaction between organisms	nucleus	nucleic acid binding|protein binding|zinc ion binding			central_nervous_system(1)	1						GTTGTGTCTCattttattttatttt	0.171													4	2	---	---	---	---	
PRPS1	5631	broad.mit.edu	37	X	106893109	106893109	+	Intron	DEL	A	-	-			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:106893109delA	uc004ene.3	+						PRPS1_uc010npg.2_Intron|PRPS1_uc011msj.1_Intron	NM_002764	NP_002755	P60891	PRPS1_HUMAN	phosphoribosyl pyrophosphate synthetase 1						5-phosphoribose 1-diphosphate biosynthetic process|hypoxanthine biosynthetic process|nervous system development|nucleoside metabolic process|purine nucleotide biosynthetic process|pyrimidine nucleotide biosynthetic process|ribonucleoside monophosphate biosynthetic process|urate biosynthetic process	cytosol	ATP binding|kinase activity|magnesium ion binding|protein homodimerization activity|ribose phosphate diphosphokinase activity			breast(3)|large_intestine(1)	4						CAGTGTCTGCAAATTGGCCAG	0.458													22	44	---	---	---	---	
PAK3	5063	broad.mit.edu	37	X	110416183	110416184	+	Intron	DEL	TC	-	-			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:110416183_110416184delTC	uc004epa.2	+						PAK3_uc010npt.1_Intron|PAK3_uc010npu.1_Intron|PAK3_uc004eoy.1_Intron|PAK3_uc004eoz.2_Intron|PAK3_uc011mst.1_Intron|PAK3_uc010npv.1_Intron|PAK3_uc010npw.1_Intron	NM_001128173	NP_001121645	O75914	PAK3_HUMAN	p21-activated kinase 3 isoform d						multicellular organismal development		ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding			lung(6)|ovary(3)|large_intestine(1)	10						AATTTCTATTtctctctctctc	0.322										TSP Lung(19;0.15)			9	4	---	---	---	---	
