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
KIF1B	23095	broad.mit.edu	37	1	10318594	10318594	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10318594A>G	uc001aqx.3	+	4	429	c.227A>G	c.(226-228)GAC>GGC	p.D76G	KIF1B_uc001aqv.3_Missense_Mutation_p.D76G|KIF1B_uc001aqw.3_Missense_Mutation_p.D76G|KIF1B_uc001aqy.2_Missense_Mutation_p.D76G|KIF1B_uc001aqz.2_Missense_Mutation_p.D76G|KIF1B_uc001ara.2_Missense_Mutation_p.D76G|KIF1B_uc001arb.2_Missense_Mutation_p.D76G|KIF1B_uc009vmt.2_RNA	NM_015074	NP_055889	O60333	KIF1B_HUMAN	kinesin family member 1B isoform b	76	Kinesin-motor.				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)		GTGTACAATGACATTGGCAAG	0.373													6	293	---	---	---	---	PASS
TMCO2	127391	broad.mit.edu	37	1	40713786	40713786	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40713786T>A	uc001cfe.2	+	1	214	c.121T>A	c.(121-123)TTG>ATG	p.L41M		NM_001008740	NP_001008740	Q7Z6W1	TMCO2_HUMAN	transmembrane and coiled-coil domains 2	41						integral to membrane				ovary(1)	1	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;6.3e-18)			GCAAACAAGTTTGGGACTATT	0.403													42	255	---	---	---	---	PASS
MAST2	23139	broad.mit.edu	37	1	46497886	46497886	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46497886C>T	uc001cov.2	+	25	3507	c.3224C>T	c.(3223-3225)TCC>TTC	p.S1075F	MAST2_uc001cow.2_Missense_Mutation_p.S1075F|MAST2_uc001cpa.2_RNA	NM_015112	NP_055927	Q6P0Q8	MAST2_HUMAN	microtubule associated serine/threonine kinase	1075					regulation of interleukin-12 biosynthetic process|spermatid differentiation	cytoplasm|cytoskeleton|plasma membrane	ATP binding|magnesium ion binding|phosphatase binding|protein serine/threonine kinase activity			ovary(5)|lung(3)|stomach(2)|breast(1)	11	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184)					AGCCCCATGTCCCCACATTCT	0.602													5	46	---	---	---	---	PASS
USP24	23358	broad.mit.edu	37	1	55559649	55559649	+	Silent	SNP	T	C	C			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55559649T>C	uc001cyg.3	-	49	5835	c.5835A>G	c.(5833-5835)AAA>AAG	p.K1945K		NM_015306	NP_056121	Q9UPU5	UBP24_HUMAN	ubiquitin specific protease 24	2105					ubiquitin-dependent protein catabolic process		binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(6)|kidney(6)|breast(1)	13						CAAACAGTCCTTTCTTCTCGC	0.438													7	550	---	---	---	---	PASS
WDR78	79819	broad.mit.edu	37	1	67303447	67303447	+	Silent	SNP	T	C	C	rs142602649		TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67303447T>C	uc001dcx.2	-	10	1583	c.1527A>G	c.(1525-1527)GGA>GGG	p.G509G	WDR78_uc001dcy.2_Silent_p.G509G|WDR78_uc009waw.2_Silent_p.G255G|WDR78_uc009wax.2_RNA	NM_024763	NP_079039	Q5VTH9	WDR78_HUMAN	WD repeat domain 78 isoform 1	509										ovary(2)	2						GCTCTTTAAATCCAAAGTGCC	0.343													6	312	---	---	---	---	PASS
FLG	2312	broad.mit.edu	37	1	152279668	152279668	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152279668G>T	uc001ezu.1	-	3	7730	c.7694C>A	c.(7693-7695)TCC>TAC	p.S2565Y		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	2565	Ser-rich.|Filaggrin 15.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)|skin(4)|upper_aerodigestive_tract(3)	16	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GCTAAAACTGGATCCCCAGTT	0.582									Ichthyosis				53	264	---	---	---	---	PASS
SPTA1	6708	broad.mit.edu	37	1	158609798	158609798	+	Splice_Site	SNP	C	G	G			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158609798C>G	uc001fst.1	-	34	4937	c.4738_splice	c.e34-1	p.E1580_splice		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1						actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|breast(1)	8	all_hematologic(112;0.0378)					CCAGTTGCTCCTAACCCAAGG	0.478													29	373	---	---	---	---	PASS
DENND1B	163486	broad.mit.edu	37	1	197704715	197704715	+	Intron	SNP	C	A	A			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197704715C>A	uc001guf.3	-						DENND1B_uc010ppe.1_Intron|DENND1B_uc010ppf.1_Intron|DENND1B_uc001gue.3_Splice_Site_p.N18_splice	NM_144977	NP_659414	Q6P3S1	DEN1B_HUMAN	DENN/MADD domain containing 1B isoform 2							clathrin-coated vesicle|cytosol	guanyl-nucleotide exchange factor activity				0						AAGGGTATTACTCGAAAATAC	0.423													35	194	---	---	---	---	PASS
NFASC	23114	broad.mit.edu	37	1	204966574	204966574	+	Intron	SNP	C	G	G			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204966574C>G	uc001hbj.2	+						NFASC_uc010pra.1_Intron|NFASC_uc001hbi.2_Intron|NFASC_uc010prb.1_Intron|NFASC_uc010prc.1_Intron|NFASC_uc001hbl.1_Intron|NFASC_uc001hbm.1_Intron|NFASC_uc001hbn.1_Missense_Mutation_p.P166R|NFASC_uc009xbh.1_Intron	NM_001005388	NP_001005388	O94856	NFASC_HUMAN	neurofascin isoform 1 precursor						axon guidance|cell adhesion|myelination|peripheral nervous system development	integral to membrane|node of Ranvier|plasma membrane	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			CCTCCTGGCCCGCCTCCCCAG	0.602													25	140	---	---	---	---	PASS
PIGR	5284	broad.mit.edu	37	1	207110826	207110826	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207110826C>A	uc001hez.2	-	4	843	c.659G>T	c.(658-660)TGC>TTC	p.C220F	PIGR_uc009xbz.2_Missense_Mutation_p.C220F	NM_002644	NP_002635	P01833	PIGR_HUMAN	polymeric immunoglobulin receptor precursor	220	Ig-like V-type 2.|Extracellular (Potential).					extracellular region|integral to plasma membrane	protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3						CCCAGCCTGGCAGAGATACTG	0.502													10	59	---	---	---	---	PASS
CR1	1378	broad.mit.edu	37	1	207758216	207758216	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207758216G>A	uc001hfy.2	+	25	4315	c.4175G>A	c.(4174-4176)CGT>CAT	p.R1392H	CR1_uc009xcl.1_Missense_Mutation_p.R942H|CR1_uc001hfx.2_Missense_Mutation_p.R1842H	NM_000573	NP_000564	P17927	CR1_HUMAN	complement receptor 1 isoform F precursor	1392	Extracellular (Potential).				complement activation, classical pathway|innate immune response	integral to plasma membrane	complement receptor activity			ovary(3)	3						CTTTCTGTTCGTGCTGGTCAG	0.488													21	143	---	---	---	---	PASS
CDC42BPA	8476	broad.mit.edu	37	1	227182038	227182038	+	Silent	SNP	G	A	A			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227182038G>A	uc001hqr.2	-	36	6034	c.5091C>T	c.(5089-5091)AGC>AGT	p.S1697S	CDC42BPA_uc001hqq.2_Silent_p.S996S|CDC42BPA_uc001hqs.2_Silent_p.S1616S|CDC42BPA_uc009xes.2_Silent_p.S1669S|CDC42BPA_uc010pvs.1_Silent_p.S1677S|CDC42BPA_uc001hqp.2_Silent_p.S915S	NM_003607	NP_003598	Q5VT25	MRCKA_HUMAN	CDC42-binding protein kinase alpha isoform B	1710					actin cytoskeleton reorganization|intracellular signal transduction	cell leading edge|cell-cell junction|cytoplasm	ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity			lung(6)|breast(2)|stomach(1)|ovary(1)|pancreas(1)	11		all_cancers(173;0.156)|Prostate(94;0.0792)				GTGAAGCTGGGCTTGGGGGGC	0.537													4	103	---	---	---	---	PASS
ROCK2	9475	broad.mit.edu	37	2	11341490	11341490	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11341490T>C	uc002rbd.1	-	22	3118	c.2669A>G	c.(2668-2670)AAG>AGG	p.K890R		NM_004850	NP_004841	O75116	ROCK2_HUMAN	Rho-associated, coiled-coil containing protein	890	Potential.				axon guidance|cytokinesis|intracellular signal transduction	cytosol|plasma membrane	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|structural molecule activity			stomach(2)|skin(2)	4	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.137)|OV - Ovarian serous cystadenocarcinoma(76;0.162)		AAGTTTGGTCTTTTCTTCACA	0.269													8	703	---	---	---	---	PASS
RAD51AP2	729475	broad.mit.edu	37	2	17697072	17697072	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17697072A>G	uc002rcl.1	-	1	2635	c.2611T>C	c.(2611-2613)TTT>CTT	p.F871L	RAD51AP2_uc010exn.1_Missense_Mutation_p.F862L	NM_001099218	NP_001092688	Q09MP3	R51A2_HUMAN	RAD51 associated protein 2	871										ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					TGTACAGAAAACATGTCATCC	0.279													5	137	---	---	---	---	PASS
NCOA1	8648	broad.mit.edu	37	2	24896334	24896334	+	Splice_Site	SNP	T	C	C			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24896334T>C	uc002rfk.2	+	5	612	c.354_splice	c.e5+2	p.E118_splice	NCOA1_uc010eye.2_Splice_Site_p.E118_splice|NCOA1_uc002rfi.2_Splice_Site|NCOA1_uc002rfj.2_Splice_Site_p.E118_splice|NCOA1_uc002rfl.2_Splice_Site_p.E118_splice	NM_003743	NP_003734	Q15788	NCOA1_HUMAN	nuclear receptor coactivator 1 isoform 1										PAX3/NCOA1(8)	soft_tissue(8)|ovary(1)|lung(1)|skin(1)	11	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTTTTGGAGGTAGGTGTCTTC	0.338			T	PAX3	alveolar rhadomyosarcoma								5	271	---	---	---	---	PASS
PLB1	151056	broad.mit.edu	37	2	28752601	28752601	+	Silent	SNP	G	A	A			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28752601G>A	uc002rmb.1	+	8	423	c.423G>A	c.(421-423)TTG>TTA	p.L141L	PLB1_uc010ezj.1_Silent_p.L141L	NM_153021	NP_694566	Q6P1J6	PLB1_HUMAN	phospholipase B1 precursor	141	4 X 308-326 AA approximate repeats.|Extracellular (Potential).|1.				lipid catabolic process|retinoid metabolic process|steroid metabolic process	apical plasma membrane|integral to membrane	lysophospholipase activity|phospholipase A2 activity|retinyl-palmitate esterase activity			ovary(4)|large_intestine(2)|skin(2)|breast(1)	9	Acute lymphoblastic leukemia(172;0.155)					ACAGAGACTTGTGGATTCAGG	0.498													41	215	---	---	---	---	PASS
XPO1	7514	broad.mit.edu	37	2	61749804	61749804	+	Missense_Mutation	SNP	T	A	A	rs76607520		TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61749804T>A	uc002sbj.2	-	4	971	c.243A>T	c.(241-243)CAA>CAT	p.Q81H	XPO1_uc010fcl.2_Missense_Mutation_p.Q77H|XPO1_uc010ypn.1_Missense_Mutation_p.Q77H|XPO1_uc002sbk.2_5'UTR	NM_003400	NP_003391	O14980	XPO1_HUMAN	exportin 1	81	Importin N-terminal.|Necessary for HTLV-1 Rex-mediated mRNA export.				intracellular protein transport|mitotic prometaphase|mRNA metabolic process|mRNA transport|viral genome transport in host cell|viral infectious cycle	annulate lamellae|Cajal body|cytosol|kinetochore|nuclear envelope|nucleolus|ribonucleoprotein complex	protein binding|protein transporter activity|RNA binding			ovary(1)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	4			LUSC - Lung squamous cell carcinoma(7;5.71e-05)|Epithelial(17;0.0662)|all cancers(80;0.226)			TTTCCAAAATTTGTAGTCCAT	0.348													42	281	---	---	---	---	PASS
SPR	6697	broad.mit.edu	37	2	73118740	73118740	+	3'UTR	SNP	A	C	C			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73118740A>C	uc002sik.2	+	3						NM_003124	NP_003115	P35270	SPRE_HUMAN	sepiapterin reductase						nitric oxide biosynthetic process|tetrahydrobiopterin biosynthetic process	cytoplasm	aldo-keto reductase (NADP) activity|NADP binding|sepiapterin reductase activity			ovary(2)	2						GGCTCCCCACACCCTGCCATA	0.557													8	19	---	---	---	---	PASS
NEB	4703	broad.mit.edu	37	2	152466540	152466540	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152466540G>A	uc010fnx.2	-	77	11575	c.11384C>T	c.(11383-11385)GCA>GTA	p.A3795V		NM_004543	NP_004534	P20929	NEBU_HUMAN	nebulin isoform 3	3795	Nebulin 104.				muscle filament sliding|muscle organ development|regulation of actin filament length|somatic muscle development	actin cytoskeleton|cytosol|Z disc	actin binding|structural constituent of muscle			ovary(8)|large_intestine(5)|breast(3)|central_nervous_system(2)|skin(1)|pancreas(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.219)		AATTTTTCCTGCATGTATGGC	0.423													6	467	---	---	---	---	PASS
DNAH7	56171	broad.mit.edu	37	2	196620981	196620981	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196620981T>G	uc002utj.3	-	62	11563	c.11462A>C	c.(11461-11463)GAA>GCA	p.E3821A	DNAH7_uc002uti.3_Missense_Mutation_p.E304A	NM_018897	NP_061720	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	3821					ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			skin(10)|ovary(2)	12						AACCACTTCTTCAAGATCTGT	0.363													34	231	---	---	---	---	PASS
DNAH7	56171	broad.mit.edu	37	2	196674542	196674542	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196674542C>A	uc002utj.3	-	52	9916	c.9815G>T	c.(9814-9816)CGG>CTG	p.R3272L		NM_018897	NP_061720	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	3272					ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			skin(10)|ovary(2)	12						AAAGAGTGACCGGCAGACATT	0.353													4	185	---	---	---	---	PASS
TMEM111	55831	broad.mit.edu	37	3	10005828	10005828	+	Silent	SNP	G	A	A	rs113658691	by1000genomes	TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10005828G>A	uc003bun.2	-	8	890	c.711C>T	c.(709-711)GTC>GTT	p.V237V	CIDEC_uc003bto.2_Intron	NM_018447	NP_060917	Q9P0I2	TM111_HUMAN	transmembrane protein 111	237						integral to membrane					0						GCTCTTCTTCGACATCATCTA	0.478													48	212	---	---	---	---	PASS
BAP1	8314	broad.mit.edu	37	3	52441304	52441304	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52441304G>A	uc003ddx.2	-	7	581	c.466C>T	c.(466-468)CAG>TAG	p.Q156*	BAP1_uc010hmh.2_5'Flank	NM_004656	NP_004647	Q92560	BAP1_HUMAN	BRCA1 associated protein-1	156					monoubiquitinated histone H2A deubiquitination|negative regulation of cell proliferation|protein K48-linked deubiquitination|regulation of cell cycle|regulation of cell growth|ubiquitin-dependent protein catabolic process	cytoplasm|nucleolus|PR-DUB complex	chromatin binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			pleura(32)|eye(28)|lung(2)|ovary(2)|breast(1)	65				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		AGGCCATTCTGCTTCTCAGGG	0.577			N|Mis|F|S|O		uveal melanoma|breast|NSCLC								22	75	---	---	---	---	PASS
NIT2	56954	broad.mit.edu	37	3	100073648	100073648	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100073648A>C	uc003dtv.2	+	9	790	c.716A>C	c.(715-717)GAA>GCA	p.E239A		NM_020202	NP_064587	Q9NQR4	NIT2_HUMAN	nitrilase family, member 2	239	CN hydrolase.				nitrogen compound metabolic process		omega-amidase activity			ovary(1)	1						GGCACAGAAGAAGCAATCGTG	0.463													11	286	---	---	---	---	PASS
DPPA2	151871	broad.mit.edu	37	3	109031519	109031519	+	Silent	SNP	T	C	C			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109031519T>C	uc003dxo.2	-	3	301	c.54A>G	c.(52-54)GTA>GTG	p.V18V		NM_138815	NP_620170	Q7Z7J5	DPPA2_HUMAN	developmental pluripotency associated 2	18						nucleus	nucleic acid binding			ovary(2)|upper_aerodigestive_tract(1)	3						CCTCATCATCTACTTCCCCCT	0.398													5	319	---	---	---	---	PASS
HEG1	57493	broad.mit.edu	37	3	124732186	124732186	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124732186A>G	uc003ehs.3	-	6	2305	c.2237T>C	c.(2236-2238)GTC>GCC	p.V746A	HEG1_uc011bke.1_Missense_Mutation_p.V846A	NM_020733	NP_065784	Q9ULI3	HEG1_HUMAN	HEG homolog 1 precursor	746	Extracellular (Potential).					extracellular region|integral to membrane	calcium ion binding			ovary(2)	2						CCTGGGCAGGACAGGGGTAGA	0.463													6	316	---	---	---	---	PASS
COL6A6	131873	broad.mit.edu	37	3	130311416	130311416	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130311416A>G	uc010htl.2	+	13	4335	c.4304A>G	c.(4303-4305)GAG>GGG	p.E1435G	COL6A6_uc003eni.3_5'UTR	NM_001102608	NP_001096078	A6NMZ7	CO6A6_HUMAN	collagen type VI alpha 6 precursor	1435	Triple-helical region.				axon guidance|cell adhesion	collagen				ovary(6)|central_nervous_system(1)|pancreas(1)	8						CCAGTGGGAGAGCAAGGTACT	0.418													6	280	---	---	---	---	PASS
MFSD1	64747	broad.mit.edu	37	3	158538031	158538031	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158538031A>G	uc003fcl.1	+	9	809	c.779A>G	c.(778-780)AAG>AGG	p.K260R	MFSD1_uc003fcm.1_RNA|MFSD1_uc003fcn.1_Missense_Mutation_p.K163R|MFSD1_uc011bow.1_Missense_Mutation_p.K221R|MFSD1_uc011box.1_Missense_Mutation_p.K187R	NM_022736	NP_073573	Q9H3U5	MFSD1_HUMAN	major facilitator superfamily domain containing	260					transmembrane transport	integral to membrane					0			Lung(72;0.00372)|LUSC - Lung squamous cell carcinoma(72;0.00523)			ACTGATGTAAAGGACTTCTCC	0.363													7	592	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195506597	195506597	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195506597G>A	uc011bto.1	-	3	11930	c.11470C>T	c.(11470-11472)CCT>TCT	p.P3824S	MUC4_uc003fva.2_5'Flank|MUC4_uc003fvb.2_5'Flank|MUC4_uc003fvc.2_5'Flank|MUC4_uc003fvd.2_5'Flank|MUC4_uc003fve.2_5'Flank|MUC4_uc010hzr.2_5'Flank|MUC4_uc011btf.1_5'Flank|MUC4_uc011btg.1_5'Flank|MUC4_uc011bth.1_5'Flank|MUC4_uc011bti.1_5'Flank|MUC4_uc011btj.1_5'Flank|MUC4_uc011btk.1_5'Flank|MUC4_uc011btl.1_5'Flank|MUC4_uc011btm.1_5'Flank|MUC4_uc011btn.1_5'Flank|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACAGGAAGAGGGGTGGTGTCA	0.602													5	4	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195507051	195507051	+	Silent	SNP	T	C	C			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195507051T>C	uc011bto.1	-	3	11476	c.11016A>G	c.(11014-11016)TCA>TCG	p.S3672S	MUC4_uc003fva.2_5'Flank|MUC4_uc003fvb.2_5'Flank|MUC4_uc003fvc.2_5'Flank|MUC4_uc003fvd.2_5'Flank|MUC4_uc003fve.2_5'Flank|MUC4_uc010hzr.2_5'Flank|MUC4_uc011btf.1_5'Flank|MUC4_uc011btg.1_5'Flank|MUC4_uc011bth.1_5'Flank|MUC4_uc011bti.1_5'Flank|MUC4_uc011btj.1_5'Flank|MUC4_uc011btk.1_5'Flank|MUC4_uc011btl.1_5'Flank|MUC4_uc011btm.1_5'Flank|MUC4_uc011btn.1_5'Flank|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CTGTGGATGCTGAGGAAGTGT	0.597													6	26	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195512665	195512665	+	Missense_Mutation	SNP	G	A	A	rs79300100	by1000genomes	TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195512665G>A	uc011bto.1	-	2	6246	c.5786C>T	c.(5785-5787)GCA>GTA	p.A1929V	MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACCTGTGGATGCTGAGGAAAG	0.582													9	234	---	---	---	---	PASS
ATP8A1	10396	broad.mit.edu	37	4	42424880	42424880	+	Silent	SNP	T	C	C			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42424880T>C	uc003gwr.2	-	35	3481	c.3249A>G	c.(3247-3249)GAA>GAG	p.E1083E	ATP8A1_uc003gwq.2_Silent_p.E309E|ATP8A1_uc003gws.2_Silent_p.E1068E	NM_006095	NP_006086	Q9Y2Q0	AT8A1_HUMAN	ATPase, aminophospholipid transporter (APLT),	1083	Cytoplasmic (Potential).				ATP biosynthetic process	chromaffin granule membrane|integral to membrane|plasma membrane	aminophospholipid transporter activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|cation-transporting ATPase activity|magnesium ion binding|phospholipid-translocating ATPase activity			skin(2)|central_nervous_system(1)	3					Phosphatidylserine(DB00144)	GCTCCTGAACTTCATCGACCA	0.343													9	527	---	---	---	---	PASS
DSPP	1834	broad.mit.edu	37	4	88536917	88536917	+	Missense_Mutation	SNP	G	A	A	rs143717970	by1000genomes	TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88536917G>A	uc003hqu.2	+	5	3223	c.3103G>A	c.(3103-3105)GAT>AAT	p.D1035N		NM_014208	NP_055023	Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein preproprotein	1035	Asp/Ser-rich.				biomineral tissue development|ossification|skeletal system development	proteinaceous extracellular matrix	calcium ion binding|collagen binding|extracellular matrix structural constituent			central_nervous_system(1)	1		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		tgacagcagcgatagcagtga	0.000													3	23	---	---	---	---	PASS
DSPP	1834	broad.mit.edu	37	4	88536919	88536919	+	Silent	SNP	T	C	C	rs147223434	by1000genomes	TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88536919T>C	uc003hqu.2	+	5	3225	c.3105T>C	c.(3103-3105)GAT>GAC	p.D1035D		NM_014208	NP_055023	Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein preproprotein	1035	Asp/Ser-rich.				biomineral tissue development|ossification|skeletal system development	proteinaceous extracellular matrix	calcium ion binding|collagen binding|extracellular matrix structural constituent			central_nervous_system(1)	1		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		acagcagcgatagcagtgaca	0.000													3	23	---	---	---	---	PASS
FAT1	2195	broad.mit.edu	37	4	187521052	187521052	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187521052C>T	uc003izf.2	-	22	12291	c.12103G>A	c.(12103-12105)GGT>AGT	p.G4035S	FAT1_uc003ize.2_5'Flank	NM_005245	NP_005236	Q14517	FAT1_HUMAN	FAT tumor suppressor 1 precursor	4035	Extracellular (Potential).|EGF-like 2.				actin filament organization|anatomical structure morphogenesis|cell migration|cell-cell signaling|establishment or maintenance of cell polarity|homophilic cell adhesion	cell-cell junction|integral to plasma membrane|nucleus|perinuclear region of cytoplasm	calcium ion binding|protein binding			ovary(10)|central_nervous_system(1)|pancreas(1)	12						CGGAGCCCACCTCCAGCAGGT	0.498										HNSCC(5;0.00058)			3	31	---	---	---	---	PASS
TRIO	7204	broad.mit.edu	37	5	14472769	14472769	+	Splice_Site	SNP	T	C	C			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14472769T>C	uc003jff.2	+	39	5985	c.5979_splice	c.e39+2	p.E1993_splice	TRIO_uc003jfg.2_Splice_Site|TRIO_uc003jfh.1_Splice_Site_p.E1642_splice	NM_007118	NP_009049	O75962	TRIO_HUMAN	triple functional domain (PTPRF interacting)						apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1)	18	Lung NSC(4;0.000742)					GTGGTTGAGGTGTGTATTGCC	0.388													7	471	---	---	---	---	PASS
ADAMTS12	81792	broad.mit.edu	37	5	33643505	33643505	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33643505C>A	uc003jia.1	-	10	1713	c.1550G>T	c.(1549-1551)GGA>GTA	p.G517V	ADAMTS12_uc010iuq.1_Missense_Mutation_p.G517V	NM_030955	NP_112217	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1	517	Disintegrin.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)	9						ACATTGAGTTCCATCTGCAGC	0.532										HNSCC(64;0.19)			9	192	---	---	---	---	PASS
SLC1A3	6507	broad.mit.edu	37	5	36677082	36677082	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36677082A>G	uc003jkj.3	+	6	1132	c.656A>G	c.(655-657)GAG>GGG	p.E219G	SLC1A3_uc011cox.1_Missense_Mutation_p.E112G|SLC1A3_uc010iuy.2_Missense_Mutation_p.E219G	NM_004172	NP_004163	P43003	EAA1_HUMAN	solute carrier family 1 (glial high affinity	219	Extracellular (Potential).				D-aspartate import|L-glutamate import|neurotransmitter uptake	integral to membrane|membrane fraction	high-affinity glutamate transmembrane transporter activity|sodium:dicarboxylate symporter activity				0	all_lung(31;0.000245)		Epithelial(62;0.0444)|Lung(74;0.111)|all cancers(62;0.128)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)		L-Glutamic Acid(DB00142)	AATGTGTCTGAGGCCATGGAG	0.463													6	313	---	---	---	---	PASS
CCL28	56477	broad.mit.edu	37	5	43382037	43382037	+	Silent	SNP	T	C	C			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43382037T>C	uc003jnu.2	-	3	379	c.309A>G	c.(307-309)AAA>AAG	p.K103K	CCL28_uc003jns.2_RNA|CCL28_uc003jnt.2_RNA|CCL28_uc010ivn.2_Silent_p.K56K	NM_148672	NP_683513	Q9NRJ3	CCL28_HUMAN	chemokine (C-C motif) ligand 28 precursor	103					chemotaxis|immune response	extracellular space	chemokine activity			ovary(1)|kidney(1)	2						TGCCATGGTGTTTCTTCCTGT	0.438													8	575	---	---	---	---	PASS
SV2C	22987	broad.mit.edu	37	5	75469440	75469440	+	Intron	SNP	A	G	G			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75469440A>G	uc003kei.1	+						uc003kej.2_RNA	NM_014979	NP_055794	Q496J9	SV2C_HUMAN	synaptic vesicle glycoprotein 2C						neurotransmitter transport	cell junction|integral to membrane|synaptic vesicle membrane	transmembrane transporter activity			skin(1)	1		all_lung(232;0.007)|Lung NSC(167;0.0148)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;1.16e-50)|all cancers(79;7.25e-40)		CAGAGCTACAATGCATTTAGT	0.418													13	202	---	---	---	---	PASS
PCDHA8	56140	broad.mit.edu	37	5	140221437	140221437	+	Silent	SNP	C	T	T			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140221437C>T	uc003lhs.2	+	1	531	c.531C>T	c.(529-531)TAC>TAT	p.Y177Y	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhr.1_Silent_p.Y177Y	NM_018911	NP_061734	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8 isoform 1 precursor	177	Cadherin 2.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			upper_aerodigestive_tract(1)|ovary(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTCATGATTACTTCATGCTAG	0.468													11	82	---	---	---	---	PASS
PCDHGA7	56108	broad.mit.edu	37	5	140764005	140764005	+	Silent	SNP	C	T	T			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140764005C>T	uc003lka.1	+	1	1539	c.1539C>T	c.(1537-1539)GTC>GTT	p.V513V	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_uc003ljz.1_Silent_p.V513V	NM_018920	NP_061743	Q9Y5G6	PCDG7_HUMAN	protocadherin gamma subfamily A, 7 isoform 1	513	Extracellular (Potential).|Cadherin 5.				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)			ACACTGGAGTCCTGTACGCGC	0.512													16	84	---	---	---	---	PASS
RNF14	9604	broad.mit.edu	37	5	141367489	141367489	+	3'UTR	SNP	T	G	G			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141367489T>G	uc003lly.2	+	8					RNF14_uc003llz.2_3'UTR|RNF14_uc003lma.2_3'UTR|RNF14_uc003lmb.2_3'UTR|RNF14_uc003lmc.2_3'UTR|RNF14_uc011dbg.1_3'UTR|RNF14_uc011dbh.1_3'UTR|RNF14_uc003lmd.2_3'UTR	NM_183399	NP_899646	Q9UBS8	RNF14_HUMAN	ring finger protein 14 isoform 1						androgen receptor signaling pathway|positive regulation of transcription, DNA-dependent|protein ubiquitination|regulation of androgen receptor signaling pathway|regulation of transcription from RNA polymerase II promoter|response to estradiol stimulus|transcription, DNA-dependent	cytoplasm|nucleus	androgen receptor binding|small conjugating protein ligase activity|transcription coactivator activity|zinc ion binding				0		all_hematologic(541;0.0536)|Ovarian(839;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;0.0407)		AGAACGAGGTTTATATTTTCA	0.333													10	82	---	---	---	---	PASS
C5orf4	10826	broad.mit.edu	37	5	154200918	154200918	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154200918C>T	uc003lvs.3	-	8	918	c.747G>A	c.(745-747)ATG>ATA	p.M249I	C5orf4_uc003lvq.2_5'Flank|C5orf4_uc003lvr.2_Translation_Start_Site|C5orf4_uc011dde.1_Missense_Mutation_p.M226I	NM_032385	NP_115761	Q96IV6	CE004_HUMAN	hypothetical protein LOC10826	249					fatty acid biosynthetic process	integral to membrane	iron ion binding|oxidoreductase activity			ovary(1)	1	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			AGGAAAACCACATGGTGATGG	0.542													109	231	---	---	---	---	PASS
KIF4B	285643	broad.mit.edu	37	5	154396586	154396586	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154396586A>G	uc010jih.1	+	1	3327	c.3167A>G	c.(3166-3168)GAA>GGA	p.E1056G		NM_001099293	NP_001092763	Q2VIQ3	KIF4B_HUMAN	kinesin family member 4B	1056	Interaction with PRC1 (By similarity).|Globular (By similarity).				axon guidance|blood coagulation|microtubule-based movement	cytosol|microtubule|nuclear matrix	ATP binding|DNA binding|microtubule motor activity			ovary(1)	1	Renal(175;0.00488)	Medulloblastoma(196;0.0523)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			AATGAGCATGAAgatggtgat	0.368													6	321	---	---	---	---	PASS
LCP2	3937	broad.mit.edu	37	5	169675746	169675746	+	Silent	SNP	A	G	G			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169675746A>G	uc003man.1	-	21	1764	c.1557T>C	c.(1555-1557)GGT>GGC	p.G519G	C5orf58_uc003mal.2_Intron|LCP2_uc011des.1_Silent_p.G314G|LCP2_uc011det.1_Silent_p.G348G	NM_005565	NP_005556	Q13094	LCP2_HUMAN	lymphocyte cytosolic protein 2	519	SH2.				immune response|platelet activation|T cell receptor signaling pathway|transmembrane receptor protein tyrosine kinase signaling pathway	cytosol	protein binding			ovary(1)	1	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0109)|all_neural(177;0.0146)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	OV - Ovarian serous cystadenocarcinoma(192;0.247)		GGTATCTGGAACCTCGGTTTT	0.463													9	413	---	---	---	---	PASS
OR5V1	81696	broad.mit.edu	37	6	29323659	29323659	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29323659A>G	uc011dlo.1	-	1	396	c.314T>C	c.(313-315)GTT>GCT	p.V105A		NM_030876	NP_110503	Q9UGF6	OR5V1_HUMAN	olfactory receptor, family 5, subfamily V,	105	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)|kidney(1)	4						TACAAAGAAAACAAATGCAAA	0.423													4	44	---	---	---	---	PASS
TAF11	6882	broad.mit.edu	37	6	34846441	34846441	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34846441T>C	uc003ojw.1	-	5	647	c.562A>G	c.(562-564)AGG>GGG	p.R188G	UHRF1BP1_uc010jvm.1_Intron|TAF11_uc011dsr.1_Nonstop_Mutation_p.*155W	NM_005643	NP_005634	Q15544	TAF11_HUMAN	TBP-associated factor 11	188					positive regulation by host of viral transcription|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|viral reproduction	transcription factor TFIID complex	protein N-terminus binding|thyroid hormone receptor binding|transcription coactivator activity|vitamin D receptor binding				0						ACGGCTTCCCTCATATGTTTG	0.408													7	549	---	---	---	---	PASS
KCNQ5	56479	broad.mit.edu	37	6	73904280	73904280	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:73904280C>A	uc003pgk.2	+	14	2289	c.1942C>A	c.(1942-1944)CCT>ACT	p.P648T	KCNQ5_uc011dyh.1_Missense_Mutation_p.P667T|KCNQ5_uc011dyi.1_Missense_Mutation_p.P658T|KCNQ5_uc010kat.2_Missense_Mutation_p.P639T|KCNQ5_uc011dyj.1_Missense_Mutation_p.P538T|KCNQ5_uc011dyk.1_Missense_Mutation_p.P398T	NM_019842	NP_062816	Q9NR82	KCNQ5_HUMAN	potassium voltage-gated channel, KQT-like	648					protein complex assembly|synaptic transmission	voltage-gated potassium channel complex	inward rectifier potassium channel activity			ovary(4)|large_intestine(2)|skin(1)	7		all_epithelial(107;0.116)|Lung NSC(302;0.219)		COAD - Colon adenocarcinoma(1;0.0107)|Colorectal(1;0.0583)		CCAGATCCCACCTTTTGAATG	0.483													10	105	---	---	---	---	PASS
KCNQ5	56479	broad.mit.edu	37	6	73904281	73904281	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:73904281C>T	uc003pgk.2	+	14	2290	c.1943C>T	c.(1942-1944)CCT>CTT	p.P648L	KCNQ5_uc011dyh.1_Missense_Mutation_p.P667L|KCNQ5_uc011dyi.1_Missense_Mutation_p.P658L|KCNQ5_uc010kat.2_Missense_Mutation_p.P639L|KCNQ5_uc011dyj.1_Missense_Mutation_p.P538L|KCNQ5_uc011dyk.1_Missense_Mutation_p.P398L	NM_019842	NP_062816	Q9NR82	KCNQ5_HUMAN	potassium voltage-gated channel, KQT-like	648					protein complex assembly|synaptic transmission	voltage-gated potassium channel complex	inward rectifier potassium channel activity			ovary(4)|large_intestine(2)|skin(1)	7		all_epithelial(107;0.116)|Lung NSC(302;0.219)		COAD - Colon adenocarcinoma(1;0.0107)|Colorectal(1;0.0583)		CAGATCCCACCTTTTGAATGT	0.478													10	104	---	---	---	---	PASS
SLC22A3	6581	broad.mit.edu	37	6	160868759	160868759	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160868759G>A	uc003qti.2	+	10	1546	c.1519G>A	c.(1519-1521)GCA>ACA	p.A507T	SLC22A3_uc011efx.1_RNA	NM_021977	NP_068812	O75751	S22A3_HUMAN	solute carrier family 22 member 3	507	Helical; (Potential).					integral to plasma membrane|membrane fraction	protein binding|quaternary ammonium group transmembrane transporter activity			skin(2)|ovary(1)|central_nervous_system(1)	4		Breast(66;0.00028)|Ovarian(120;0.0308)|Prostate(117;0.218)		OV - Ovarian serous cystadenocarcinoma(65;9.47e-17)|BRCA - Breast invasive adenocarcinoma(81;9.75e-06)		AGGTATCCTGGCATCCATCTG	0.522													5	285	---	---	---	---	PASS
FOXK1	221937	broad.mit.edu	37	7	4794839	4794839	+	Intron	SNP	C	T	T			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4794839C>T	uc003snc.1	+						FOXK1_uc003sna.1_Intron|FOXK1_uc003snb.1_3'UTR	NM_001037165	NP_001032242	P85037	FOXK1_HUMAN	forkhead box K1						cell differentiation|embryo development|muscle organ development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|magnesium ion binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			upper_aerodigestive_tract(1)|skin(1)	2		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;7.43e-15)		CTTGCTGGAGCTCATCCCGTG	0.642													3	18	---	---	---	---	PASS
NFE2L3	9603	broad.mit.edu	37	7	26225394	26225394	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26225394G>T	uc003sxq.2	+	4	2348	c.2076G>T	c.(2074-2076)AAG>AAT	p.K692N		NM_004289	NP_004280	Q9Y4A8	NF2L3_HUMAN	nuclear factor erythroid 2-like 3	692					transcription from RNA polymerase II promoter	nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			skin(3)|ovary(1)	4						AAAAGGGAAAGAGAAAGTGAG	0.403													8	66	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	38402596	38402596	+	Intron	SNP	C	T	T			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38402596C>T	uc003tgp.1	+						uc003tgs.1_Missense_Mutation_p.V75I					Homo sapiens cDNA FLJ43658 fis, clone SYNOV4004184.																		TCCAACACAACCTTGGAGTTG	0.453													5	261	---	---	---	---	PASS
ZNF735	730291	broad.mit.edu	37	7	63680408	63680408	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63680408T>A	uc011kdn.1	+	4	979	c.979T>A	c.(979-981)TGT>AGT	p.C327S		NM_001159524	NP_001152996	P0CB33	ZN735_HUMAN	zinc finger protein 735	327	C2H2-type 7.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						ACCCTACACATGTGAAGAATG	0.428													6	37	---	---	---	---	PASS
DNAJC2	27000	broad.mit.edu	37	7	102957389	102957389	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102957389T>C	uc003vbo.2	-	13	1566	c.1315A>G	c.(1315-1317)AAC>GAC	p.N439D	PMPCB_uc011kll.1_Intron|DNAJC2_uc003vbn.2_Missense_Mutation_p.N64D|DNAJC2_uc010lix.2_Missense_Mutation_p.N386D|DNAJC2_uc003vbp.2_Missense_Mutation_p.N64D	NM_014377	NP_055192	Q99543	DNJC2_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 2	439					'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						TTCTCTGTGTTCTTAGATGCT	0.388													7	573	---	---	---	---	PASS
AASS	10157	broad.mit.edu	37	7	121753716	121753716	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121753716C>A	uc003vka.2	-	9	1198	c.1102G>T	c.(1102-1104)GAG>TAG	p.E368*	AASS_uc011knu.1_RNA|AASS_uc011knv.1_RNA|AASS_uc003vkb.2_Nonsense_Mutation_p.E368*|AASS_uc011knw.1_Intron	NM_005763	NP_005754	Q9UDR5	AASS_HUMAN	aminoadipate-semialdehyde synthase precursor	368	Lysine-ketoglutarate reductase.				protein tetramerization	mitochondrial matrix	binding|saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity|saccharopine dehydrogenase (NADP+, L-lysine-forming) activity			upper_aerodigestive_tract(1)|ovary(1)	2					L-Glutamic Acid(DB00142)|NADH(DB00157)	GTTGTACACTCAGTCATAAAC	0.383													8	195	---	---	---	---	PASS
AKR1B10	57016	broad.mit.edu	37	7	134212563	134212563	+	5'UTR	SNP	A	G	G			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134212563A>G	uc003vrr.2	+	1						NM_020299	NP_064695	O60218	AK1BA_HUMAN	aldo-keto reductase family 1, member B10						cellular aldehyde metabolic process|digestion|steroid metabolic process	cytoplasm	aldo-keto reductase (NADP) activity|protein binding			skin(5)	5						gcaccactgcactctagcctt	0.159													7	64	---	---	---	---	PASS
CALD1	800	broad.mit.edu	37	7	134618353	134618353	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134618353A>T	uc003vrz.2	+	5	1292	c.833A>T	c.(832-834)GAA>GTA	p.E278V	CALD1_uc003vry.2_Intron|CALD1_uc003vsa.2_Intron|CALD1_uc003vsb.2_Intron|CALD1_uc010lmm.2_Intron|CALD1_uc011kpt.1_Intron|CALD1_uc003vsc.2_Intron|CALD1_uc003vsd.2_Intron|CALD1_uc011kpu.1_Intron|CALD1_uc011kpv.1_Intron|CALD1_uc003vse.2_Missense_Mutation_p.E142V	NM_033138	NP_149129	Q05682	CALD1_HUMAN	caldesmon 1 isoform 1	278					cellular component movement|muscle contraction	cytosol|focal adhesion|myofibril	actin binding|calmodulin binding|myosin binding|tropomyosin binding				0						GAAGAAAGAGAAAGAATTAAA	0.413													14	120	---	---	---	---	PASS
NUP205	23165	broad.mit.edu	37	7	135261021	135261021	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135261021A>G	uc003vsw.2	+	4	378	c.347A>G	c.(346-348)GAG>GGG	p.E116G	NUP205_uc011kqa.1_RNA	NM_015135	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa	116					carbohydrate metabolic process|glucose transport|mRNA transport|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6						TTTTTAGGAGAGCATCAACAG	0.363													6	279	---	---	---	---	PASS
HOOK3	84376	broad.mit.edu	37	8	42821725	42821725	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42821725C>T	uc003xpr.2	+	10	1131	c.889C>T	c.(889-891)CAG>TAG	p.Q297*	HOOK3_uc010lxq.1_Nonsense_Mutation_p.Q297*	NM_032410	NP_115786	Q86VS8	HOOK3_HUMAN	golgi-associated microtubule-binding protein	297	Potential.				cytoplasmic microtubule organization|early endosome to late endosome transport|endosome organization|endosome to lysosome transport|Golgi localization|interkinetic nuclear migration|lysosome organization|microtubule anchoring|negative regulation of neurogenesis|protein localization to centrosome|protein transport	cis-Golgi network|FHF complex|microtubule|pericentriolar material	identical protein binding|microtubule binding			ovary(1)|breast(1)	2	Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.000105)|Lung NSC(58;0.000419)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.048)|LUSC - Lung squamous cell carcinoma(45;0.114)			AGATGAAGCTCAGTCTCTGAA	0.453			T	RET	papillary thyroid								35	142	---	---	---	---	PASS
MCM4	4173	broad.mit.edu	37	8	48889311	48889311	+	Silent	SNP	G	T	T			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48889311G>T	uc003xqk.1	+	17	2660	c.2565G>T	c.(2563-2565)GTG>GTT	p.V855V	MCM4_uc003xql.1_Silent_p.V855V|MCM4_uc011ldi.1_Silent_p.V842V	NM_182746	NP_877423	P33991	MCM4_HUMAN	minichromosome maintenance complex component 4	855					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|DNA binding|helicase activity|protein binding			ovary(2)|skin(2)	4		all_cancers(86;0.026)|all_epithelial(80;0.000748)|Lung NSC(129;0.00327)|all_lung(136;0.00354)				TCCTGACAGTGACTGGGAAGA	0.498													26	183	---	---	---	---	PASS
UBXN2B	137886	broad.mit.edu	37	8	59360028	59360028	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59360028C>T	uc003xtl.2	+	8	1036	c.914C>T	c.(913-915)CCG>CTG	p.P305L		NM_001077619	NP_001071087	Q14CS0	UBX2B_HUMAN	UBX domain protein 2B	305	UBX.					cytosol|endoplasmic reticulum|Golgi apparatus|nucleus				ovary(2)	2						ACTTCATTTCCGAATAAAGAG	0.388													5	270	---	---	---	---	PASS
ABRA	137735	broad.mit.edu	37	8	107773724	107773724	+	Silent	SNP	C	T	T			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107773724C>T	uc003ymm.3	-	2	741	c.687G>A	c.(685-687)GAG>GAA	p.E229E		NM_139166	NP_631905	Q8N0Z2	ABRA_HUMAN	actin-binding Rho activating protein	229					positive regulation of Rho protein signal transduction|positive regulation of sequence-specific DNA binding transcription factor activity|transcription, DNA-dependent|transmembrane transport	actin cytoskeleton|plasma membrane|sarcomere	actin binding			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(57;3.83e-09)			AGTTGAGTTTCTCTGTAAATC	0.433													9	68	---	---	---	---	PASS
ANGPT1	284	broad.mit.edu	37	8	108359248	108359248	+	Silent	SNP	A	G	G			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108359248A>G	uc003ymn.2	-	2	843	c.375T>C	c.(373-375)GCT>GCC	p.A125A	ANGPT1_uc003ymo.2_Silent_p.A125A	NM_001146	NP_001137	Q15389	ANGP1_HUMAN	angiopoietin 1 precursor	125					activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|blood coagulation|cell differentiation|heparin biosynthetic process|leukocyte migration|negative regulation of cell adhesion|negative regulation of endothelial cell apoptosis|negative regulation of vascular permeability|positive chemotaxis|positive regulation of blood vessel endothelial cell migration|positive regulation of ERK1 and ERK2 cascade|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of protein ubiquitination|positive regulation of receptor internalization|protein localization at cell surface|regulation of satellite cell proliferation|sprouting angiogenesis|Tie receptor signaling pathway	extracellular space|membrane raft|microvillus|plasma membrane	receptor tyrosine kinase binding			ovary(3)|skin(3)|upper_aerodigestive_tract(1)	7	Breast(1;5.06e-08)		OV - Ovarian serous cystadenocarcinoma(57;5.53e-09)			CCAGCATGGTAGCCGTGTGGT	0.502													5	293	---	---	---	---	PASS
ZNF623	9831	broad.mit.edu	37	8	144732657	144732657	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144732657G>T	uc003yzd.2	+	1	704	c.615G>T	c.(613-615)AAG>AAT	p.K205N	ZNF623_uc011lkp.1_Missense_Mutation_p.K165N|ZNF623_uc003yzc.2_Missense_Mutation_p.K165N	NM_014789	NP_055604	O75123	ZN623_HUMAN	zinc finger protein 623 isoform 1	205					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;5.28e-40)|all cancers(56;5.23e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			CAGGAGAAAAGCCCTTCAAAT	0.468													12	66	---	---	---	---	PASS
MAPK15	225689	broad.mit.edu	37	8	144800451	144800451	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144800451T>A	uc003yzj.2	+	4	306	c.265T>A	c.(265-267)TAC>AAC	p.Y89N		NM_139021	NP_620590	Q8TD08	MK15_HUMAN	mitogen-activated protein kinase 15	89	Protein kinase.				protein autophosphorylation	extracellular region	ATP binding|MAP kinase activity|SH3 domain binding			lung(2)	2	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			CAGGGACATTTACCTGGTGTT	0.542													10	23	---	---	---	---	PASS
VLDLR	7436	broad.mit.edu	37	9	2644978	2644978	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2644978C>T	uc003zhk.1	+	9	1605	c.1208C>T	c.(1207-1209)CCA>CTA	p.P403L	VLDLR_uc003zhl.1_Missense_Mutation_p.P403L|VLDLR_uc003zhm.1_RNA|VLDLR_uc003zhn.1_Missense_Mutation_p.P362L	NM_003383	NP_003374	P98155	VLDLR_HUMAN	very low density lipoprotein receptor isoform a	403	Extracellular (Potential).|EGF-like 2; calcium-binding (Potential).				cholesterol metabolic process|endocytosis|lipid transport|memory|very-low-density lipoprotein particle clearance	coated pit|integral to membrane|membrane fraction|plasma membrane|very-low-density lipoprotein particle	apolipoprotein binding|calcium ion binding|low-density lipoprotein receptor activity|very-low-density lipoprotein particle receptor activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3				GBM - Glioblastoma multiforme(50;0.0668)|Lung(218;0.123)		TGCCAAAATCCAGGAATCTGC	0.433													6	321	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	9	68413581	68413581	+	RNA	SNP	G	C	C	rs1809619		TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68413581G>C	uc004aex.2	+	1		c.136G>C								Homo sapiens mRNA; cDNA DKFZp564N0763 (from clone DKFZp564N0763).																		CCGGATCTAGGAAAGGTTGTG	0.602													7	14	---	---	---	---	PASS
RNF20	56254	broad.mit.edu	37	9	104309448	104309448	+	Silent	SNP	A	G	G			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104309448A>G	uc004bbn.2	+	8	1014	c.924A>G	c.(922-924)GGA>GGG	p.G308G		NM_019592	NP_062538	Q5VTR2	BRE1A_HUMAN	ring finger protein 20	308	Potential.				histone H2B ubiquitination|histone monoubiquitination|negative regulation of cell migration|positive regulation of transcription, DNA-dependent|protein polyubiquitination|ubiquitin-dependent protein catabolic process	nucleolus|ubiquitin ligase complex	histone binding|p53 binding|transcription coactivator activity|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(1)|breast(1)|kidney(1)|skin(1)	8		all_hematologic(171;8.99e-06)|Acute lymphoblastic leukemia(62;0.000365)|Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;2.88e-19)|STAD - Stomach adenocarcinoma(157;0.00311)		AGGTGTATGGAGCGGGGAGCA	0.413													5	135	---	---	---	---	PASS
RNF20	56254	broad.mit.edu	37	9	104323473	104323473	+	Silent	SNP	T	C	C			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104323473T>C	uc004bbn.2	+	18	2700	c.2610T>C	c.(2608-2610)GTT>GTC	p.V870V		NM_019592	NP_062538	Q5VTR2	BRE1A_HUMAN	ring finger protein 20	870	Potential.				histone H2B ubiquitination|histone monoubiquitination|negative regulation of cell migration|positive regulation of transcription, DNA-dependent|protein polyubiquitination|ubiquitin-dependent protein catabolic process	nucleolus|ubiquitin ligase complex	histone binding|p53 binding|transcription coactivator activity|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(1)|breast(1)|kidney(1)|skin(1)	8		all_hematologic(171;8.99e-06)|Acute lymphoblastic leukemia(62;0.000365)|Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;2.88e-19)|STAD - Stomach adenocarcinoma(157;0.00311)		AGAACAGTGTTACCAAAGAAA	0.453													4	168	---	---	---	---	PASS
POLR3A	11128	broad.mit.edu	37	10	79753035	79753035	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79753035C>T	uc001jzn.2	-	20	2801	c.2707G>A	c.(2707-2709)GGA>AGA	p.G903R		NM_007055	NP_008986	O14802	RPC1_HUMAN	polymerase (RNA) III (DNA directed) polypeptide	903					innate immune response|positive regulation of interferon-beta production|response to virus|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase III promoter	DNA-directed RNA polymerase III complex	DNA binding|DNA-directed RNA polymerase activity|ribonucleoside binding|zinc ion binding				0	all_cancers(46;0.0356)|all_epithelial(25;0.00102)|Breast(12;0.00124)|Prostate(51;0.0095)		Epithelial(14;0.00161)|OV - Ovarian serous cystadenocarcinoma(4;0.00323)|all cancers(16;0.00646)			CCATCTCCTCCATAAATGAAC	0.408													5	244	---	---	---	---	PASS
ALDH18A1	5832	broad.mit.edu	37	10	97366699	97366699	+	Silent	SNP	T	G	G			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97366699T>G	uc001kkz.2	-	18	2450	c.2208A>C	c.(2206-2208)GGA>GGC	p.G736G	ALDH18A1_uc001kky.2_Silent_p.G734G|ALDH18A1_uc010qog.1_Silent_p.G625G|ALDH18A1_uc010qoh.1_Silent_p.G524G	NM_002860	NP_002851	P54886	P5CS_HUMAN	pyrroline-5-carboxylate synthetase isoform 1	736	Gamma-glutamyl phosphate reductase.				proline biosynthetic process	mitochondrial inner membrane	ATP binding|glutamate 5-kinase activity|glutamate-5-semialdehyde dehydrogenase activity			pancreas(1)|central_nervous_system(1)|skin(1)	3		Colorectal(252;0.0402)		Epithelial(162;9.1e-07)|all cancers(201;2.55e-05)	L-Glutamic Acid(DB00142)	CCACTTCAGCTCCTGTGAAAA	0.542													23	114	---	---	---	---	PASS
DUSP5	1847	broad.mit.edu	37	10	112269965	112269965	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112269965G>T	uc001kzd.2	+	4	1191	c.936G>T	c.(934-936)CAG>CAT	p.Q312H		NM_004419	NP_004410	Q16690	DUS5_HUMAN	dual specificity phosphatase 5	312	Tyrosine-protein phosphatase.				endoderm formation|inactivation of MAPK activity	nucleoplasm	MAP kinase tyrosine/serine/threonine phosphatase activity|protein tyrosine phosphatase activity			upper_aerodigestive_tract(1)	1		Breast(234;0.0848)		Epithelial(162;0.000276)|all cancers(201;0.00465)|BRCA - Breast invasive adenocarcinoma(275;0.12)		AGCTCCTGCAGTACGAATCTG	0.582													7	78	---	---	---	---	PASS
DUSP5	1847	broad.mit.edu	37	10	112269966	112269966	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112269966T>C	uc001kzd.2	+	4	1192	c.937T>C	c.(937-939)TAC>CAC	p.Y313H		NM_004419	NP_004410	Q16690	DUS5_HUMAN	dual specificity phosphatase 5	313	Tyrosine-protein phosphatase.				endoderm formation|inactivation of MAPK activity	nucleoplasm	MAP kinase tyrosine/serine/threonine phosphatase activity|protein tyrosine phosphatase activity			upper_aerodigestive_tract(1)	1		Breast(234;0.0848)		Epithelial(162;0.000276)|all cancers(201;0.00465)|BRCA - Breast invasive adenocarcinoma(275;0.12)		GCTCCTGCAGTACGAATCTGA	0.587													7	79	---	---	---	---	PASS
TCF7L2	6934	broad.mit.edu	37	10	114710470	114710470	+	5'UTR	SNP	C	T	T			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114710470C>T	uc001lae.3	+	1					TCF7L2_uc001lac.3_5'UTR|TCF7L2_uc010qrk.1_5'UTR|TCF7L2_uc010qrl.1_5'UTR|TCF7L2_uc010qrm.1_5'UTR|TCF7L2_uc010qrn.1_5'UTR|TCF7L2_uc001lad.3_5'UTR|TCF7L2_uc001lag.3_5'UTR|TCF7L2_uc001laf.3_5'UTR|TCF7L2_uc010qro.1_5'UTR|TCF7L2_uc001lah.2_5'UTR|TCF7L2_uc010qrp.1_5'UTR|TCF7L2_uc010qrq.1_5'UTR|TCF7L2_uc010qrr.1_5'Flank|TCF7L2_uc010qrs.1_5'Flank|TCF7L2_uc010qrt.1_5'Flank	NM_001146274	NP_001139746	Q9NQB0	TF7L2_HUMAN	transcription factor 7-like 2 isoform 1						anti-apoptosis|blood vessel development|canonical Wnt receptor signaling pathway involved in positive regulation of epithelial to mesenchymal transition|cell cycle arrest|cell proliferation|fat cell differentiation|glucose homeostasis|maintenance of DNA repeat elements|myoblast cell fate commitment|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|pancreas development|positive regulation of heparan sulfate proteoglycan biosynthetic process|positive regulation of insulin secretion|positive regulation of protein binding|positive regulation of protein export from nucleus|positive regulation of protein kinase B signaling cascade|positive regulation of transcription from RNA polymerase II promoter|regulation of hormone metabolic process|regulation of smooth muscle cell proliferation|response to glucose stimulus	beta-catenin-TCF7L2 complex|PML body|protein-DNA complex	armadillo repeat domain binding|beta-catenin binding|gamma-catenin binding|nuclear hormone receptor binding|protein kinase binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding			large_intestine(3)|ovary(1)	4		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)		GCTTTTCTTCCTCCTTCATTT	0.463													6	36	---	---	---	---	PASS
PNLIPRP1	5407	broad.mit.edu	37	10	118359584	118359584	+	Silent	SNP	T	C	C			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118359584T>C	uc001lco.1	+	9	858	c.840T>C	c.(838-840)AAT>AAC	p.N280N	PNLIPRP1_uc001lcp.2_Silent_p.N280N	NM_006229	NP_006220	P54315	LIPR1_HUMAN	pancreatic lipase-related protein 1 precursor	280					lipid metabolic process		calcium ion binding|triglyceride lipase activity			ovary(1)|breast(1)	2				all cancers(201;0.0161)		TGGCTTGCAATCACCTAAGAA	0.483													13	190	---	---	---	---	PASS
OR52A4	390053	broad.mit.edu	37	11	5142378	5142378	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5142378A>G	uc001lzz.1	-	1	431	c.431T>C	c.(430-432)CTA>CCA	p.L144P		NM_001005222	NP_001005222			olfactory receptor, family 52, subfamily A,											ovary(2)	2		Medulloblastoma(188;0.0049)|all_neural(188;0.0442)|Breast(177;0.0675)		Epithelial(150;1.7e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.2)		ATAAGTGACTAGCTGTCGAGT	0.463													10	48	---	---	---	---	PASS
DNHD1	144132	broad.mit.edu	37	11	6541001	6541001	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6541001C>T	uc001mdw.3	+	8	2128	c.1564C>T	c.(1564-1566)CGC>TGC	p.R522C	DNHD1_uc001mdp.2_Missense_Mutation_p.R522C|DNHD1_uc001mdq.2_Missense_Mutation_p.R211C	NM_144666	NP_653267	Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1 isoform 1	522					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)		AAAGTTTGCCCGCCTGGTTGA	0.527													4	167	---	---	---	---	PASS
IPO7	10527	broad.mit.edu	37	11	9451227	9451227	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9451227A>G	uc001mho.2	+	15	1740	c.1598A>G	c.(1597-1599)GAA>GGA	p.E533G		NM_006391	NP_006382	O95373	IPO7_HUMAN	importin 7	533					interspecies interaction between organisms|signal transduction	Golgi apparatus|nuclear pore|soluble fraction	protein transporter activity|Ran GTPase binding|small GTPase regulator activity			lung(1)|breast(1)	2				all cancers(16;8.29e-09)|Epithelial(150;4.76e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0217)		ACAGCTAAAGAATATATCACA	0.308													5	140	---	---	---	---	PASS
TPH1	7166	broad.mit.edu	37	11	18042621	18042621	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18042621T>C	uc001mnp.2	-	10	1278	c.1252A>G	c.(1252-1254)ACC>GCC	p.T418A	TPH1_uc009yhe.2_RNA	NM_004179	NP_004170	P17752	TPH1_HUMAN	tryptophan hydroxylase 1	418					aromatic amino acid family metabolic process|hormone biosynthetic process|serotonin biosynthetic process	cytosol	amino acid binding|iron ion binding|tryptophan 5-monooxygenase activity				0					L-Tryptophan(DB00150)|Tetrahydrobiopterin(DB00360)	ATGGCACTGGTTATGCTCTTG	0.428													6	358	---	---	---	---	PASS
GAS2	2620	broad.mit.edu	37	11	22759290	22759290	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:22759290T>C	uc009yie.2	+	5	755	c.449T>C	c.(448-450)CTA>CCA	p.L150P	GAS2_uc001mqm.2_Missense_Mutation_p.L150P|GAS2_uc001mqn.2_RNA|GAS2_uc001mqo.2_Missense_Mutation_p.L150P	NM_001143830	NP_001137302	O43903	GAS2_HUMAN	growth arrest-specific 2	150	CH.				cell cycle arrest|cellular component disassembly involved in apoptosis|regulation of cell shape	actin filament|cytosol|membrane				ovary(1)|skin(1)	2						CTCTGTCTGCTAGAGCTTGGC	0.483													5	179	---	---	---	---	PASS
ARFGAP2	84364	broad.mit.edu	37	11	47193866	47193866	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47193866A>G	uc001ndt.2	-	8	653	c.638T>C	c.(637-639)ATT>ACT	p.I213T	ARFGAP2_uc010rha.1_5'UTR|ARFGAP2_uc010rhb.1_Missense_Mutation_p.I185T|ARFGAP2_uc001ndu.2_Intron|ARFGAP2_uc010rhc.1_Intron	NM_032389	NP_115765	Q8N6H7	ARFG2_HUMAN	ADP-ribosylation factor GTPase activating	213	Required for interaction with coatomer.				protein transport|regulation of ARF GTPase activity|vesicle-mediated transport	Golgi membrane|nucleolus|plasma membrane	ARF GTPase activator activity|zinc ion binding			ovary(1)	1						CTTCTTGCCAATGATGGAGCT	0.353													74	417	---	---	---	---	PASS
EHBP1L1	254102	broad.mit.edu	37	11	65348529	65348529	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65348529A>C	uc001oeo.3	+	7	900	c.635A>C	c.(634-636)GAT>GCT	p.D212A	EHBP1L1_uc001oep.1_5'Flank	NM_001099409	NP_001092879	Q8N3D4	EH1L1_HUMAN	tangerin	212										central_nervous_system(1)	1						CCATTCCCAGATCCCTCTCGA	0.647													5	31	---	---	---	---	PASS
TYR	7299	broad.mit.edu	37	11	88911056	88911056	+	5'UTR	SNP	C	T	T			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:88911056C>T	uc001pcs.2	+	1						NM_000372	NP_000363	P14679	TYRO_HUMAN	tyrosinase precursor						eye pigment biosynthetic process|melanin biosynthetic process from tyrosine|visual perception	Golgi-associated vesicle|integral to membrane|lysosome|melanosome membrane|perinuclear region of cytoplasm	copper ion binding|monophenol monooxygenase activity|protein heterodimerization activity|protein homodimerization activity			ovary(2)|central_nervous_system(1)	3		Acute lymphoblastic leukemia(157;2.33e-05)|all_hematologic(158;0.0033)			Azelaic Acid(DB00548)|Mimosine(DB01055)|NADH(DB00157)	GTAGTAGTAGCTGGAAAGAGA	0.438									Oculocutaneous_Albinism				4	122	---	---	---	---	PASS
POU2AF1	5450	broad.mit.edu	37	11	111228240	111228240	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111228240G>C	uc001plg.3	-	4	641	c.386C>G	c.(385-387)CCC>CGC	p.P129R		NM_006235	NP_006226	Q16633	OBF1_HUMAN	POU class 2 associating factor 1	129					humoral immune response|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	protein binding|transcription coactivator activity			kidney(1)	1		all_cancers(61;1.36e-12)|all_epithelial(67;1.87e-07)|Melanoma(852;1.46e-05)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|all_neural(223;0.0146)|Medulloblastoma(222;0.0245)|Breast(348;0.0389)		Epithelial(105;1.01e-06)|BRCA - Breast invasive adenocarcinoma(274;3.12e-06)|all cancers(92;1.8e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0364)		CGTGTAGCTGGGGCACACGGG	0.602			T	BCL6	NHL								9	57	---	---	---	---	PASS
C12orf32	83695	broad.mit.edu	37	12	2997444	2997444	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2997444T>C	uc001qlh.2	+	3	704	c.536T>C	c.(535-537)CTT>CCT	p.L179P	TULP3_uc010sef.1_Intron|TULP3_uc009zec.1_5'Flank|TULP3_uc010seg.1_5'Flank|TULP3_uc001qlj.2_5'Flank|TULP3_uc010seh.1_5'Flank|TULP3_uc010sei.1_5'Flank|C12orf32_uc010see.1_Missense_Mutation_p.L165P|C12orf32_uc001qli.2_Missense_Mutation_p.L40P	NR_027363				RecName: Full=Uncharacterized protein C12orf32;												0			OV - Ovarian serous cystadenocarcinoma(31;0.000622)			GAAAACAGCCTTCTAAGCTGC	0.483													5	106	---	---	---	---	PASS
TAS2R31	259290	broad.mit.edu	37	12	11183307	11183307	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11183307G>T	uc001qzo.1	-	1	700	c.628C>A	c.(628-630)CAG>AAG	p.Q210K	PRR4_uc009zhp.2_Intron|PRH1_uc001qzb.3_Intron|PRH1_uc001qzc.2_Intron|PRB4_uc001qzf.1_Intron|PRH1_uc001qzj.2_Intron	NM_176885	NP_795366	P59538	T2R31_HUMAN	taste receptor, type 2, member 31	210	Cytoplasmic (Potential).				sensory perception of taste	integral to membrane	G-protein coupled receptor activity				0						CCATGGAGCTGCATCTTCTTG	0.428													37	187	---	---	---	---	PASS
CMAS	55907	broad.mit.edu	37	12	22213839	22213839	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22213839T>C	uc001rfm.2	+	5	846	c.767T>C	c.(766-768)ATT>ACT	p.I256T	CMAS_uc001rfn.2_RNA	NM_018686	NP_061156	Q8NFW8	NEUA_HUMAN	cytidine monophospho-N-acetylneuraminic acid	256					lipopolysaccharide biosynthetic process	nucleus	N-acylneuraminate cytidylyltransferase activity			ovary(1)|pancreas(1)|skin(1)	3						GATTGGCCTATTGCAGAGCAA	0.308													5	216	---	---	---	---	PASS
NAP1L1	4673	broad.mit.edu	37	12	76462768	76462768	+	Silent	SNP	T	C	C			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76462768T>C	uc001sxw.2	-	3	436	c.24A>G	c.(22-24)GAA>GAG	p.E8E	NAP1L1_uc001sxv.2_5'UTR|NAP1L1_uc001sxz.2_5'UTR|NAP1L1_uc001sxx.2_Silent_p.E8E|NAP1L1_uc001sxy.2_Intron|NAP1L1_uc010sty.1_Intron|NAP1L1_uc010stz.1_Intron|NAP1L1_uc010sua.1_Silent_p.E8E|NAP1L1_uc001syb.2_Silent_p.E8E|NAP1L1_uc001sya.2_5'UTR|NAP1L1_uc001syc.2_Silent_p.E8E	NM_139207	NP_631946	P55209	NP1L1_HUMAN	nucleosome assembly protein 1-like 1	8					DNA replication|nucleosome assembly|positive regulation of cell proliferation	chromatin assembly complex|melanosome	protein binding			ovary(1)|skin(1)	2		Colorectal(145;0.09)				GTTCAGACTGTTCTTTGCTAT	0.289													7	618	---	---	---	---	PASS
PTPRQ	374462	broad.mit.edu	37	12	80887186	80887186	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80887186A>G	uc001sze.2	+	7	1492	c.1492A>G	c.(1492-1494)AAA>GAA	p.K498E		NM_001145026	NP_001138498			protein tyrosine phosphatase, receptor type, Q												0						CCATCCAGATAAAAACTTTCC	0.393													28	158	---	---	---	---	PASS
HIP1R	9026	broad.mit.edu	37	12	123343703	123343703	+	Silent	SNP	C	T	T			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123343703C>T	uc001udj.1	+	22	2313	c.2254C>T	c.(2254-2256)CTG>TTG	p.L752L	HIP1R_uc001udk.1_Silent_p.L17L	NM_003959	NP_003950	O75146	HIP1R_HUMAN	huntingtin interacting protein-1-related	752					receptor-mediated endocytosis	clathrin coated vesicle membrane|coated pit|perinuclear region of cytoplasm	actin binding|phosphatidylinositol binding			ovary(1)	1	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;4.6e-05)|Epithelial(86;0.000119)|BRCA - Breast invasive adenocarcinoma(302;0.2)		GCAGGCCAGCCTGGTGCGGAC	0.682													3	7	---	---	---	---	PASS
GJA3	2700	broad.mit.edu	37	13	20717063	20717063	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20717063G>A	uc001umx.1	-	2	537	c.365C>T	c.(364-366)CCC>CTC	p.P122L		NM_021954	NP_068773	Q9Y6H8	CXA3_HUMAN	connexin 46	122	Cytoplasmic (Potential).				cell-cell signaling|visual perception	connexon complex|integral to membrane				pancreas(1)	1		all_cancers(29;1.4e-21)|all_epithelial(30;8.75e-19)|all_lung(29;1.28e-17)|Lung SC(185;0.0257)|Ovarian(182;0.0822)		all cancers(112;0.000554)|Epithelial(112;0.000872)|OV - Ovarian serous cystadenocarcinoma(117;0.0105)|Lung(94;0.0251)|LUSC - Lung squamous cell carcinoma(192;0.0784)		TGGCTCCTTGGGGCTGGGGCt	0.502													4	21	---	---	---	---	PASS
PABPC3	5042	broad.mit.edu	37	13	25670501	25670501	+	Silent	SNP	G	A	A			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25670501G>A	uc001upy.2	+	1	226	c.165G>A	c.(163-165)GCG>GCA	p.A55A		NM_030979	NP_112241	Q9H361	PABP3_HUMAN	poly(A) binding protein, cytoplasmic 3	55	RRM 1.				mRNA metabolic process	cytoplasm	nucleotide binding|poly(A) RNA binding			ovary(3)|skin(1)	4		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.0071)|Epithelial(112;0.0398)|OV - Ovarian serous cystadenocarcinoma(117;0.151)|GBM - Glioblastoma multiforme(144;0.222)|Lung(94;0.241)		CCAACTACGCGTATGTGAACT	0.547													8	70	---	---	---	---	PASS
OLFM4	10562	broad.mit.edu	37	13	53603018	53603018	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53603018G>T	uc001vhl.2	+	1	47	c.47G>T	c.(46-48)GGC>GTC	p.G16V	OLFM4_uc001vhk.1_Missense_Mutation_p.G16V	NM_006418	NP_006409	Q6UX06	OLFM4_HUMAN	olfactomedin 4 precursor	16					cell adhesion	extracellular space				skin(1)	1		Breast(56;0.000776)|Lung NSC(96;0.000814)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.13e-08)		TTCTTCCTTGGCCAAGCTGCA	0.512													11	112	---	---	---	---	PASS
RNF219	79596	broad.mit.edu	37	13	79219134	79219134	+	Splice_Site	SNP	T	C	C			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:79219134T>C	uc001vkw.1	-	2	132	c.73_splice	c.e2-1	p.V25_splice	RNF219_uc010afb.1_Splice_Site|RNF219_uc010afc.2_Splice_Site_p.V25_splice	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)		CTGACGTACCTTTGAAAAAAG	0.363													5	200	---	---	---	---	PASS
NFATC4	4776	broad.mit.edu	37	14	24845237	24845237	+	Silent	SNP	C	T	T			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24845237C>T	uc001wpc.2	+	8	2307	c.1986C>T	c.(1984-1986)GTC>GTT	p.V662V	NFATC4_uc010tok.1_Silent_p.V725V|NFATC4_uc010tol.1_Silent_p.V725V|NFATC4_uc010alr.2_Silent_p.V725V|NFATC4_uc010tom.1_Silent_p.V675V|NFATC4_uc010ton.1_Silent_p.V675V|NFATC4_uc010too.1_Silent_p.V675V|NFATC4_uc010alt.2_Silent_p.V694V|NFATC4_uc010top.1_Silent_p.V694V|NFATC4_uc010toq.1_Silent_p.V694V|NFATC4_uc010tor.1_Silent_p.V662V|NFATC4_uc010tos.1_Silent_p.V592V|NFATC4_uc010tot.1_Silent_p.V650V|NFATC4_uc010tou.1_Silent_p.V592V|NFATC4_uc010tov.1_Silent_p.V650V|NFATC4_uc010tow.1_Silent_p.V592V|NFATC4_uc010alv.2_Silent_p.V650V|NFATC4_uc010tox.1_Silent_p.V592V|NFATC4_uc001wpd.2_Silent_p.V197V|NFATC4_uc010toy.1_Silent_p.V197V|NFATC4_uc010toz.1_Silent_p.V197V|NFATC4_uc010tpa.1_5'UTR|NFATC4_uc010tpb.1_5'UTR	NM_004554	NP_004545	Q14934	NFAC4_HUMAN	nuclear factor of activated T-cells,	662	IPT/TIG.				cell differentiation|inflammatory response|transcription from RNA polymerase II promoter	cytoplasm|intermediate filament cytoskeleton|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(1)|central_nervous_system(1)|skin(1)	3				GBM - Glioblastoma multiforme(265;0.018)		CCCGGCCAGTCCAGGTCTACT	0.582													13	42	---	---	---	---	PASS
ADSSL1	122622	broad.mit.edu	37	14	105196283	105196283	+	Intron	SNP	G	T	T			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105196283G>T	uc001ypd.2	+						INF2_uc010tyi.1_Intron|ADSSL1_uc001ype.2_Missense_Mutation_p.R18S|ADSSL1_uc001ypf.2_RNA	NM_152328	NP_689541	Q8N142	PURA1_HUMAN	adenylosuccinate synthase like 1 isoform 2						AMP biosynthetic process|immune system process|purine base metabolic process	cytosol	adenylosuccinate synthase activity|GTP binding|magnesium ion binding|phosphate binding			ovary(1)|central_nervous_system(1)	2		all_cancers(154;0.0896)|Melanoma(154;0.155)|all_epithelial(191;0.172)	all cancers(16;0.00153)|OV - Ovarian serous cystadenocarcinoma(23;0.0148)|Epithelial(46;0.0396)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.18)	L-Aspartic Acid(DB00128)	gtgGGCAGAGGCCCACGAACC	0.358													5	15	---	---	---	---	PASS
TRPM1	4308	broad.mit.edu	37	15	31362254	31362254	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31362254C>T	uc001zfm.2	-	3	321	c.193G>A	c.(193-195)GGA>AGA	p.G65R	TRPM1_uc010azy.2_5'Flank|TRPM1_uc001zfl.2_5'Flank|TRPM1_uc001zfn.3_Missense_Mutation_p.G65R|uc010ubn.1_RNA	NM_002420	NP_002411	Q7Z4N2	TRPM1_HUMAN	transient receptor potential cation channel,	65	Extracellular (Potential).				cellular response to light stimulus|visual perception	integral to plasma membrane	calcium channel activity|receptor activity			ovary(2)|pancreas(1)|skin(1)	4		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)		TTGGAATATCCGCCACCCTGG	0.507													4	183	---	---	---	---	PASS
FBN1	2200	broad.mit.edu	37	15	48748913	48748913	+	Silent	SNP	C	A	A	rs140649	byFrequency	TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48748913C>A	uc001zwx.1	-	44	5671	c.5343G>T	c.(5341-5343)GTG>GTT	p.V1781V	FBN1_uc010beo.1_RNA	NM_000138	NP_000129	P35555	FBN1_HUMAN	fibrillin 1 precursor	1781	EGF-like 29; calcium-binding.				heart development|negative regulation of BMP signaling pathway by extracellular sequestering of BMP|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|skeletal system development	basement membrane|extracellular space|microfibril	calcium ion binding|extracellular matrix structural constituent|protein binding			ovary(2)|large_intestine(1)	3		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		TGTTGATACACACTCCATTTT	0.453													22	137	---	---	---	---	PASS
POLR3E	55718	broad.mit.edu	37	16	22345052	22345052	+	3'UTR	SNP	C	A	A			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22345052C>A	uc002dkk.2	+	21					POLR3E_uc002dkm.2_3'UTR|POLR3E_uc010vbr.1_3'UTR|POLR3E_uc002dkl.2_3'UTR|POLR3E_uc010vbs.1_3'UTR|POLR3E_uc010vbt.1_3'UTR	NM_018119	NP_060589	Q9NVU0	RPC5_HUMAN	RNA polymerase III polypeptide E						innate immune response|response to virus|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase III promoter	nucleoplasm	DNA-directed RNA polymerase activity			ovary(1)|central_nervous_system(1)	2				GBM - Glioblastoma multiforme(48;0.012)		CCCAGCAAATCTAAGCCCAAG	0.488													7	224	---	---	---	---	PASS
LOC653786	653786	broad.mit.edu	37	16	22588020	22588020	+	3'UTR	SNP	G	A	A			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22588020G>A	uc002dlh.3	+	9						NR_003676				RecName: Full=Otoancorin; Flags: Precursor;												0						TGAGCACATCGTCCTGTGTTG	0.572													32	298	---	---	---	---	PASS
CES7	221223	broad.mit.edu	37	16	55903470	55903470	+	Intron	SNP	C	A	A			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55903470C>A	uc002eip.2	-						CES7_uc002eio.2_Intron|CES7_uc002eiq.2_5'UTR|CES7_uc002eir.2_Intron	NM_001143685	NP_001137157	Q6NT32	EST5A_HUMAN	carboxylesterase 7 isoform 1							extracellular region	carboxylesterase activity|methyl indole-3-acetate esterase activity|methyl jasmonate esterase activity|methyl salicylate esterase activity				0				all cancers(182;0.229)|Epithelial(162;0.231)		TCTATGGCTACTGCACTGCTG	0.448													3	26	---	---	---	---	PASS
KIAA0174	9798	broad.mit.edu	37	16	71956438	71956438	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71956438A>C	uc002fbj.1	+	9	936	c.653A>C	c.(652-654)AAG>ACG	p.K218T	KIAA0174_uc010cgh.1_Missense_Mutation_p.K218T|KIAA0174_uc002fbk.1_Missense_Mutation_p.K205T|KIAA0174_uc002fbm.1_Missense_Mutation_p.K205T|KIAA0174_uc002fbl.1_Missense_Mutation_p.K205T|KIAA0174_uc002fbn.1_Missense_Mutation_p.K57T|KIAA0174_uc010cgi.1_5'UTR|KIAA0174_uc010cgj.1_Missense_Mutation_p.K137T|KIAA0174_uc010vml.1_RNA|KIAA0174_uc010vmk.1_Missense_Mutation_p.K57T			P53990	IST1_HUMAN	SubName: Full=cDNA FLJ32696 fis, clone TESTI2000358; SubName: Full=cDNA FLJ77725;	205	Interaction with VPS37B.|Interaction with VTA1.				cell cycle|cell division	cytoplasmic membrane-bounded vesicle|ER-Golgi intermediate compartment	protein binding			ovary(1)	1						GATGATGTGAAGAAAGGAGGC	0.413													25	144	---	---	---	---	PASS
ATMIN	23300	broad.mit.edu	37	16	81077602	81077602	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81077602G>A	uc002ffz.1	+	4	1517	c.1499G>A	c.(1498-1500)AGT>AAT	p.S500N	ATMIN_uc002fga.2_Missense_Mutation_p.S342N|ATMIN_uc010vnn.1_Missense_Mutation_p.S271N|ATMIN_uc002fgb.1_Missense_Mutation_p.S342N	NM_015251	NP_056066	O43313	ATMIN_HUMAN	ATM interactor	500					response to DNA damage stimulus	nucleus	zinc ion binding				0						GGGATAGAAAGTCCAACGGAT	0.428													4	147	---	---	---	---	PASS
SLFN12	55106	broad.mit.edu	37	17	33749820	33749820	+	Silent	SNP	T	C	C			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33749820T>C	uc002hji.3	-	2	605	c.228A>G	c.(226-228)GGA>GGG	p.G76G	SLFN12_uc002hjj.3_Silent_p.G76G|SLFN12_uc010cts.2_Silent_p.G76G	NM_018042	NP_060512	Q8IYM2	SLN12_HUMAN	schlafen family member 12	76							ATP binding			skin(1)	1		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CCAAATCTAGTCCTATTCCAT	0.368													6	241	---	---	---	---	PASS
C17orf66	256957	broad.mit.edu	37	17	34192324	34192324	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34192324C>T	uc002hke.1	-	3	364	c.215G>A	c.(214-216)TGC>TAC	p.C72Y	C17orf66_uc010wck.1_RNA|C17orf66_uc010wcl.1_Missense_Mutation_p.C72Y|C17orf66_uc010wcm.1_Missense_Mutation_p.C38Y	NM_152781	NP_689994	A2RTY3	CQ066_HUMAN	hypothetical protein LOC256957	72							binding			breast(2)|skin(1)	3		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0184)		CTTGAAGTAGCAGTACGGGAC	0.522													6	338	---	---	---	---	PASS
KRTAP1-1	81851	broad.mit.edu	37	17	39197549	39197549	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39197549G>C	uc002hvw.1	-	1	165	c.101C>G	c.(100-102)TCC>TGC	p.S34C		NM_030967	NP_112229	Q07627	KRA11_HUMAN	keratin associated protein 1-1	34			Missing (in allele KAP1.7).|PSCSTSGTCGSSCCQPSCCETSSCQPRCCETSCCQPSCCQT SFCGFP -> R (in allele KAP1.6).			extracellular region|keratin filament					0		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			TGGCTGGCAGGAGCTGGTCTC	0.612													3	7	---	---	---	---	PASS
AXIN2	8313	broad.mit.edu	37	17	63554465	63554465	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63554465C>T	uc002jfi.2	-	2	563	c.274G>A	c.(274-276)GCT>ACT	p.A92T	AXIN2_uc010den.1_Missense_Mutation_p.A92T|AXIN2_uc002jfh.2_Missense_Mutation_p.A92T|AXIN2_uc002jfj.1_Missense_Mutation_p.A92T	NM_004655	NP_004646	Q9Y2T1	AXIN2_HUMAN	axin 2	92	RGS.				cellular protein localization|cellular response to organic cyclic compound|dorsal/ventral axis specification|intramembranous ossification|maintenance of DNA repeat elements|mRNA stabilization|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|negative regulation of cell proliferation|negative regulation of osteoblast differentiation|odontogenesis|positive regulation of cell death|positive regulation of epithelial to mesenchymal transition|positive regulation of protein phosphorylation|regulation of centromeric sister chromatid cohesion|regulation of mismatch repair|Wnt receptor signaling pathway involved in somitogenesis	Axin-APC-beta-catenin-GSK3B complex|cell cortex|centrosome|cytoplasmic membrane-bounded vesicle|cytoplasmic microtubule|nucleus|plasma membrane|postsynaptic density	armadillo repeat domain binding|beta-catenin binding|GTPase activator activity|protein kinase binding|signal transducer activity|ubiquitin protein ligase binding			central_nervous_system(1)|skin(1)	2						AACAGGTAAGCACCGTCTTGA	0.552									Oligodontia_Ectodermal_Dysplasia_and_Colorectal_Polyp_syndrome				15	81	---	---	---	---	PASS
NARF	26502	broad.mit.edu	37	17	80436689	80436689	+	Silent	SNP	C	T	T			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80436689C>T	uc002kfg.3	+	6	674	c.534C>T	c.(532-534)TAC>TAT	p.Y178Y	NARF_uc002kff.3_Silent_p.Y119Y|NARF_uc010wvo.1_Silent_p.Y133Y|NARF_uc010wvp.1_Silent_p.Y50Y|NARF_uc010dit.2_Silent_p.Y178Y|NARF_uc002kfj.3_Silent_p.Y130Y|NARF_uc002kfi.3_RNA|NARF_uc002kfh.3_Silent_p.Y178Y|NARF_uc002kfk.2_RNA	NM_012336	NP_036468	Q9UHQ1	NARF_HUMAN	nuclear prelamin A recognition factor isoform a	178						lamin filament	lamin binding			skin(1)	1	Breast(20;0.00106)|all_neural(118;0.0804)		OV - Ovarian serous cystadenocarcinoma(97;0.0143)|BRCA - Breast invasive adenocarcinoma(99;0.0369)			GGGTCCGATACGCCGAGCGGG	0.617													8	30	---	---	---	---	PASS
FAM38B	63895	broad.mit.edu	37	18	10762537	10762537	+	Silent	SNP	G	A	A			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10762537G>A	uc002kos.1	-	4	643	c.606C>T	c.(604-606)GTC>GTT	p.V202V	FAM38B_uc002kou.1_Silent_p.V326V			Q9H5I5	PIEZ2_HUMAN	SubName: Full=cDNA FLJ45725 fis, clone HCHON2009766; Flags: Fragment;	1045						integral to membrane	ion channel activity			ovary(1)	1						TCCGCAGGCCGACCCACTCTG	0.458													5	148	---	---	---	---	PASS
DSC1	1823	broad.mit.edu	37	18	28713925	28713925	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28713925T>C	uc002kwn.2	-	13	2307	c.2045A>G	c.(2044-2046)GAC>GGC	p.D682G	DSC1_uc002kwm.2_Missense_Mutation_p.D682G	NM_024421	NP_077739	Q08554	DSC1_HUMAN	desmocollin 1 isoform Dsc1a preproprotein	682	Extracellular (Potential).|Cadherin 5.				homophilic cell adhesion	desmosome|gap junction|integral to membrane|membrane fraction	calcium ion binding			ovary(3)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(10;0.00778)			TGGTCTAACGTCTCTTGTACT	0.348													6	315	---	---	---	---	PASS
CCDC11	220136	broad.mit.edu	37	18	47792751	47792751	+	Silent	SNP	G	A	A			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47792751G>A	uc002lee.2	-	1	115	c.24C>T	c.(22-24)ACC>ACT	p.T8T		NM_145020	NP_659457	Q96M91	CCD11_HUMAN	coiled-coil domain containing 11	8										ovary(1)|pancreas(1)|skin(1)	3				STAD - Stomach adenocarcinoma(97;2.66e-05)|Colorectal(21;7.57e-05)|Lung(128;0.00932)|READ - Rectum adenocarcinoma(32;0.164)		CCCGCTGTACGGTGCCAAACC	0.637													11	55	---	---	---	---	PASS
OR7D2	162998	broad.mit.edu	37	19	9297041	9297041	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9297041A>G	uc002mkz.1	+	1	772	c.584A>G	c.(583-585)AAC>AGC	p.N195S		NM_175883	NP_787079	Q96RA2	OR7D2_HUMAN	olfactory receptor, family 7, subfamily D,	195	Extracellular (Potential).				regulation of transcription, DNA-dependent|sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|upper_aerodigestive_tract(1)	3						ACCTTCCTGAACAGCACGTTG	0.428													6	369	---	---	---	---	PASS
ZNF30	90075	broad.mit.edu	37	19	35424605	35424605	+	Silent	SNP	A	G	G			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35424605A>G	uc010edp.1	+	4	612	c.234A>G	c.(232-234)AAA>AAG	p.K78K	ZNF30_uc002nxf.2_5'UTR|ZNF30_uc010edq.1_Silent_p.K79K|ZNF30_uc010edr.1_Silent_p.K79K	NM_194325	NP_919306	P17039	ZNF30_HUMAN	zinc finger protein 30 isoform b	78	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2	all_lung(56;8.38e-08)|Lung NSC(56;1.31e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)	GBM - Glioblastoma multiforme(1328;0.0265)		CAGTGAGGAAAGATGGAAGAA	0.478													6	294	---	---	---	---	PASS
PSENEN	55851	broad.mit.edu	37	19	36236501	36236501	+	5'UTR	SNP	A	T	T			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36236501A>T	uc002obi.1	+	1					TMEM149_uc010xsy.1_5'Flank|TMEM149_uc010eej.2_5'Flank|U2AF1L4_uc002obh.1_5'Flank|U2AF1L4_uc002obe.2_5'Flank|U2AF1L4_uc002obf.2_5'Flank|U2AF1L4_uc002obg.2_5'Flank|PSENEN_uc002obj.1_5'UTR|PSENEN_uc002obk.1_RNA	NM_172341	NP_758844	Q9NZ42	PEN2_HUMAN	presenilin enhancer 2						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 membrane|Golgi cisterna membrane|integral to plasma membrane	aspartic-type endopeptidase activity|protein binding			ovary(2)	2	all_lung(56;3.33e-07)|Lung NSC(56;5.02e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			TGCCTCGCCCAAAGAAGACTA	0.607													3	12	---	---	---	---	PASS
SUPT5H	6829	broad.mit.edu	37	19	39966815	39966815	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39966815A>G	uc002olo.3	+	29	3298	c.3119A>G	c.(3118-3120)AAG>AGG	p.K1040R	SUPT5H_uc002olp.3_Missense_Mutation_p.K1040R|SUPT5H_uc002olq.3_Missense_Mutation_p.K1036R|SUPT5H_uc002oln.3_Missense_Mutation_p.K1040R|SUPT5H_uc002olr.3_Missense_Mutation_p.K1040R	NM_001111020	NP_001104490	O00267	SPT5H_HUMAN	suppressor of Ty 5 homolog isoform a	1040					cell cycle|chromatin remodeling|mRNA capping|negative regulation of transcription elongation, DNA-dependent|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription elongation from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|response to organic substance|retroviral genome replication|transcription elongation from RNA polymerase II promoter	nucleoplasm	enzyme binding|protein heterodimerization activity			ovary(3)|pancreas(1)	4	all_cancers(60;6.69e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;1.57e-06)|Ovarian(47;0.159)		Epithelial(26;3.9e-26)|all cancers(26;1.35e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			AAGAACAACAAGGTAAGGGCA	0.577													4	60	---	---	---	---	PASS
LAIR2	3904	broad.mit.edu	37	19	55020248	55020248	+	Missense_Mutation	SNP	G	C	C	rs12949	by1000genomes	TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55020248G>C	uc002qgc.2	+	4	490	c.368G>C	c.(367-369)AGC>ACC	p.S123T	LAIR2_uc002qgd.2_Intron|LAIR2_uc010erl.2_Missense_Mutation_p.A92P	NM_002288	NP_002279	Q6ISS4	LAIR2_HUMAN	leukocyte-associated immunoglobulin-like	123						extracellular region	receptor activity			ovary(1)	1	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0967)		TTTACAGAAAGCTCTGGAGGC	0.627													5	86	---	---	---	---	PASS
ZNF264	9422	broad.mit.edu	37	19	57723635	57723635	+	Silent	SNP	T	C	C			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57723635T>C	uc002qob.2	+	4	1583	c.1170T>C	c.(1168-1170)TAT>TAC	p.Y390Y		NM_003417	NP_003408	O43296	ZN264_HUMAN	zinc finger protein 264	390	C2H2-type 7.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0135)		TTCACCACTATGTCATCCACA	0.547													4	70	---	---	---	---	PASS
RBCK1	10616	broad.mit.edu	37	20	402784	402784	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:402784G>A	uc002wdp.3	+	8	1624	c.931G>A	c.(931-933)GGC>AGC	p.G311S	RBCK1_uc010zpm.1_RNA|RBCK1_uc002wdq.3_Missense_Mutation_p.G269S|RBCK1_uc010fzy.2_RNA|RBCK1_uc002wdr.3_Missense_Mutation_p.G141S	NM_031229	NP_112506	Q9BYM8	HOIL1_HUMAN	RanBP-type and C3HC4-type zinc finger containing	311	RING-type.				interspecies interaction between organisms|negative regulation of NF-kappaB transcription factor activity|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|proteasomal ubiquitin-dependent protein catabolic process|protein linear polyubiquitination|T cell receptor signaling pathway	LUBAC complex	protein binding|ubiquitin binding|ubiquitin-protein ligase activity|zinc ion binding				0		all_epithelial(17;0.172)|Lung NSC(37;0.191)|Breast(17;0.231)				GTGCCTGCAGGGCACCATCCG	0.612													8	57	---	---	---	---	PASS
C20orf194	25943	broad.mit.edu	37	20	3277596	3277596	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3277596C>A	uc002wii.2	-	23	1981	c.1930G>T	c.(1930-1932)GTC>TTC	p.V644F	C20orf194_uc002wij.3_Missense_Mutation_p.V383F|C20orf194_uc002wik.2_Missense_Mutation_p.V318F	NM_001009984	NP_001009984	Q5TEA3	CT194_HUMAN	hypothetical protein LOC25943	644											0						AGGGAGAAGACCTAAACAAAA	0.408													10	195	---	---	---	---	PASS
C20orf191	149934	broad.mit.edu	37	20	26084303	26084303	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26084303G>T	uc002wvj.3	-	2	168	c.113C>A	c.(112-114)CCA>CAA	p.P38Q		NR_003678				SubName: Full=Putative uncharacterized protein ENSP00000323172;												0						TCCAAATGCTGGATCCTTTAG	0.398													6	216	---	---	---	---	PASS
FRG1B	284802	broad.mit.edu	37	20	29632707	29632707	+	Intron	SNP	G	A	A	rs6057187		TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29632707G>A	uc010ztl.1	+						FRG1B_uc002wvm.1_RNA|FRG1B_uc010ztj.1_RNA|FRG1B_uc010ztk.1_Silent_p.E96E					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						TTTTGCATGAGACGCTTCTGG	0.313													9	58	---	---	---	---	PASS
SPAG4	6676	broad.mit.edu	37	20	34207221	34207221	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34207221G>T	uc002xdb.1	+	9	1015	c.898G>T	c.(898-900)GTT>TTT	p.V300F	SPAG4_uc010zvi.1_Missense_Mutation_p.V223F	NM_003116	NP_003107	Q9NPE6	SPAG4_HUMAN	sperm associated antigen 4	300	SUN.				spermatogenesis	cilium|flagellar axoneme|integral to membrane	structural molecule activity				0	Lung NSC(9;0.0053)|all_lung(11;0.00785)		BRCA - Breast invasive adenocarcinoma(18;0.0127)			GCCGCCCACGGTTATCCTGGA	0.602													11	66	---	---	---	---	PASS
KRTAP10-6	386674	broad.mit.edu	37	21	46011170	46011170	+	3'UTR	SNP	T	C	C	rs233302	by1000genomes	TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46011170T>C	uc002zfm.2	-	1					C21orf29_uc002zfe.1_Intron|C21orf29_uc010gpv.1_Intron	NM_198688	NP_941961	P60371	KR106_HUMAN	keratin associated protein 10-6							keratin filament					0						GCCTGCCCCATCTTCTGAGGG	0.607													3	17	---	---	---	---	PASS
POTEH	23784	broad.mit.edu	37	22	16278057	16278057	+	Intron	SNP	G	A	A	rs146119771		TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:16278057G>A	uc010gqp.2	-						POTEH_uc002zlg.1_Intron|POTEH_uc002zlh.1_Intron|POTEH_uc002zlj.1_Intron|uc002zlk.2_RNA	NM_001136213	NP_001129685	Q6S545	POTEH_HUMAN	ANKRD26-like family C, member 3											skin(1)	1						CACCAAGGTTGAAAGGAAGGG	0.368													11	59	---	---	---	---	PASS
TCF20	6942	broad.mit.edu	37	22	42606432	42606432	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42606432T>C	uc003bcj.1	-	1	5014	c.4880A>G	c.(4879-4881)AAG>AGG	p.K1627R	TCF20_uc003bck.1_Missense_Mutation_p.K1627R|TCF20_uc003bnt.2_Missense_Mutation_p.K1627R	NM_005650	NP_005641	Q9UGU0	TCF20_HUMAN	transcription factor 20 isoform 1	1627					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|transcription coactivator activity|zinc ion binding			ovary(4)|skin(1)	5						AGACTTGTTCTTGGCATCAGT	0.408													6	361	---	---	---	---	PASS
ARSE	415	broad.mit.edu	37	X	2876320	2876320	+	Silent	SNP	G	A	A			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2876320G>A	uc004crc.3	-	3	430	c.180C>T	c.(178-180)ACC>ACT	p.T60T	ARSE_uc011mhi.1_Intron|ARSE_uc011mhh.1_Silent_p.T85T	NM_000047	NP_000038	P51690	ARSE_HUMAN	arylsulfatase E precursor	60					skeletal system development	Golgi stack	arylsulfatase activity|metal ion binding			ovary(1)|central_nervous_system(1)	2		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				CTTGCCTCATGGTGTTGTTGC	0.522													5	190	---	---	---	---	PASS
SHROOM4	57477	broad.mit.edu	37	X	50376299	50376299	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:50376299C>A	uc004dpe.2	-	4	2800	c.2774G>T	c.(2773-2775)CGG>CTG	p.R925L	SHROOM4_uc004dpd.3_RNA|SHROOM4_uc004dpf.1_Missense_Mutation_p.R809L	NM_020717	NP_065768	Q9ULL8	SHRM4_HUMAN	shroom family member 4	925	Cys-rich.				actin filament organization|brain development|cell morphogenesis|cognition	apical plasma membrane|basal plasma membrane|internal side of plasma membrane|nucleus	actin filament binding			upper_aerodigestive_tract(1)	1	Ovarian(276;0.236)					GTGGTGGCACCGGCAGTTGTA	0.488													4	147	---	---	---	---	PASS
ACRC	93953	broad.mit.edu	37	X	70824426	70824426	+	Silent	SNP	T	C	C			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70824426T>C	uc004eae.2	+	8	1800	c.1299T>C	c.(1297-1299)AAT>AAC	p.N433N	BCYRN1_uc011mpt.1_Intron	NM_052957	NP_443189	Q96QF7	ACRC_HUMAN	ACRC protein	433	Arg/Lys/Pro-rich.					nucleus				ovary(3)	3	Renal(35;0.156)					AGACCAAAAATATAGTGGAGC	0.453													18	124	---	---	---	---	PASS
PHKA1	5255	broad.mit.edu	37	X	71802392	71802392	+	Silent	SNP	T	C	C			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:71802392T>C	uc004eax.3	-	31	3655	c.3354A>G	c.(3352-3354)GTA>GTG	p.V1118V	PHKA1_uc004eay.3_Silent_p.V1105V|PHKA1_uc011mqi.1_Silent_p.V1046V|PHKA1_uc010nll.2_Silent_p.V150V	NM_002637	NP_002628	P46020	KPB1_HUMAN	phosphorylase kinase, alpha 1 (muscle) isoform	1118					glucose metabolic process|glycogen catabolic process	cytosol|plasma membrane	calmodulin binding|glucan 1,4-alpha-glucosidase activity|phosphorylase kinase activity			ovary(3)|skin(1)	4	Renal(35;0.156)					CTGGCTGAGGTACACGATTCA	0.453													5	144	---	---	---	---	PASS
FAM122C	159091	broad.mit.edu	37	X	133955426	133955426	+	Intron	SNP	T	C	C			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:133955426T>C	uc004exz.1	+						FAM122C_uc010nru.1_3'UTR|FAM122C_uc004exw.2_Intron|FAM122C_uc004exx.2_RNA|FAM122C_uc011mvq.1_Intron|FAM122C_uc004exy.1_Intron	NM_138819	NP_620174	Q6P4D5	F222C_HUMAN	hypothetical protein LOC159091												0	Acute lymphoblastic leukemia(192;0.000127)					CTATGCCTTCTCCCAAATCGC	0.458													7	484	---	---	---	---	PASS
MAMLD1	10046	broad.mit.edu	37	X	149638089	149638089	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:149638089A>C	uc004fee.1	+	3	320	c.244A>C	c.(244-246)AAA>CAA	p.K82Q	MAMLD1_uc011mxt.1_Missense_Mutation_p.K44Q|MAMLD1_uc011mxu.1_Missense_Mutation_p.K57Q|MAMLD1_uc011mxv.1_Missense_Mutation_p.K57Q|MAMLD1_uc011mxw.1_Missense_Mutation_p.K9Q	NM_005491	NP_005482	Q13495	MAMD1_HUMAN	mastermind-like domain containing 1	82					male gonad development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0	Acute lymphoblastic leukemia(192;6.56e-05)					CTACCCTAATAAAATTAAGAG	0.443													10	28	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	2861139	2861140	+	IGR	INS	-	GT	GT			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2861139_2861140insGT								MMEL1 (296658 upstream) : ACTRT2 (76906 downstream)																							tccatgcgtgggtgtgtgtgag	0.109													4	2	---	---	---	---	
MTHFR	4524	broad.mit.edu	37	1	11852585	11852585	+	Intron	DEL	G	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11852585delG	uc001atc.1	-						MTHFR_uc001atb.1_Intron	NM_005957	NP_005948	P42898	MTHR_HUMAN	5,10-methylenetetrahydrofolate reductase						blood circulation|folic acid metabolic process	cytosol	methylenetetrahydrofolate reductase (NADPH) activity|protein binding				0	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00826)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)	Benazepril(DB00542)|Cyanocobalamin(DB00115)|Folic Acid(DB00158)|L-Methionine(DB00134)|Menadione(DB00170)|Methotrexate(DB00563)|Pyridoxal Phosphate(DB00114)|Pyridoxine(DB00165)|Raltitrexed(DB00293)|Riboflavin(DB00140)|S-Adenosylmethionine(DB00118)|Tetrahydrofolic acid(DB00116)	TGAGGGGAGTGGGGACGTGAG	0.547													4	2	---	---	---	---	
LOC440563	440563	broad.mit.edu	37	1	13184079	13184080	+	5'Flank	INS	-	T	T	rs146762683	by1000genomes	TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:13184079_13184080insT	uc010obg.1	-							NM_001136561	NP_001130033	B2RXH8	B2RXH8_HUMAN	heterogeneous nuclear ribonucleoprotein C-like							ribonucleoprotein complex	nucleic acid binding|nucleotide binding				0						GAAAAGCACAACAACATTTTTG	0.342													7	4	---	---	---	---	
PAX7	5081	broad.mit.edu	37	1	19071184	19071191	+	Intron	DEL	ATGGATGG	-	-	rs3916683	by1000genomes	TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19071184_19071191delATGGATGG	uc010oct.1	+							NM_001135254	NP_001128726	P23759	PAX7_HUMAN	paired box 7 isoform 3						anti-apoptosis	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		PAX7/FOXO1(197)	soft_tissue(197)|lung(3)|prostate(1)|ovary(1)|breast(1)	203		Colorectal(325;3.46e-05)|all_lung(284;0.000439)|Renal(390;0.000518)|Lung NSC(340;0.000543)|Breast(348;0.00093)|Ovarian(437;0.00768)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00609)|BRCA - Breast invasive adenocarcinoma(304;4.71e-05)|Kidney(64;0.000279)|KIRC - Kidney renal clear cell carcinoma(64;0.00371)|STAD - Stomach adenocarcinoma(196;0.00658)|READ - Rectum adenocarcinoma(331;0.0576)		ggatggataaatggatggatggatggat	0.082			T	FOXO1A	alveolar rhabdomyosarcoma								8	4	---	---	---	---	
SFRS4	6429	broad.mit.edu	37	1	29501130	29501130	+	Intron	DEL	A	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29501130delA	uc001bro.2	-						SFRS4_uc010ofy.1_Intron|SFRS4_uc009vtp.2_Intron	NM_005626	NP_005617	Q08170	SRSF4_HUMAN	splicing factor, arginine/serine-rich 4						mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	nuclear speck	nucleotide binding|RNA binding				0		Colorectal(325;0.00161)|Breast(348;0.0364)|Myeloproliferative disorder(586;0.0393)|all_neural(195;0.0529)|Lung NSC(340;0.0654)|all_lung(284;0.074)|Ovarian(437;0.104)|Medulloblastoma(700;0.151)		Colorectal(126;1.01e-07)|COAD - Colon adenocarcinoma(152;6.21e-06)|STAD - Stomach adenocarcinoma(196;0.0196)|BRCA - Breast invasive adenocarcinoma(304;0.0531)|READ - Rectum adenocarcinoma(331;0.0649)|KIRC - Kidney renal clear cell carcinoma(1967;0.138)		ccaagtttggaaaaaaaAAAG	0.124													6	3	---	---	---	---	
BSDC1	55108	broad.mit.edu	37	1	32855592	32855592	+	Intron	DEL	G	-	-	rs67545706		TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32855592delG	uc001bvh.3	-						BSDC1_uc010ohg.1_Intron|BSDC1_uc010ohh.1_Intron|BSDC1_uc010ohi.1_Intron|BSDC1_uc001bvg.3_Intron|BSDC1_uc001bvj.2_Intron|BSDC1_uc001bvi.2_Intron	NM_018045	NP_060515	Q9NW68	BSDC1_HUMAN	BSD domain containing 1 isoform b								protein binding			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				aaaaaaaaaagaaCAggagtc	0.005													6	3	---	---	---	---	
ZNF643	65243	broad.mit.edu	37	1	40920061	40920061	+	Intron	DEL	T	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40920061delT	uc001cfn.1	+						ZNF643_uc001cfl.1_Intron|ZNF643_uc001cfm.1_Intron	NM_023070	NP_075558	Q9UJL9	ZN643_HUMAN	zinc finger protein 643						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;5.25e-18)			TTGGCTtttctttttttttct	0.199													4	2	---	---	---	---	
ACOT11	26027	broad.mit.edu	37	1	55080092	55080093	+	Intron	DEL	TG	-	-	rs71767684		TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55080092_55080093delTG	uc001cxm.1	+						FAM151A_uc001cxn.2_Intron	NM_015547	NP_056362	Q8WXI4	ACO11_HUMAN	thioesterase, adipose associated isoform BFIT1						fatty acid metabolic process|intracellular signal transduction|response to cold		acyl-CoA thioesterase activity|carboxylesterase activity			central_nervous_system(1)	1						aagtcagggctgtgttagaagg	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	64160665	64160665	+	IGR	DEL	G	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:64160665delG								PGM1 (34751 upstream) : ROR1 (79025 downstream)																							tactgtgcttggcactttttc	0.000													4	2	---	---	---	---	
NBPF10	100132406	broad.mit.edu	37	1	145310834	145310834	+	Intron	DEL	A	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145310834delA	uc001end.3	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NBPF10_uc001emp.3_Intron|NBPF10_uc010oyi.1_Intron|NBPF10_uc010oyk.1_5'Flank|NBPF10_uc010oyl.1_5'Flank|NBPF10_uc001emq.1_Intron|NBPF10_uc010oyj.1_5'Flank	NM_001039703	NP_001034792	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC100132406												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		TTTATTGGGGAAAAAATTGCT	0.368													10	5	---	---	---	---	
BCL9	607	broad.mit.edu	37	1	147086644	147086644	+	Intron	DEL	T	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:147086644delT	uc001epq.2	+						BCL9_uc010ozr.1_Intron	NM_004326	NP_004317	O00512	BCL9_HUMAN	B-cell CLL/lymphoma 9						Wnt receptor signaling pathway	nucleus	protein binding			ovary(2)|large_intestine(2)|breast(1)|skin(1)	6	all_hematologic(923;0.115)					TCTCtttttcttttttttttt	0.179			T	IGH@|IGL@	B-ALL								4	2	---	---	---	---	
UBAP2L	9898	broad.mit.edu	37	1	154215938	154215938	+	Intron	DEL	T	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154215938delT	uc001fep.3	+						UBAP2L_uc009wot.2_Intron|UBAP2L_uc010pek.1_Intron|UBAP2L_uc010pel.1_Intron|UBAP2L_uc010pen.1_Intron	NM_014847	NP_055662	Q14157	UBP2L_HUMAN	ubiquitin associated protein 2-like isoform a						binding of sperm to zona pellucida		protein binding			ovary(1)|central_nervous_system(1)	2	all_lung(78;1.09e-30)|Lung NSC(65;1.66e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			GAGAGACttcttttttttttt	0.179													11	5	---	---	---	---	
RNPEP	6051	broad.mit.edu	37	1	201966296	201966296	+	Intron	DEL	G	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201966296delG	uc001gxd.2	+						RNPEP_uc001gxe.2_Intron|RNPEP_uc001gxf.2_Intron	NM_020216	NP_064601	Q9H4A4	AMPB_HUMAN	arginyl aminopeptidase						leukotriene biosynthetic process		epoxide hydrolase activity|zinc ion binding			upper_aerodigestive_tract(1)	1				KIRC - Kidney renal clear cell carcinoma(1967;3.23e-08)|Colorectal(1306;0.005)		TGAGGAGCCTGGGCTTTATTT	0.572													10	5	---	---	---	---	
KCNH1	3756	broad.mit.edu	37	1	211111106	211111106	+	Intron	DEL	T	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211111106delT	uc001hib.2	-						KCNH1_uc001hic.2_Intron	NM_172362	NP_758872	O95259	KCNH1_HUMAN	potassium voltage-gated channel, subfamily H,						myoblast fusion|regulation of transcription, DNA-dependent	voltage-gated potassium channel complex	calmodulin binding|delayed rectifier potassium channel activity|two-component sensor activity			ovary(4)|central_nervous_system(1)	5				OV - Ovarian serous cystadenocarcinoma(81;0.0109)|all cancers(67;0.141)|Epithelial(68;0.185)		tttaataaccttttttcctcc	0.144													4	2	---	---	---	---	
TRAF5	7188	broad.mit.edu	37	1	211538511	211538512	+	Intron	INS	-	A	A			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211538511_211538512insA	uc001hih.2	+						TRAF5_uc001hii.2_Intron|TRAF5_uc010psx.1_Intron|TRAF5_uc010psy.1_Intron|TRAF5_uc001hij.2_Intron	NM_004619	NP_004610	O00463	TRAF5_HUMAN	TNF receptor-associated factor 5						apoptosis|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|regulation of apoptosis	CD40 receptor complex|centrosome|internal side of plasma membrane	protein binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)|breast(2)|ovary(1)	5				OV - Ovarian serous cystadenocarcinoma(81;0.00946)|all cancers(67;0.0808)|Epithelial(68;0.144)		caggctgtctcaaaaaaaaaac	0.173													5	3	---	---	---	---	
ARID4B	51742	broad.mit.edu	37	1	235420786	235420786	+	Intron	DEL	T	-	-	rs72514522		TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235420786delT	uc001hwq.2	-						ARID4B_uc001hwr.2_Intron|ARID4B_uc001hws.3_Intron|ARID4B_uc001hwu.1_Intron	NM_016374	NP_057458	Q4LE39	ARI4B_HUMAN	AT rich interactive domain 4B isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding			ovary(2)|lung(1)	3	Ovarian(103;0.0473)|Breast(184;0.23)	all_cancers(173;0.000782)|Prostate(94;0.0132)|all_epithelial(177;0.0808)|Lung SC(1967;0.24)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)			CCACATGTCAttttttttttt	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	1593548	1593548	+	IGR	DEL	A	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1593548delA								TPO (47050 upstream) : PXDN (42112 downstream)																							GGTGGGAGTGAAAGGTGCTGC	0.572													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	7050484	7050485	+	IGR	DEL	TG	-	-	rs145080587		TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7050484_7050485delTG								RSAD2 (12121 upstream) : RNF144A (7038 downstream)																							GTGGTGGCGAtgtgtgtgtgtg	0.327													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91766185	91766187	+	IGR	DEL	ATG	-	-	rs142832221		TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91766185_91766187delATG								None (None upstream) : LOC654342 (39005 downstream)																							CTTTTTTACCATGATAGTTTAGT	0.305													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	107087588	107087589	+	IGR	INS	-	T	T			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107087588_107087589insT								RGPD3 (2787 upstream) : ST6GAL2 (330469 downstream)																							TGTTGGTATAAtttcttttttt	0.139													4	3	---	---	---	---	
NXPH2	11249	broad.mit.edu	37	2	139477701	139477701	+	Intron	DEL	A	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:139477701delA	uc002tvi.2	-							NM_007226	NP_009157	O95156	NXPH2_HUMAN	neurexophilin 2 precursor						neuropeptide signaling pathway	extracellular region				ovary(3)|skin(1)	4				BRCA - Breast invasive adenocarcinoma(221;0.101)		ttttaaggttaaaaaaaaaaa	0.025													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	159574914	159574914	+	Intron	DEL	C	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:159574914delC	uc002uab.1	-											Homo sapiens cDNA FLJ44380 fis, clone TRACH3035482.																		CTTCCAGTCTCCCCCACTGGC	0.542													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	181673828	181673829	+	IGR	INS	-	T	T			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:181673828_181673829insT								CWC22 (801988 upstream) : UBE2E3 (171283 downstream)																							TTTCAAACTTCTTTTTTTTctt	0.153													4	2	---	---	---	---	
COL5A2	1290	broad.mit.edu	37	2	189916369	189916373	+	Intron	DEL	AAAAG	-	-	rs72902374		TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:189916369_189916373delAAAAG	uc002uqk.2	-						COL5A2_uc010frx.2_Intron	NM_000393	NP_000384	P05997	CO5A2_HUMAN	alpha 2 type V collagen preproprotein						axon guidance|collagen fibril organization|eye morphogenesis|skin development	collagen type V	extracellular matrix structural constituent			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.127)			aaaacaaaacaaaagaaaacaCAGC	0.341													3	3	---	---	---	---	
HECW2	57520	broad.mit.edu	37	2	197280257	197280258	+	Intron	INS	-	TTCCTG	TTCCTG	rs144634819	by1000genomes	TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197280257_197280258insTTCCTG	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						gtgtttgctgcttcctgtggtg	0.084													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	13201294	13201294	+	IGR	DEL	A	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13201294delA								IQSEC1 (86677 upstream) : NUP210 (156443 downstream)																							GTGCTGGGGGAAAAAAGATAA	0.443													4	2	---	---	---	---	
MLH1	4292	broad.mit.edu	37	3	37063728	37063728	+	Intron	DEL	G	-	-	rs28754348	by1000genomes	TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37063728delG	uc003cgl.2	+						MLH1_uc011aye.1_Intron|MLH1_uc011ayb.1_Intron|MLH1_uc010hge.2_Intron|MLH1_uc003cgn.3_Intron|MLH1_uc011ayc.1_Intron|MLH1_uc011ayd.1_Intron|MLH1_uc003cgo.2_Intron|MLH1_uc010hgg.1_Intron|MLH1_uc010hgh.1_Intron|MLH1_uc010hgi.1_Intron|MLH1_uc010hgj.1_Intron|MLH1_uc010hgk.2_Intron|MLH1_uc010hgl.1_Intron	NM_000249	NP_000240	P40692	MLH1_HUMAN	MutL protein homolog 1						mismatch repair|somatic hypermutation of immunoglobulin genes	chiasma|MutLalpha complex|MutLbeta complex|synaptonemal complex	ATP binding|ATPase activity|protein binding	p.0?(1)		large_intestine(40)|haematopoietic_and_lymphoid_tissue(8)|ovary(6)|pancreas(5)|stomach(3)|central_nervous_system(3)|endometrium(3)|breast(3)|prostate(3)|skin(2)|NS(1)	77						cttgggtggtggggtctgggc	0.095		1	D|Mis|N|F|S		colorectal|endometrial|ovarian|CNS	colorectal|endometrial|ovarian|CNS		MMR	Lynch_syndrome|Muir-Torre_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				4	2	---	---	---	---	
CTNNB1	1499	broad.mit.edu	37	3	41277009	41277009	+	Intron	DEL	G	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41277009delG	uc010hia.1	+						CTNNB1_uc003ckp.2_Intron|CTNNB1_uc003ckq.2_Intron|CTNNB1_uc003ckr.2_Intron|CTNNB1_uc011azf.1_Intron|CTNNB1_uc011azg.1_Intron|CTNNB1_uc003cks.2_3'UTR|CTNNB1_uc003ckt.1_5'Flank	NM_001904	NP_001895	P35222	CTNB1_HUMAN	beta-catenin						adherens junction assembly|androgen receptor signaling pathway|branching involved in ureteric bud morphogenesis|canonical Wnt receptor signaling pathway involved in negative regulation of apoptosis|canonical Wnt receptor signaling pathway involved in positive regulation of epithelial to mesenchymal transition|cell-cell adhesion|cell-matrix adhesion|cellular component disassembly involved in apoptosis|cellular response to growth factor stimulus|cellular response to indole-3-methanol|central nervous system vasculogenesis|cytoskeletal anchoring at plasma membrane|determination of dorsal/ventral asymmetry|dorsal/ventral axis specification|ectoderm development|embryonic axis specification|embryonic foregut morphogenesis|embryonic leg joint morphogenesis|endodermal cell fate commitment|endothelial tube morphogenesis|epithelial to mesenchymal transition|gastrulation with mouth forming second|glial cell fate determination|hair follicle morphogenesis|hair follicle placode formation|hindbrain development|liver development|lung cell differentiation|lung induction|lung-associated mesenchyme development|male genitalia development|mesenchymal cell proliferation involved in lung development|mesenchymal to epithelial transition involved in metanephros morphogenesis|negative regulation of cell proliferation|negative regulation of chondrocyte differentiation|negative regulation of heart induction by canonical Wnt receptor signaling pathway|negative regulation of osteoclast differentiation|negative regulation of transcription from RNA polymerase II promoter|nephron tubule formation|odontogenesis of dentine-containing tooth|oocyte development|pancreas development|positive regulation of anti-apoptosis|positive regulation of apoptosis|positive regulation of branching involved in lung morphogenesis|positive regulation of epithelial cell proliferation involved in prostate gland development|positive regulation of fibroblast growth factor receptor signaling pathway|positive regulation of heparan sulfate proteoglycan biosynthetic process|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of MAPKKK cascade|positive regulation of muscle cell differentiation|positive regulation of osteoblast differentiation|positive regulation of transcription from RNA polymerase II promoter|protein localization at cell surface|proximal/distal pattern formation|regulation of angiogenesis|regulation of calcium ion import|regulation of centriole-centriole cohesion|regulation of centromeric sister chromatid cohesion|regulation of fibroblast proliferation|regulation of nephron tubule epithelial cell differentiation|regulation of protein localization at cell surface|regulation of smooth muscle cell proliferation|regulation of T cell proliferation|renal inner medulla development|renal outer medulla development|renal vesicle formation|response to drug|response to estradiol stimulus|Schwann cell proliferation|smooth muscle cell differentiation|synapse organization|synaptic vesicle transport|T cell differentiation in thymus|thymus development|trachea formation	APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin-TCF7L2 complex|catenin complex|cell cortex|cell-substrate adherens junction|centrosome|dendritic shaft|desmosome|fascia adherens|internal side of plasma membrane|lamellipodium|lateral plasma membrane|microvillus membrane|perinuclear region of cytoplasm|protein-DNA complex|synapse|transcription factor complex|Z disc|zonula adherens	alpha-catenin binding|androgen receptor binding|cadherin binding|estrogen receptor binding|I-SMAD binding|ion channel binding|protein binding|protein C-terminus binding|protein kinase binding|protein phosphatase binding|R-SMAD binding|RPTP-like protein binding|signal transducer activity|specific RNA polymerase II transcription factor activity|structural molecule activity|transcription coactivator activity|transcription regulatory region DNA binding		CTNNB1/PLAG1(60)	liver(806)|soft_tissue(609)|large_intestine(243)|endometrium(222)|kidney(172)|stomach(157)|central_nervous_system(139)|ovary(104)|skin(97)|pancreas(91)|adrenal_gland(85)|pituitary(81)|salivary_gland(62)|haematopoietic_and_lymphoid_tissue(57)|thyroid(55)|biliary_tract(41)|lung(38)|prostate(24)|bone(20)|small_intestine(17)|cervix(9)|parathyroid(9)|urinary_tract(8)|breast(7)|oesophagus(5)|NS(3)|pleura(2)|upper_aerodigestive_tract(2)|eye(1)	3166				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)	Lithium(DB01356)	CACTGTGTATGGGGGAGGGGT	0.438		15	H|Mis|T	PLAG1	colorectal|cvarian| hepatoblastoma|others|pleomorphic salivary adenoma				Pilomatrixoma_Familial_Clustering_of				4	2	---	---	---	---	
KIAA1143	57456	broad.mit.edu	37	3	44795447	44795447	+	Intron	DEL	A	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44795447delA	uc011bac.1	-							NM_020696	NP_065747	Q96AT1	K1143_HUMAN	hypothetical protein LOC57456												0				BRCA - Breast invasive adenocarcinoma(193;0.00847)|KIRC - Kidney renal clear cell carcinoma(197;0.0465)|Kidney(197;0.0582)		CCATCTATTTAAAAAAAAAAA	0.154													3	3	---	---	---	---	
SEMA3G	56920	broad.mit.edu	37	3	52472646	52472646	+	Intron	DEL	A	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52472646delA	uc003dea.1	-							NM_020163	NP_064548	Q9NS98	SEM3G_HUMAN	semaphorin sem2 precursor						multicellular organismal development	extracellular region|membrane	receptor activity			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(193;1.69e-05)|Kidney(197;0.00173)|KIRC - Kidney renal clear cell carcinoma(197;0.00196)|OV - Ovarian serous cystadenocarcinoma(275;0.0333)		GTAGGCCTCTAAAAAGTGGCC	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	129717843	129717844	+	IGR	DEL	AG	-	-	rs75643277		TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129717843_129717844delAG								TRH (21067 upstream) : ALG1L2 (82830 downstream)																							AAAAAAAAAAAGGAAGcagtct	0.183													6	3	---	---	---	---	
STAG1	10274	broad.mit.edu	37	3	136287405	136287405	+	Intron	DEL	T	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136287405delT	uc003era.1	-						STAG1_uc003erb.1_Intron|STAG1_uc003erc.1_Intron|STAG1_uc010hua.1_Intron|STAG1_uc003erd.2_Intron|STAG1_uc003ere.2_Intron	NM_005862	NP_005853	Q8WVM7	STAG1_HUMAN	stromal antigen 1						cell division|chromosome segregation|mitotic metaphase/anaphase transition|mitotic prometaphase	cell junction|chromatin|chromosome, centromeric region|nucleoplasm	protein binding			ovary(2)	2						TATAAATGTATTACTTTATAG	0.249													4	2	---	---	---	---	
ZNF595	152687	broad.mit.edu	37	4	66227	66227	+	Intron	DEL	T	-	-	rs28445159		TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:66227delT	uc003fzv.1	+						ZNF595_uc003fzu.1_Intron|ZNF718_uc003fzt.3_Intron|ZNF595_uc010iay.1_Intron|ZNF595_uc011bus.1_Intron|ZNF595_uc011but.1_Intron	NM_182524	NP_872330	Q7Z3I0	Q7Z3I0_HUMAN	zinc finger protein 595						regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding				0		all_cancers(4;0.0738)|all_epithelial(65;0.139)		Lung(54;0.0654)|Epithelial(2;0.0921)|all cancers(2;0.146)|LUSC - Lung squamous cell carcinoma(95;0.173)		taactttttgttttttttttg	0.000													8	4	---	---	---	---	
CPLX1	10815	broad.mit.edu	37	4	786602	786602	+	Intron	DEL	G	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:786602delG	uc003gbi.2	-						CPLX1_uc003gbj.2_Intron	NM_006651	NP_006642	O14810	CPLX1_HUMAN	complexin 1						glutamate secretion	cytosol					0				Colorectal(103;0.187)		CCAGTGTGCTGGGGTCTCCTG	0.557													4	2	---	---	---	---	
GRK4	2868	broad.mit.edu	37	4	2993725	2993725	+	Intron	DEL	A	-	-	rs148317231		TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2993725delA	uc003ggn.1	+						GRK4_uc003ggo.1_Intron|GRK4_uc003ggp.1_Intron|GRK4_uc003ggq.1_Intron	NM_182982	NP_892027	P32298	GRK4_HUMAN	G protein-coupled receptor kinase 4 isoform							cell cortex	ATP binding|G-protein coupled receptor kinase activity|signal transducer activity			lung(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		ATATCAAACCAAATAATTTGA	0.274													3	7	---	---	---	---	
CC2D2A	57545	broad.mit.edu	37	4	15542781	15542781	+	Intron	DEL	A	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15542781delA	uc010idv.2	+						CC2D2A_uc003gnx.2_Intron|CC2D2A_uc003gnz.1_Intron|CC2D2A_uc003goa.1_Intron	NM_001080522	NP_001073991	Q9P2K1	C2D2A_HUMAN	coiled-coil and C2 domain containing 2A isoform						cell projection organization	cilium|microtubule basal body				pancreas(2)|ovary(1)	3						ctgtaaatacaaaaaaaaaaa	0.000													4	2	---	---	---	---	
PROM1	8842	broad.mit.edu	37	4	16018089	16018089	+	Intron	DEL	A	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:16018089delA	uc003goo.2	-						PROM1_uc003gor.2_Intron|PROM1_uc003gos.2_Intron|PROM1_uc003got.2_Intron|PROM1_uc003gou.2_Intron|PROM1_uc003gop.2_Intron|PROM1_uc003goq.3_Intron|PROM1_uc010iec.1_Intron	NM_006017	NP_006008	O43490	PROM1_HUMAN	prominin 1 isoform 1						camera-type eye photoreceptor cell differentiation|photoreceptor cell maintenance|retina layer formation	apical plasma membrane|cell surface|integral to plasma membrane|microvillus membrane|photoreceptor outer segment membrane|plasma membrane	beta-actinin binding|cadherin binding			ovary(3)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)|central_nervous_system(1)	7						gtaaccagctaaaaaaaagag	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	57598648	57598649	+	IGR	DEL	CA	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57598648_57598649delCA								HOPX (50776 upstream) : SPINK2 (77385 downstream)																							CGGTCCAGGTCACATGCCACTG	0.490													4	2	---	---	---	---	
GSTCD	79807	broad.mit.edu	37	4	106751937	106751937	+	Intron	DEL	A	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:106751937delA	uc003hxz.3	+						GSTCD_uc003hxy.3_Intron|GSTCD_uc011cfb.1_Intron	NM_001031720	NP_001026890	Q8NEC7	GSTCD_HUMAN	glutathione S-transferase, C-terminal domain							cytoplasm	rRNA methyltransferase activity			breast(1)|central_nervous_system(1)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;3.15e-07)|READ - Rectum adenocarcinoma(30;0.139)		CTTGGATGTTAAAAAAACAAG	0.289													4	2	---	---	---	---	
PLK4	10733	broad.mit.edu	37	4	128817629	128817629	+	Intron	DEL	A	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128817629delA	uc003ifo.2	+						PLK4_uc011cgs.1_Intron|PLK4_uc011cgt.1_Intron	NM_014264	NP_055079	O00444	PLK4_HUMAN	polo-like kinase 4						G2/M transition of mitotic cell cycle|positive regulation of centriole replication|trophoblast giant cell differentiation	centriole|cleavage furrow|cytosol|nucleolus	ATP binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity				0						CTTGTGGGGGAAAAAAACCAA	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	160138218	160138218	+	IGR	DEL	T	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:160138218delT								C4orf45 (114113 upstream) : RAPGEF2 (50780 downstream)																							GCTTGCAAGGTTTTTTTTAGT	0.388													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	179007442	179007443	+	IGR	INS	-	C	C			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:179007442_179007443insC								LOC285501 (95539 upstream) : None (None downstream)																							ATTTTCCGATTTTTTTCTGTTC	0.337													4	2	---	---	---	---	
SUB1	10923	broad.mit.edu	37	5	32592819	32592819	+	Intron	DEL	A	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32592819delA	uc003jhs.2	+						SUB1_uc003jht.2_Intron	NM_006713	NP_006704	P53999	TCP4_HUMAN	activated RNA polymerase II transcription						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleolus|transcription factor complex	protein binding|single-stranded DNA binding|transcription coactivator activity				0						GATGTGATTGAAAAAAAAAAT	0.398													4	2	---	---	---	---	
NIPBL	25836	broad.mit.edu	37	5	37052271	37052271	+	Intron	DEL	T	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37052271delT	uc003jkl.3	+						NIPBL_uc003jkk.3_Intron|NIPBL_uc003jkn.2_Intron	NM_133433	NP_597677	Q6KC79	NIPBL_HUMAN	delangin isoform A						brain development|cellular protein localization|cellular response to X-ray|cognition|developmental growth|ear morphogenesis|embryonic arm morphogenesis|embryonic digestive tract morphogenesis|external genitalia morphogenesis|eye morphogenesis|face morphogenesis|gall bladder development|maintenance of mitotic sister chromatid cohesion|metanephros development|negative regulation of transcription from RNA polymerase II promoter|outflow tract morphogenesis|positive regulation of histone deacetylation|regulation of developmental growth|regulation of embryonic development|regulation of hair cycle|response to DNA damage stimulus|sensory perception of sound|uterus morphogenesis	SMC loading complex	chromo shadow domain binding|histone deacetylase binding|protein C-terminus binding|protein N-terminus binding			ovary(4)|lung(2)|large_intestine(1)|breast(1)|kidney(1)	9	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			ctgggcctcattttttttttc	0.065													5	3	---	---	---	---	
FER	2241	broad.mit.edu	37	5	108207524	108207526	+	Intron	DEL	GCG	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:108207524_108207526delGCG	uc003kop.1	+						FER_uc011cvf.1_Intron|FER_uc011cvg.1_Intron	NM_005246	NP_005237	P16591	FER_HUMAN	fer (fps/fes related) tyrosine kinase						intracellular signal transduction|peptidyl-tyrosine phosphorylation	cytoplasm|nucleus	ATP binding|non-membrane spanning protein tyrosine kinase activity			lung(2)|stomach(1)|ovary(1)|kidney(1)	5		all_cancers(142;2.86e-06)|all_epithelial(76;9.81e-08)|Prostate(80;0.00972)|Lung NSC(167;0.039)|Ovarian(225;0.0448)|all_lung(232;0.0496)|Colorectal(57;0.0986)|Breast(839;0.152)		OV - Ovarian serous cystadenocarcinoma(64;6.77e-10)|Epithelial(69;4.13e-08)|COAD - Colon adenocarcinoma(37;0.0174)		actttatgatgcgccaaatactt	0.015													4	2	---	---	---	---	
HSPA4	3308	broad.mit.edu	37	5	132432653	132432653	+	Intron	DEL	T	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132432653delT	uc003kyj.2	+							NM_002154	NP_002145	P34932	HSP74_HUMAN	heat shock 70kDa protein 4						cellular chaperone-mediated protein complex assembly|protein import into mitochondrial outer membrane|response to unfolded protein	cytoplasm|nucleus	ATP binding			lung(1)|breast(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TCTATTGTTCTTTTTTTTAAT	0.303													4	2	---	---	---	---	
PHF15	23338	broad.mit.edu	37	5	133902795	133902795	+	Intron	DEL	C	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133902795delC	uc003kzo.1	+						PHF15_uc011cxt.1_Intron|PHF15_uc003kzk.2_Intron|PHF15_uc003kzl.2_Intron|PHF15_uc003kzm.2_Intron|PHF15_uc003kzn.2_Intron|PHF15_uc003kzp.2_Intron	NM_015288	NP_056103	Q9NQC1	JADE2_HUMAN	PHD finger protein 15						histone H3 acetylation|histone H4-K12 acetylation|histone H4-K5 acetylation|histone H4-K8 acetylation	histone acetyltransferase complex	zinc ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TGGGTAAACGCGGCTCCGTGG	0.617													4	2	---	---	---	---	
PDE6A	5145	broad.mit.edu	37	5	149300989	149300990	+	Intron	INS	-	T	T			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149300989_149300990insT	uc003lrg.3	-							NM_000440	NP_000431	P16499	PDE6A_HUMAN	phosphodiesterase 6A						cytosolic calcium ion homeostasis|GMP metabolic process|platelet activation|signal transduction|visual perception	cytosol|plasma membrane	3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding			ovary(1)|pancreas(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)			TATTGTTGCTGTTTTTTTTTTA	0.257													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	174821993	174821993	+	IGR	DEL	T	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174821993delT								MSX2 (664092 upstream) : DRD1 (45683 downstream)																							AAACCAGGGATTTTTTTTTCC	0.418													6	5	---	---	---	---	
B4GALT7	11285	broad.mit.edu	37	5	177027607	177027607	+	Intron	DEL	C	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177027607delC	uc003mhy.2	+							NM_007255	NP_009186	Q9UBV7	B4GT7_HUMAN	xylosylprotein beta 1,4-galactosyltransferase 7						fibril organization|glycosaminoglycan biosynthetic process|negative regulation of fibroblast proliferation|protein modification process|proteoglycan metabolic process	Golgi cisterna membrane|integral to membrane	metal ion binding|xylosylprotein 4-beta-galactosyltransferase activity			pancreas(1)	1	all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	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)			CTGTGTTTCTCCACCAGCCTC	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	4400006	4400007	+	IGR	INS	-	ATTTATCCAACACAG	ATTTATCCAACACAG	rs140658133	by1000genomes	TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:4400006_4400007insATTTATCCAACACAG								PECI (264175 upstream) : CDYL (306386 downstream)																							CCAGGCAATCCATTTATCCAAC	0.480													16	9	---	---	---	---	
MAK	4117	broad.mit.edu	37	6	10802526	10802526	+	Intron	DEL	T	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10802526delT	uc003mzl.2	-						SYCP2L_uc011dim.1_Intron|TMEM14B_uc010jos.1_Intron|MAK_uc010jot.2_Intron|MAK_uc010jou.2_Intron|MAK_uc003mzm.2_Intron|MAK_uc010jov.1_Intron	NM_005906	NP_005897	P20794	MAK_HUMAN	male germ cell-associated kinase						cell differentiation|multicellular organismal development|spermatogenesis		ATP binding|cyclin-dependent protein kinase activity			breast(2)|skin(1)	3	Breast(50;0.107)|Ovarian(93;0.107)	all_hematologic(90;0.117)				CTTTTATAGCTtttttttgtt	0.174													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	15872986	15872986	+	IGR	DEL	T	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15872986delT								DTNBP1 (209715 upstream) : MYLIP (256331 downstream)																							AAGCAGTCTGTAACACATGAG	0.448													4	2	---	---	---	---	
HLA-H	3136	broad.mit.edu	37	6	29856941	29856941	+	3'UTR	DEL	A	-	-	rs147655138		TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29856941delA	uc010jro.2	+	3					HLA-G_uc011dmb.1_Intron|HLA-H_uc003nod.2_Intron					SubName: Full=cDNA FLJ52667, highly similar to HLA class I histocompatibility antigen, alpha chain H;												0						TTTTCCACGGAATAGGAGATT	0.567													6	3	---	---	---	---	
CFB	629	broad.mit.edu	37	6	31918204	31918204	+	Intron	DEL	G	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31918204delG	uc003nyj.3	+						CFB_uc011dor.1_Intron|CFB_uc003nyi.2_Frame_Shift_Del_p.G550fs	NM_001710	NP_001701	P00751	CFAB_HUMAN	complement factor B preproprotein						complement activation, alternative pathway|proteolysis	extracellular region|plasma membrane	complement binding|serine-type endopeptidase activity			skin(1)	1						TGAAGGTCCTGGGCTGCACCT	0.522													4	2	---	---	---	---	
PKHD1	5314	broad.mit.edu	37	6	51923570	51923573	+	Intron	DEL	TCTA	-	-	rs66624918		TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51923570_51923573delTCTA	uc003pah.1	-						PKHD1_uc003pai.2_Intron	NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1						cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1)	44	Lung NSC(77;0.0605)					TCTCCAGCTCtctatctatctatc	0.333													3	4	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57413897	57413898	+	Intron	INS	-	TT	TT	rs139691483		TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57413897_57413898insTT	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|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|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		AAGGTGGACTCTTTTTTGCCAA	0.366													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	96444187	96444187	+	IGR	DEL	T	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:96444187delT								MANEA (386861 upstream) : FUT9 (19658 downstream)																							tttccttaggtttttttttgg	0.000													4	2	---	---	---	---	
C6orf167	253714	broad.mit.edu	37	6	97715519	97715519	+	Intron	DEL	A	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97715519delA	uc003ppb.2	-						C6orf167_uc011eaf.1_Intron|C6orf167_uc010kcn.1_Intron|C6orf167_uc010kco.1_Intron|C6orf167_uc003ppc.2_Intron	NM_198468	NP_940870	Q6ZRQ5	MMS22_HUMAN	hypothetical protein LOC253714						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)		TATTTTTCTTaaaaaaaaaaa	0.259													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	107213598	107213599	+	Intron	INS	-	TAACAAGA	TAACAAGA	rs149433339	by1000genomes	TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107213598_107213599insTAACAAGA	uc003pro.1	-											Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 1534000.																		gatggaagaggtaacaagatcc	0.000													2	4	---	---	---	---	
SLC35F1	222553	broad.mit.edu	37	6	118598986	118598986	+	Intron	DEL	A	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:118598986delA	uc003pxx.3	+						SLC35F1_uc003pxy.1_Intron	NM_001029858	NP_001025029	Q5T1Q4	S35F1_HUMAN	solute carrier family 35, member F1						transport	integral to membrane				breast(1)	1				GBM - Glioblastoma multiforme(226;0.217)		ACACCAACAGAAAAAAAAAAC	0.383													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	136043724	136043724	+	IGR	DEL	C	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136043724delC								C6orf217 (6532 upstream) : PDE7B (129110 downstream)																							CTTTTCCCCTCCCTGACTCCA	0.378													4	2	---	---	---	---	
REPS1	85021	broad.mit.edu	37	6	139253596	139253597	+	Intron	INS	-	C	C	rs148100051	by1000genomes	TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139253596_139253597insC	uc003qii.2	-						REPS1_uc003qig.3_Intron|REPS1_uc011edr.1_Intron|REPS1_uc003qij.2_Intron|REPS1_uc003qik.2_Intron	NM_031922	NP_114128	Q96D71	REPS1_HUMAN	RALBP1 associated Eps domain containing 1							coated pit|plasma membrane	calcium ion binding|SH3 domain binding			lung(1)|breast(1)	2				GBM - Glioblastoma multiforme(68;0.000434)|OV - Ovarian serous cystadenocarcinoma(155;0.000548)		tgtattccttacccccccccac	0.000													7	4	---	---	---	---	
PHACTR2	9749	broad.mit.edu	37	6	143929697	143929698	+	Intron	INS	-	TATTT	TATTT	rs144166110	by1000genomes	TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:143929697_143929698insTATTT	uc003qjq.3	+						PHACTR2_uc010khh.2_Intron	NM_014721	NP_055536	O75167	PHAR2_HUMAN	phosphatase and actin regulator 2 isoform 3								actin binding|protein phosphatase inhibitor activity			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(155;1.58e-05)|GBM - Glioblastoma multiforme(68;0.0386)		AAGACTACTGCTATTTAGGCTG	0.396													4	2	---	---	---	---	
MAD1L1	8379	broad.mit.edu	37	7	1906096	1906096	+	Intron	DEL	A	-	-	rs35613646		TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1906096delA	uc003slh.1	-						MAD1L1_uc003sle.1_Intron|MAD1L1_uc003slf.1_Intron|MAD1L1_uc003slg.1_Intron|MAD1L1_uc010ksh.1_Intron|MAD1L1_uc003sli.1_Intron|MAD1L1_uc003sld.1_Intron	NM_001013836	NP_001013858	Q9Y6D9	MD1L1_HUMAN	MAD1-like 1 protein						cell division|mitotic anaphase|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase|mitotic prometaphase|mitotic telophase	actin cytoskeleton|centrosome|condensed chromosome kinetochore|cytosol|mitochondrion|nucleus|spindle	protein binding			lung(1)|central_nervous_system(1)	2		Ovarian(82;0.0272)		UCEC - Uterine corpus endometrioid carcinoma (27;0.134)|OV - Ovarian serous cystadenocarcinoma(56;3.63e-14)		GGGCTGAAGCAAGAGATGAGA	0.587													2	4	---	---	---	---	
EIF2AK1	27102	broad.mit.edu	37	7	6064007	6064008	+	3'UTR	INS	-	AGA	AGA	rs146929595	by1000genomes	TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6064007_6064008insAGA	uc003spp.2	-	15					EIF2AK1_uc003spq.2_3'UTR|EIF2AK1_uc011jwm.1_Intron	NM_014413	NP_055228	Q9BQI3	E2AK1_HUMAN	eukaryotic translation initiation factor 2-alpha						negative regulation of hemoglobin biosynthetic process|negative regulation of translational initiation by iron|protein autophosphorylation|response to external stimulus|response to stress	cytoplasm	ATP binding|eukaryotic translation initiation factor 2alpha kinase activity|heme binding|protein homodimerization activity			upper_aerodigestive_tract(1)|stomach(1)|lung(1)|central_nervous_system(1)	4		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.106)|OV - Ovarian serous cystadenocarcinoma(56;5.22e-14)		ATTTCTGCGGTACCTTCTAGAG	0.495													1	7	---	---	---	---	
RSPH10B2	728194	broad.mit.edu	37	7	6835946	6835946	+	Intron	DEL	A	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6835946delA	uc003sqw.1	+						RSPH10B2_uc010ktk.1_Intron|RSPH10B2_uc011jxc.1_Intron|RSPH10B2_uc010ktl.1_Intron	NM_173565	NP_775836	B2RC85	R10B2_HUMAN	radial spoke head 10 homolog B											ovary(1)|pancreas(1)|skin(1)	3						ctctgtctccaaaaaaaaaaa	0.219													3	3	---	---	---	---	
SCIN	85477	broad.mit.edu	37	7	12618090	12618090	+	Intron	DEL	T	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:12618090delT	uc003ssn.3	+						SCIN_uc010ktt.2_Intron	NM_001112706	NP_001106177	Q9Y6U3	ADSV_HUMAN	scinderin isoform 1						actin filament capping|actin filament severing|actin nucleation|calcium ion-dependent exocytosis|negative regulation of cell proliferation|positive regulation of apoptosis|positive regulation of megakaryocyte differentiation|positive regulation of secretion|regulation of chondrocyte differentiation	cell cortex|cytoskeleton	1-phosphatidylinositol binding|actin filament binding|calcium ion binding|phosphatidylinositol-4,5-bisphosphate binding|phosphatidylserine binding			ovary(2)	2				UCEC - Uterine corpus endometrioid carcinoma (126;0.195)		GATAGGTTAATTTTTTAAAAG	0.184													4	2	---	---	---	---	
WBSCR27	155368	broad.mit.edu	37	7	73249451	73249456	+	Intron	DEL	CTCTCC	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73249451_73249456delCTCTCC	uc003tzj.2	-						RFC2_uc011kfa.1_Intron	NM_152559	NP_689772	Q8N6F8	WBS27_HUMAN	Williams-Beuren syndrome chromosome region 27											central_nervous_system(1)	1		Lung NSC(55;0.159)				TGGGGACGCTctctccctctccctct	0.277													1	5	---	---	---	---	
CDK14	5218	broad.mit.edu	37	7	90742138	90742139	+	Intron	DEL	GT	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90742138_90742139delGT	uc003uky.2	+						CDK14_uc003ukz.1_Intron|CDK14_uc010les.1_Intron|CDK14_uc011khl.1_Intron	NM_012395	NP_036527	O94921	CDK14_HUMAN	PFTAIRE protein kinase 1						cell division|G2/M transition of mitotic cell cycle|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane	ATP binding|cyclin binding|cyclin-dependent protein kinase activity			lung(3)|ovary(1)	4						TGCATTACAGgtgtgtgtgtgt	0.272													4	3	---	---	---	---	
SPDYE2	441273	broad.mit.edu	37	7	102197796	102197800	+	Intron	DEL	TTTTG	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102197796_102197800delTTTTG	uc011kkx.1	+						UPK3BL_uc003uzy.2_Intron|POLR2J3_uc003uzw.2_Intron|POLR2J3_uc011kkw.1_Intron|SPDYE2_uc003vaa.1_Intron	NM_001031618	NP_001026789	Q495Y8	SPDE2_HUMAN	speedy homolog E2												0						ttttttttttttttgtgtgtgtgtg	0.263													6	5	---	---	---	---	
BPGM	669	broad.mit.edu	37	7	134331753	134331753	+	Intron	DEL	T	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134331753delT	uc003vrv.2	+						BPGM_uc003vrw.2_Intron	NM_199186	NP_954655	P07738	PMGE_HUMAN	bisphosphoglycerate mutase						glycolysis|respiratory gaseous exchange		2,3-bisphospho-D-glycerate 2-phosphohydrolase activity|bisphosphoglycerate mutase activity|phosphoglycerate mutase activity				0						TGATGTTTTATTTTTGGGTGC	0.433													4	2	---	---	---	---	
C7orf34	135927	broad.mit.edu	37	7	142637880	142637880	+	3'UTR	DEL	T	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142637880delT	uc003wca.2	+	2						NM_178829	NP_849151	Q96L11	CG034_HUMAN	hypothetical protein LOC135927							extracellular region					0	Melanoma(164;0.059)					CCCACACCTCTCCTGGTTTTG	0.483													4	2	---	---	---	---	
CSMD1	64478	broad.mit.edu	37	8	3492059	3492059	+	Intron	DEL	T	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3492059delT	uc011kwk.1	-							NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor							integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		acctcttcccttttttgcctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	48080932	48080933	+	IGR	INS	-	G	G	rs148795212	by1000genomes	TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48080932_48080933insG								BEYLA (313525 upstream) : KIAA0146 (92609 downstream)																							TGCTGGTGTCTGGCCATAAATC	0.441													7	7	---	---	---	---	
PRKDC	5591	broad.mit.edu	37	8	48848624	48848624	+	Intron	DEL	A	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48848624delA	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)				TGATTGCCTTAAAAAAAAAAC	0.303								NHEJ					3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	52092715	52092716	+	IGR	DEL	CA	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52092715_52092716delCA								SNTG1 (387288 upstream) : PXDNL (139428 downstream)																							gaactaaatgcacacacacaca	0.000													7	4	---	---	---	---	
FABP4	2167	broad.mit.edu	37	8	82393021	82393021	+	Intron	DEL	A	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82393021delA	uc003ycd.2	-							NM_001442	NP_001433	P15090	FABP4_HUMAN	fatty acid binding protein 4, adipocyte						triglyceride catabolic process	cytoplasm|nucleus|soluble fraction	fatty acid binding|protein binding|transporter activity			breast(1)	1			Epithelial(68;0.213)			aaaaaaaaagaaaacccacaa	0.333													4	2	---	---	---	---	
RRM2B	50484	broad.mit.edu	37	8	103238407	103238407	+	Intron	DEL	A	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103238407delA	uc003ykn.2	-						RRM2B_uc003yko.2_Intron|RRM2B_uc010mbv.1_Intron|RRM2B_uc010mbw.1_Intron|RRM2B_uc010mbx.1_Intron|RRM2B_uc010mby.1_Intron	NM_015713	NP_056528	Q7LG56	RIR2B_HUMAN	ribonucleotide reductase M2 B (TP53 inducible)						deoxyribonucleoside diphosphate metabolic process|DNA repair|nucleobase, nucleoside and nucleotide interconversion	nucleoplasm	ribonucleoside-diphosphate reductase activity|transition metal ion binding			ovary(2)	2	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000728)			GCAAAGAAATAAAAAAAAAAG	0.313								Direct_reversal_of_damage|Modulation_of_nucleotide_pools					9	4	---	---	---	---	
ERMP1	79956	broad.mit.edu	37	9	5785678	5785679	+	3'UTR	INS	-	TACT	TACT	rs140253913	by1000genomes	TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5785678_5785679insTACT	uc003zjm.1	-	15					ERMP1_uc011lme.1_Intron|ERMP1_uc010mhs.1_3'UTR	NM_024896	NP_079172	Q7Z2K6	ERMP1_HUMAN	aminopeptidase Fxna						proteolysis	endoplasmic reticulum membrane|integral to membrane	metal ion binding|metallopeptidase activity			ovary(1)	1		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00115)|Lung(218;0.111)		CCGGCAATGCATACTTACTGTG	0.450													14	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	38596616	38596617	+	5'Flank	INS	-	AC	AC	rs145697360	by1000genomes	TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:38596616_38596617insAC	uc004abf.1	-						uc004abg.3_Intron|uc010mme.2_Intron					RecName: Full=Ankyrin repeat domain-containing protein 18B;																		ATCCATAAAATACACACACACA	0.292													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	85532743	85532745	+	IGR	DEL	TCC	-	-	rs72408650		TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:85532743_85532745delTCC								FLJ46321 (922573 upstream) : RASEF (64572 downstream)																							tgcctcagtttcctcatctcaaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	110099372	110099372	+	IGR	DEL	G	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110099372delG								RAD23B (4903 upstream) : KLF4 (147763 downstream)																							CCACCTGCTTGGAGTTTAGGA	0.517													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	117459484	117459484	+	IGR	DEL	T	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117459484delT								C9orf91 (50788 upstream) : TNFSF15 (92129 downstream)																							TTATACTTAATTTTTTTTTGT	0.488													4	2	---	---	---	---	
ADARB2	105	broad.mit.edu	37	10	1620871	1620872	+	Intron	INS	-	AG	AG	rs138276650	by1000genomes	TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1620871_1620872insAG	uc009xhq.2	-							NM_018702	NP_061172	Q9NS39	RED2_HUMAN	adenosine deaminase, RNA-specific, B2						mRNA processing	mitochondrion|nucleus	adenosine deaminase activity|double-stranded RNA binding|metal ion binding|single-stranded RNA binding			large_intestine(2)|central_nervous_system(1)	3		all_epithelial(10;0.059)|Colorectal(49;0.0815)		all cancers(11;0.0224)|GBM - Glioblastoma multiforme(2;0.0414)|Epithelial(11;0.165)		cacacacacacagagagaagtg	0.243													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	8842709	8842709	+	IGR	DEL	T	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8842709delT								GATA3 (725547 upstream) : None (None downstream)																							CTGTGCTGTGTTTTTTTGTTT	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	14524064	14524064	+	IGR	DEL	T	-	-	rs71984985		TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14524064delT								FRMD4A (19921 upstream) : FAM107B (36495 downstream)																							TCTCCAATGGttttttttttg	0.279													4	2	---	---	---	---	
BAMBI	25805	broad.mit.edu	37	10	28967576	28967579	+	Intron	DEL	GTGA	-	-	rs150503415		TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28967576_28967579delGTGA	uc001iuj.1	+						BAMBI_uc001iui.2_Intron	NM_012342	NP_036474	Q13145	BAMBI_HUMAN	BMP and activin membrane-bound inhibitor						cell migration|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of cell proliferation|positive regulation of epithelial to mesenchymal transition|positive regulation of protein binding|positive regulation of transcription, DNA-dependent|regulation of cell shape	cytoplasm|integral to membrane|plasma membrane	frizzled binding|type II transforming growth factor beta receptor binding			central_nervous_system(4)	4						gagtctctgtgtgagtgtgtctct	0.132													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	38944608	38944609	+	IGR	DEL	AT	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38944608_38944609delAT								LOC399744 (203528 upstream) : None (None downstream)																							TTATAGTGACATGTATGAAAAC	0.282													5	3	---	---	---	---	
SLC16A9	220963	broad.mit.edu	37	10	61427832	61427832	+	Intron	DEL	T	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61427832delT	uc010qig.1	-							NM_194298	NP_919274	Q7RTY1	MOT9_HUMAN	solute carrier family 16 (monocarboxylic acid						urate metabolic process	integral to membrane|plasma membrane	symporter activity			skin(2)|ovary(1)	3						CCTCCTCATCTTTTTTTTTTA	0.413													8	4	---	---	---	---	
COL13A1	1305	broad.mit.edu	37	10	71696843	71696844	+	Intron	DEL	GG	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71696843_71696844delGG	uc001jpr.1	+						COL13A1_uc001jqj.1_Intron|COL13A1_uc001jps.1_Intron|COL13A1_uc001jpt.1_Intron|COL13A1_uc001jpu.1_Intron|COL13A1_uc001jpv.1_Intron|COL13A1_uc001jpx.1_Intron|COL13A1_uc001jpw.1_Intron|COL13A1_uc001jpy.1_Intron|COL13A1_uc001jpz.1_Intron|COL13A1_uc001jqa.1_Intron|COL13A1_uc001jqc.1_Intron|COL13A1_uc001jqb.1_Intron|COL13A1_uc001jql.2_Intron|COL13A1_uc001jqd.1_Intron|COL13A1_uc001jqe.1_Intron|COL13A1_uc001jqf.1_Intron|COL13A1_uc001jqg.1_Intron|COL13A1_uc001jqh.1_Intron|COL13A1_uc001jqi.1_Intron|COL13A1_uc010qjf.1_Intron	NM_005203	NP_005194	Q5TAT6	CODA1_HUMAN	alpha 1 type XIII collagen isoform 1						cell differentiation|cell-cell adhesion|cell-matrix adhesion|endochondral ossification|morphogenesis of a branching structure	collagen type XIII|integral to membrane	extracellular matrix structural constituent|heparin binding|protein binding			ovary(1)	1					Atorvastatin(DB01076)|Simvastatin(DB00641)	GAGTAGAGGTGGGAGAGAGACA	0.554													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	81784335	81784337	+	IGR	DEL	AAT	-	-	rs67544556		TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81784335_81784337delAAT								MBL1P (73552 upstream) : LOC219347 (21654 downstream)																							TAAAGATAACAATCTTTGGAGAG	0.256													4	3	---	---	---	---	
HTR7	3363	broad.mit.edu	37	10	92502858	92502859	+	Intron	INS	-	A	A	rs149957585	by1000genomes	TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:92502858_92502859insA	uc001kha.2	-						HTR7_uc001kgz.2_Intron|HTR7_uc001khb.2_Intron	NM_019859	NP_062873	P34969	5HT7R_HUMAN	5-hydroxytryptamine receptor 7 isoform d						blood circulation|circadian rhythm	integral to plasma membrane	protein binding|serotonin receptor activity			ovary(1)	1					Eletriptan(DB00216)|Methysergide(DB00247)|Ziprasidone(DB00246)	GGCCTCAACTTACCACACTACA	0.530													2	4	---	---	---	---	
TNKS2	80351	broad.mit.edu	37	10	93582313	93582314	+	Intron	INS	-	TGTTT	TGTTT	rs139143201	by1000genomes	TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93582313_93582314insTGTTT	uc001khp.2	+							NM_025235	NP_079511	Q9H2K2	TNKS2_HUMAN	tankyrase, TRF1-interacting ankyrin-related						positive regulation of canonical Wnt receptor signaling pathway|protein auto-ADP-ribosylation|protein localization to chromosome, telomeric region|protein polyubiquitination|Wnt receptor signaling pathway	Golgi membrane|microsome|nuclear envelope|pericentriolar material|perinuclear region of cytoplasm	NAD+ ADP-ribosyltransferase activity|protein binding			kidney(3)|skin(3)|ovary(1)|lung(1)	8		Colorectal(252;0.162)				GAGATACCATAtgttttgtttt	0.149													3	3	---	---	---	---	
BLNK	29760	broad.mit.edu	37	10	97960101	97960101	+	Intron	DEL	T	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97960101delT	uc001kls.3	-						BLNK_uc001kme.3_Intron|BLNK_uc001klt.3_Intron|BLNK_uc009xvc.2_Intron|BLNK_uc001klu.3_Intron|BLNK_uc001klv.3_Intron|BLNK_uc001klw.3_Intron|BLNK_uc001klx.3_Intron|BLNK_uc001kly.3_Intron|BLNK_uc001klz.3_Intron|BLNK_uc001kma.3_Intron|BLNK_uc001kmb.3_Intron|BLNK_uc001kmc.3_Intron|BLNK_uc001kmd.3_Intron|BLNK_uc009xvd.2_Intron	NM_013314	NP_037446	Q8WV28	BLNK_HUMAN	B-cell linker isoform 1						B cell differentiation|humoral immune response|inflammatory response|intracellular signal transduction	cytoplasm|plasma membrane	SH3/SH2 adaptor activity|transmembrane receptor protein tyrosine kinase adaptor activity			skin(2)	2		Colorectal(252;0.083)		Epithelial(162;7.89e-08)|all cancers(201;2.27e-06)		GTTTTTTGTATTTTTTTTTCA	0.294													4	2	---	---	---	---	
C10orf28	27291	broad.mit.edu	37	10	99994572	99994572	+	Intron	DEL	A	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99994572delA	uc001kow.3	+						C10orf28_uc001kox.3_Intron|C10orf28_uc001koy.3_Intron|C10orf28_uc009xvx.2_Intron|C10orf28_uc009xvy.2_Intron|C10orf28_uc001koz.3_Intron	NM_014472	NP_055287	Q4KMY3	Q4KMY3_HUMAN	growth inhibition and differentiation related								nucleotide binding			large_intestine(1)|skin(1)	2		Colorectal(252;0.234)		Epithelial(162;7.18e-11)|all cancers(201;8.75e-09)		TGGGGCTCTTAAAATATTGGT	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	123202080	123202080	+	IGR	DEL	A	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123202080delA								WDR11 (533045 upstream) : FGFR2 (35765 downstream)																							ataatgggataaggaagagac	0.000													4	2	---	---	---	---	
FGFR2	2263	broad.mit.edu	37	10	123263119	123263119	+	Intron	DEL	T	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123263119delT	uc010qtk.1	-						FGFR2_uc010qtg.1_Intron|FGFR2_uc010qth.1_Intron|FGFR2_uc010qti.1_Intron|FGFR2_uc010qtj.1_Intron|FGFR2_uc010qtl.1_Intron|FGFR2_uc010qtm.1_Intron|FGFR2_uc001lfl.3_Intron|FGFR2_uc001lfm.2_Intron|FGFR2_uc001lfg.3_Intron	NM_000141	NP_000132	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2 isoform 1						angiogenesis|axonogenesis|bone mineralization|bone morphogenesis|branch elongation involved in salivary gland morphogenesis|branching involved in embryonic placenta morphogenesis|branching morphogenesis of a nerve|bud elongation involved in lung branching|cell fate commitment|cell growth|cell-cell signaling|cellular response to protein stimulus|embryonic digestive tract morphogenesis|embryonic pattern specification|epithelial cell proliferation involved in salivary gland morphogenesis|fibroblast growth factor receptor signaling pathway involved in hemopoiesis|fibroblast growth factor receptor signaling pathway involved in mammary gland specification|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptosis in bone marrow|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow|hair follicle morphogenesis|insulin receptor signaling pathway|lacrimal gland development|lateral sprouting from an epithelium|limb bud formation|lung alveolus development|lung lobe morphogenesis|lung-associated mesenchyme development|mammary gland bud formation|membranous septum morphogenesis|mesenchymal cell differentiation involved in lung development|mesenchymal cell proliferation involved in lung development|midbrain development|multicellular organism growth|negative regulation of transcription from RNA polymerase II promoter|odontogenesis|organ growth|otic vesicle formation|outflow tract septum morphogenesis|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell cycle|positive regulation of cell division|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of ERK1 and ERK2 cascade|positive regulation of mesenchymal cell proliferation|positive regulation of transcription from RNA polymerase II promoter|post-embryonic development|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis|prostate epithelial cord elongation|pyramidal neuron development|regulation of branching involved in prostate gland morphogenesis|regulation of cell fate commitment|regulation of fibroblast growth factor receptor signaling pathway|regulation of multicellular organism growth|regulation of smooth muscle cell differentiation|regulation of smoothened signaling pathway|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development|ureteric bud development|ventricular cardiac muscle tissue morphogenesis|ventricular zone neuroblast division	cell cortex|cell surface|excitatory synapse|extracellular region|integral to membrane|nucleus|plasma membrane	ATP binding|fibroblast growth factor binding|fibroblast growth factor binding|fibroblast growth factor receptor activity|heparin binding|protein binding			endometrium(44)|skin(28)|lung(11)|ovary(4)|cervix(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|soft_tissue(1)|central_nervous_system(1)	96		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	Palifermin(DB00039)	CAAGGAGTTATTTTTTTTTTT	0.393		5	Mis		gastric. NSCLC|endometrial		Crouzon|Pfeiffer|and Apert syndromes		Apert_syndrome|Saethre-Chotzen_syndrome				4	2	---	---	---	---	
ST5	6764	broad.mit.edu	37	11	8738009	8738009	+	Intron	DEL	C	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8738009delC	uc001mgt.2	-						ST5_uc009yfr.2_Intron|ST5_uc001mgu.2_Intron|ST5_uc001mgv.2_Intron|ST5_uc010rbq.1_Intron|ST5_uc010rbp.1_Intron	NM_213618	NP_998783	P78524	ST5_HUMAN	suppression of tumorigenicity 5 isoform 1						positive regulation of ERK1 and ERK2 cascade		protein binding			upper_aerodigestive_tract(1)	1				Epithelial(150;2.63e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0352)		ATCCTTGTCGCGGACCCTGTC	0.587													4	2	---	---	---	---	
TPH1	7166	broad.mit.edu	37	11	18042322	18042322	+	3'UTR	DEL	A	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18042322delA	uc001mnp.2	-	10					TPH1_uc009yhe.2_RNA	NM_004179	NP_004170	P17752	TPH1_HUMAN	tryptophan hydroxylase 1						aromatic amino acid family metabolic process|hormone biosynthetic process|serotonin biosynthetic process	cytosol	amino acid binding|iron ion binding|tryptophan 5-monooxygenase activity				0					L-Tryptophan(DB00150)|Tetrahydrobiopterin(DB00360)	AGCTGCTACCAAAAAAAAAAA	0.303													5	4	---	---	---	---	
QSER1	79832	broad.mit.edu	37	11	32977177	32977178	+	Intron	INS	-	T	T			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32977177_32977178insT	uc001mty.2	+						QSER1_uc001mtz.1_Intron|QSER1_uc001mua.2_Intron	NM_001076786	NP_001070254	Q2KHR3	QSER1_HUMAN	glutamine and serine rich 1											ovary(3)|central_nervous_system(2)|skin(1)	6	Breast(20;0.158)					TATTGTTTAACTTTTTTTTTTA	0.262													4	2	---	---	---	---	
AMBRA1	55626	broad.mit.edu	37	11	46567012	46567012	+	Intron	DEL	A	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46567012delA	uc010rgu.1	-						AMBRA1_uc010rgt.1_5'Flank|AMBRA1_uc009ylc.1_Intron|AMBRA1_uc001ncu.1_Intron|AMBRA1_uc001ncv.2_Intron|AMBRA1_uc001ncw.2_Intron|AMBRA1_uc001ncx.2_Intron	NM_017749	NP_060219	Q9C0C7	AMRA1_HUMAN	activating molecule in beclin-1-regulated						autophagy|cell differentiation|nervous system development	autophagic vacuole|cytoplasmic vesicle				large_intestine(1)|ovary(1)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(35;0.0435)|Lung(87;0.182)		accctgtctcaaaaaaaaaaT	0.219													4	2	---	---	---	---	
SLC39A13	91252	broad.mit.edu	37	11	47378844	47378844	+	Intron	DEL	C	-	-	rs11290095		TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47378844delC	uc001nfd.2	+						SPI1_uc001nfb.1_Intron|SPI1_uc001nfc.1_Intron			Q96H72	S39AD_HUMAN	RecName: Full=Zinc transporter ZIP13; AltName: Full=Zrt- and Irt-like protein 13;          Short=ZIP-13; AltName: Full=Solute carrier family 39 member 13; AltName: Full=LIV-1 subfamily of ZIP zinc transporter 9; AltName: Full=LZT-Hs9;						zinc ion transport	integral to membrane	metal ion transmembrane transporter activity				0				Lung(87;0.0936)		GCTCACTTATCACTCACACGC	0.303													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	59244444	59244444	+	IGR	DEL	A	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59244444delA								OR4D6 (19067 upstream) : OR4D10 (459 downstream)																							CCACAACATTAAAAAAAAAAC	0.343													4	2	---	---	---	---	
EEF1G	1937	broad.mit.edu	37	11	62339883	62339884	+	Intron	INS	-	T	T			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62339883_62339884insT	uc001ntm.1	-						EEF1G_uc010rlw.1_Intron|EEF1G_uc001ntn.1_Intron	NM_001404	NP_001395	P26641	EF1G_HUMAN	eukaryotic translation elongation factor 1						response to virus	cytosol|eukaryotic translation elongation factor 1 complex	protein binding|translation elongation factor activity				0						atagctctgtattttttttcac	0.243													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	91495000	91495001	+	IGR	INS	-	A	A	rs147350711	by1000genomes	TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:91495000_91495001insA								MIR1261 (892630 upstream) : FAT3 (590261 downstream)																							TAGAACAAAAGAAAAAAGACCA	0.450													4	2	---	---	---	---	
RDX	5962	broad.mit.edu	37	11	110104422	110104423	+	Intron	INS	-	GTC	GTC	rs151016852	by1000genomes	TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110104422_110104423insGTC	uc001pku.2	-						RDX_uc009yxx.1_Intron|RDX_uc009yxy.2_Intron|RDX_uc009yxz.2_Intron|RDX_uc009yya.2_Intron|RDX_uc001pks.2_Intron|RDX_uc001pkt.2_Intron|RDX_uc010rwe.1_Intron	NM_002906	NP_002897	P35241	RADI_HUMAN	radixin						actin filament capping	cleavage furrow|cytoskeleton|extrinsic to membrane|Golgi apparatus|nucleolus|plasma membrane	actin binding				0		all_cancers(61;7.18e-13)|all_epithelial(67;2.61e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.13e-06)|BRCA - Breast invasive adenocarcinoma(274;9.75e-06)|all cancers(92;5.9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0248)		GTGAGCTTCAAAGTGACAGATT	0.099													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	111760184	111760185	+	IGR	INS	-	T	T	rs34987928		TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111760184_111760185insT								C11orf1 (5389 upstream) : CRYAB (19165 downstream)																							TTCCGACtttcttttttttttt	0.233													11	5	---	---	---	---	
SORL1	6653	broad.mit.edu	37	11	121340515	121340515	+	Intron	DEL	A	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121340515delA	uc001pxx.2	+							NM_003105	NP_003096	Q92673	SORL_HUMAN	sortilin-related receptor containing LDLR class						cholesterol metabolic process|lipid transport|receptor-mediated endocytosis	integral to plasma membrane|low-density lipoprotein particle	low-density lipoprotein particle binding|transmembrane receptor activity			ovary(5)|breast(4)|large_intestine(2)|skin(2)|central_nervous_system(1)|pancreas(1)	15		Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113)		BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108)		CCAAAATAGCAGGGGACTCAT	0.428													4	2	---	---	---	---	
HDAC7	51564	broad.mit.edu	37	12	48184817	48184818	+	Intron	INS	-	C	C	rs147772246	by1000genomes	TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48184817_48184818insC	uc010slo.1	-						HDAC7_uc009zku.2_Intron|HDAC7_uc001rqe.2_Intron|HDAC7_uc001rqj.3_Intron|HDAC7_uc001rqk.3_Intron|HDAC7_uc010slp.1_5'Flank	NM_015401	NP_056216	Q8WUI4	HDAC7_HUMAN	histone deacetylase 7 isoform a						negative regulation of interleukin-2 production|negative regulation of osteoblast differentiation|positive regulation of cell migration involved in sprouting angiogenesis|transcription, DNA-dependent	cytoplasm|histone deacetylase complex	activating transcription factor binding|histone deacetylase activity (H3-K16 specific)|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|protein kinase C binding|repressing transcription factor binding			lung(1)|breast(1)	2				GBM - Glioblastoma multiforme(48;0.137)		CCTTCTAGGGGAAGGCTTAGGC	0.594													6	5	---	---	---	---	
RHEBL1	121268	broad.mit.edu	37	12	49463362	49463374	+	Intron	DEL	CCTCCACTCTTCC	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49463362_49463374delCCTCCACTCTTCC	uc001rtc.1	-						RHEBL1_uc001rtd.1_Intron|RHEBL1_uc009zlc.1_Intron	NM_144593	NP_653194	Q8TAI7	REBL1_HUMAN	Ras homolog enriched in brain like 1 precursor						positive regulation of NF-kappaB transcription factor activity|small GTPase mediated signal transduction|TOR signaling cascade	cytoplasm|plasma membrane	GTP binding|GTPase activity|protein binding			lung(1)|breast(1)	2						CTCTTCCAATCCTCCACTCTTCCATTCCTCCAC	0.573													7	4	---	---	---	---	
CPSF6	11052	broad.mit.edu	37	12	69655902	69655903	+	Intron	INS	-	A	A	rs146620973	by1000genomes	TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69655902_69655903insA	uc001sut.3	+						CPSF6_uc001suu.3_Intron|CPSF6_uc010stk.1_Intron	NM_007007	NP_008938	Q16630	CPSF6_HUMAN	cleavage and polyadenylation specific factor 6,						mRNA polyadenylation|protein tetramerization	mRNA cleavage factor complex|paraspeckles|ribonucleoprotein complex	mRNA binding|nucleotide binding|protein binding				0	all_epithelial(5;2.47e-36)|Lung NSC(4;1.1e-32)|all_lung(4;6.26e-31)|Breast(13;1.59e-06)|Esophageal squamous(21;0.187)		Epithelial(6;4.89e-17)|BRCA - Breast invasive adenocarcinoma(5;8.5e-10)|Lung(24;6.04e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.0151)|LUSC - Lung squamous cell carcinoma(43;0.171)|Kidney(9;0.241)			GCTACTAGTTTAATAGATGATG	0.337													4	2	---	---	---	---	
PHLDA1	22822	broad.mit.edu	37	12	76424953	76424955	+	In_Frame_Del	DEL	TGG	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76424953_76424955delTGG	uc001sxu.2	-	1	602_604	c.567_569delCCA	c.(565-570)CACCAG>CAG	p.H189del		NM_007350	NP_031376	Q8WV24	PHLA1_HUMAN	pleckstrin homology-like domain, family A,	189	PH.|Poly-Gln.				apoptosis	cytoplasmic vesicle membrane|nucleolus|plasma membrane	protein binding				0		Colorectal(145;0.09)				ctgctgctgctggtgttgcagct	0.468													9	4	---	---	---	---	
TCTN1	79600	broad.mit.edu	37	12	111084202	111084202	+	Intron	DEL	T	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111084202delT	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						ATTTTAAAGCttttttttttt	0.214													4	3	---	---	---	---	
C12orf43	64897	broad.mit.edu	37	12	121443031	121443031	+	Intron	DEL	A	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121443031delA	uc001tzh.1	-						C12orf43_uc009zxa.1_Intron|C12orf43_uc010szo.1_Intron|C12orf43_uc010szp.1_Intron|C12orf43_uc001tzi.1_Intron	NM_022895	NP_075046	Q96C57	CL043_HUMAN	hypothetical protein LOC64897												0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					aaagagaaacaaaaaaaaaat	0.025													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	126653265	126653265	+	IGR	DEL	T	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:126653265delT								TMEM132B (509676 upstream) : LOC100128554 (273762 downstream)																							ATGCTGCAGCTTTTTCTTATC	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	59783742	59783743	+	IGR	INS	-	G	G	rs144037370	by1000genomes	TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:59783742_59783743insG								None (None upstream) : DIAPH3 (455982 downstream)																							ATATACTGGGCGGGGGGGAAAA	0.351													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	111604153	111604153	+	IGR	DEL	A	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111604153delA								ANKRD10 (36737 upstream) : ARHGEF7 (163471 downstream)																							AAGAACATGGAAAAAATGGGA	0.368													4	2	---	---	---	---	
ADCY4	196883	broad.mit.edu	37	14	24799926	24799926	+	Intron	DEL	C	-	-	rs76270919		TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24799926delC	uc001wov.2	-						ADCY4_uc001wow.2_Intron|ADCY4_uc010toh.1_Intron|ADCY4_uc001wox.2_Intron|ADCY4_uc001woy.2_Intron	NM_139247	NP_640340	Q8NFM4	ADCY4_HUMAN	adenylate cyclase 4						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|integral to membrane|plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding|protein binding			ovary(1)|lung(1)|pancreas(1)	3				GBM - Glioblastoma multiforme(265;0.0192)		CAGAACGTCTCTATAGATTTG	0.493													2	5	---	---	---	---	
FOXN3	1112	broad.mit.edu	37	14	89876303	89876303	+	Intron	DEL	C	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89876303delC	uc001xxo.3	-						FOXN3_uc001xxn.3_Intron|FOXN3_uc010atk.2_Intron	NM_001085471	NP_001078940	O00409	FOXN3_HUMAN	checkpoint suppressor 1 isoform 1						DNA damage checkpoint|embryo development|G2 phase of mitotic cell cycle|negative regulation of transcription, DNA-dependent|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein C-terminus binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			skin(2)|ovary(1)	3						AAAATAAGGACCTGGGGAGGA	0.458													4	2	---	---	---	---	
IFI27L1	122509	broad.mit.edu	37	14	94568638	94568639	+	Intron	INS	-	C	C	rs146844483	by1000genomes	TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94568638_94568639insC	uc001ycl.2	+						IFI27L1_uc001yck.2_Intron	NM_206949	NP_996832	Q96BM0	I27L1_HUMAN	interferon, alpha-inducible protein 27-like 1							integral to membrane					0						TCCTCTTCGGGCAGTGGCCTGC	0.589													4	5	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	106846004	106846005	+	Intron	INS	-	A	A			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106846004_106846005insA	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0						TACAAATAAAGAAAAAAAAACA	0.426													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	22488189	22488189	+	IGR	DEL	T	-	-	rs112177113		TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22488189delT								OR4N3P (73804 upstream) : MIR1268 (25040 downstream)																							TGTCTCCAGATAACAATAATG	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	37546474	37546475	+	IGR	INS	-	TAT	TAT	rs147091078	by1000genomes	TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:37546474_37546475insTAT								MEIS2 (152974 upstream) : TMCO5A (680352 downstream)																							aaaattGATTCTATTATACTTA	0.262													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	39156940	39156941	+	IGR	INS	-	T	T	rs66807263		TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:39156940_39156941insT								C15orf53 (164701 upstream) : C15orf54 (385944 downstream)																							aataaagccacccaggtggtaa	0.153													3	3	---	---	---	---	
MYO5A	4644	broad.mit.edu	37	15	52720402	52720403	+	Intron	INS	-	C	C			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52720402_52720403insC	uc002aby.2	-						MYO5A_uc002abx.3_Intron|MYO5A_uc010uge.1_Intron	NM_000259	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA isoform 1						actin filament-based movement|transport	cytoplasm|growth cone|myosin complex|ruffle	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(3)|central_nervous_system(1)	4				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)		ATTTTTAGCAAAATTATGTAAG	0.337													4	2	---	---	---	---	
MAP2K1	5604	broad.mit.edu	37	15	66739549	66739549	+	Intron	DEL	T	-	-	rs113189634		TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66739549delT	uc010bhq.2	+						MAP2K1_uc010ujp.1_Intron	NM_002755	NP_002746	Q02750	MP2K1_HUMAN	mitogen-activated protein kinase kinase 1						activation of MAPK activity|activation of MAPKK activity|axon guidance|cell cycle arrest|cellular senescence|epidermal growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of cell proliferation|nerve growth factor receptor signaling pathway|Ras protein signal transduction|stress-activated MAPK cascade|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	cytosol|plasma membrane	ATP binding|MAP kinase kinase activity|protein serine/threonine kinase activity|protein tyrosine kinase activity				0						CCTGGATGCATTTTTTTTTTT	0.458									Cardiofaciocutaneous_syndrome				4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	88062432	88062432	+	IGR	DEL	A	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88062432delA								AGBL1 (490149 upstream) : NCRNA00052 (57728 downstream)																							aacaggctataaattggaggt	0.000													4	2	---	---	---	---	
HMOX2	3163	broad.mit.edu	37	16	4538827	4538827	+	Intron	DEL	T	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4538827delT	uc010bts.2	+						HMOX2_uc002cwr.3_Intron|HMOX2_uc002cwq.3_Intron|HMOX2_uc002cws.3_Intron	NM_001127206	NP_001120678	P30519	HMOX2_HUMAN	heme oxygenase (decyclizing) 2						cellular iron ion homeostasis|heme catabolic process|heme oxidation|response to hypoxia|transmembrane transport	endoplasmic reticulum membrane|microsome|plasma membrane	electron carrier activity|heme oxygenase (decyclizing) activity|metal ion binding|protein binding				0					NADH(DB00157)	TGTACAtttcttttttttttt	0.214													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33537029	33537030	+	IGR	INS	-	T	T			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33537029_33537030insT								SLC6A10P (640566 upstream) : MIR1826 (428478 downstream)																							TTTTCCAACAATTTTTTTTCAG	0.292													11	5	---	---	---	---	
OGFOD1	55239	broad.mit.edu	37	16	56510317	56510317	+	3'UTR	DEL	A	-	-	rs76812608		TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56510317delA	uc002ejb.2	+	13					OGFOD1_uc002ejc.2_3'UTR	NM_018233	NP_060703	Q8N543	OGFD1_HUMAN	2-oxoglutarate and iron-dependent oxygenase								iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			skin(1)	1					Vitamin C(DB00126)	TCTCTTGATTAAAAAAAAAAA	0.294													3	3	---	---	---	---	
MPRIP	23164	broad.mit.edu	37	17	17064775	17064776	+	Intron	INS	-	C	C	rs72535824		TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17064775_17064776insC	uc002gqu.1	+						MPRIP_uc002gqv.1_Intron|MPRIP_uc002gqw.1_Intron	NM_201274	NP_958431	Q6WCQ1	MPRIP_HUMAN	myosin phosphatase-Rho interacting protein							cytoplasm|cytoskeleton	actin binding				0						CTGAGCAGGGGTGTCTCCCAGG	0.569													5	4	---	---	---	---	
RAI1	10743	broad.mit.edu	37	17	17628679	17628679	+	Intron	DEL	G	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17628679delG	uc002grm.2	+							NM_030665	NP_109590	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1							cytoplasm|nucleus	zinc ion binding			central_nervous_system(1)|skin(1)	2				READ - Rectum adenocarcinoma(1115;0.0276)		ACGCTGCTCCGGTGACCCGGA	0.483													3	5	---	---	---	---	
ACACA	31	broad.mit.edu	37	17	35550600	35550600	+	Intron	DEL	A	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35550600delA	uc002hnm.2	-						ACACA_uc002hnk.2_Intron|ACACA_uc002hnl.2_Intron|ACACA_uc002hnn.2_Intron|ACACA_uc002hno.2_Intron|ACACA_uc010cuy.2_Intron	NM_198836	NP_942133	Q13085	ACACA_HUMAN	acetyl-Coenzyme A carboxylase alpha isoform 2						acetyl-CoA metabolic process|energy reserve metabolic process|fatty acid biosynthetic process|long-chain fatty-acyl-CoA biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|triglyceride biosynthetic process	cytosol	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			large_intestine(1)|ovary(1)	2		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	CTCCCAGGGGAAAAAAAATGT	0.348													4	2	---	---	---	---	
CRHR1	1394	broad.mit.edu	37	17	43853968	43853968	+	Intron	DEL	A	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43853968delA	uc002ijp.2	+						CRHR1_uc010wjx.1_Intron			P34998	CRFR1_HUMAN	SubName: Full=cDNA FLJ60308, highly similar to Corticotropin-releasing factor receptor 1;						female pregnancy|immune response|parturition	integral to plasma membrane	corticotrophin-releasing factor receptor activity|protein binding			lung(3)	3	Colorectal(2;0.0416)			BRCA - Breast invasive adenocarcinoma(366;0.161)		gttgttttttaaaatctgtta	0.040													4	2	---	---	---	---	
FN3K	64122	broad.mit.edu	37	17	80696192	80696193	+	Intron	INS	-	G	G	rs140281589	by1000genomes	TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80696192_80696193insG	uc010wvs.1	+						FN3K_uc002kfw.1_5'UTR	NM_022158	NP_071441	Q9H479	FN3K_HUMAN	fructosamine 3 kinase						fructoselysine metabolic process		fructosamine-3-kinase activity				0	Breast(20;0.000523)|all_neural(118;0.0952)		BRCA - Breast invasive adenocarcinoma(99;0.0344)|OV - Ovarian serous cystadenocarcinoma(97;0.061)			TCGTCTCCGACGGGGGGCCCCT	0.653													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	70664098	70664099	+	IGR	DEL	AC	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:70664098_70664099delAC								NETO1 (129288 upstream) : None (None downstream)																							ACTCGAGGAAACACACACACAG	0.465													4	2	---	---	---	---	
PNPLA6	10908	broad.mit.edu	37	19	7623628	7623629	+	Intron	INS	-	CTC	CTC	rs149281719		TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7623628_7623629insCTC	uc010xjq.1	+						PNPLA6_uc002mgq.1_Intron|PNPLA6_uc010xjp.1_Intron|PNPLA6_uc002mgr.1_Intron|PNPLA6_uc002mgs.2_Intron|PNPLA6_uc002mgt.1_Intron	NM_006702	NP_006693	Q8IY17	PLPL6_HUMAN	neuropathy target esterase isoform b						cell death|lipid catabolic process|phosphatidylcholine metabolic process	endoplasmic reticulum membrane|integral to membrane	lysophospholipase activity			ovary(3)	3						GTATTCTCTCTTTTTTTTTTGC	0.545													4	2	---	---	---	---	
ILF3	3609	broad.mit.edu	37	19	10790178	10790178	+	Intron	DEL	T	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10790178delT	uc002mpn.2	+						ILF3_uc002mpm.2_Intron|ILF3_uc002mpl.2_Intron|ILF3_uc002mpk.2_Intron|ILF3_uc010xli.1_Intron|ILF3_uc002mpo.2_Intron|ILF3_uc002mpp.2_Intron	NM_012218	NP_036350	Q12906	ILF3_HUMAN	interleukin enhancer binding factor 3 isoform a						M phase|negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	mitochondrion|nucleolus|ribonucleoprotein complex	DNA binding|double-stranded RNA binding|protein binding|protein binding			ovary(3)	3			Epithelial(33;6.86e-06)|all cancers(31;1.65e-05)			AGTTGCACCCTTTTTTTTTTC	0.428													4	3	---	---	---	---	
HSH2D	84941	broad.mit.edu	37	19	16254263	16254263	+	Intron	DEL	G	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16254263delG	uc002ndp.3	+						HSH2D_uc002ndr.2_5'Flank|HSH2D_uc010ead.2_5'Flank	NM_032855	NP_116244	Q96JZ2	HSH2D_HUMAN	hematopoietic SH2 domain containing							cytoplasm|nucleus					0						ccaggagtcagggggcctgca	0.119													4	2	---	---	---	---	
HAMP	57817	broad.mit.edu	37	19	35775510	35775510	+	Intron	DEL	T	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35775510delT	uc002nyw.2	+							NM_021175	NP_066998	P81172	HEPC_HUMAN	hepcidin antimicrobial peptide preproprotein						defense response to bacterium|defense response to fungus|immune response|killing of cells of other organism	extracellular region	hormone activity			central_nervous_system(1)	1	all_lung(56;2.37e-08)|Lung NSC(56;3.66e-08)|Esophageal squamous(110;0.162)		Epithelial(14;7.4e-20)|OV - Ovarian serous cystadenocarcinoma(14;6.47e-19)|all cancers(14;4.17e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)			atctgggaggttttttttttt	0.209													3	5	---	---	---	---	
CIC	23152	broad.mit.edu	37	19	42792902	42792902	+	Intron	DEL	T	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42792902delT	uc002otf.1	+							NM_015125	NP_055940	Q96RK0	CIC_HUMAN	capicua homolog						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding			ovary(4)|breast(4)|lung(1)|central_nervous_system(1)|skin(1)	11		Prostate(69;0.00682)				TGGGTGGTGGTTTTTTTTTTT	0.542			T	DUX4	soft tissue sarcoma								6	3	---	---	---	---	
ZNF155	7711	broad.mit.edu	37	19	44489179	44489179	+	Intron	DEL	A	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44489179delA	uc002oxy.1	+						ZNF155_uc002oxz.1_Intron|ZNF155_uc010xwt.1_Intron	NM_003445	NP_003436	Q12901	ZN155_HUMAN	zinc finger protein 155							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			large_intestine(1)|ovary(1)	2		Prostate(69;0.0352)				TTCTCTTTTTAAAAAAAAGTT	0.269													4	2	---	---	---	---	
APOC1P1	342	broad.mit.edu	37	19	45431268	45431268	+	Intron	DEL	A	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45431268delA	uc010eju.2	+											Homo sapiens clone DKFZp781C1677 mRNA sequence.												0						GAACAGATTGAAAAAAAAAAC	0.527													6	3	---	---	---	---	
CABP5	56344	broad.mit.edu	37	19	48537049	48537049	+	Intron	DEL	C	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48537049delC	uc002phu.1	-							NM_019855	NP_062829	Q9NP86	CABP5_HUMAN	calcium binding protein 5						signal transduction	cytoplasm	calcium ion binding			skin(1)	1		all_cancers(25;1.86e-08)|all_lung(116;1.14e-06)|all_epithelial(76;1.16e-06)|Lung NSC(112;2.54e-06)|all_neural(266;0.0138)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;4.09e-05)|all cancers(93;0.000322)|Epithelial(262;0.01)|GBM - Glioblastoma multiforme(486;0.058)		aagggagtagcataagccaca	0.045													4	2	---	---	---	---	
PLEKHA4	57664	broad.mit.edu	37	19	49351415	49351415	+	Intron	DEL	T	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49351415delT	uc002pkx.2	-						PLEKHA4_uc002pkw.1_Intron|PLEKHA4_uc010eml.2_Intron	NM_020904	NP_065955	Q9H4M7	PKHA4_HUMAN	pleckstrin homology domain containing family A							cytoplasm|membrane	1-phosphatidylinositol binding			ovary(1)|central_nervous_system(1)|skin(1)	3		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;0.000108)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.00027)|all cancers(93;0.00084)|GBM - Glioblastoma multiforme(486;0.0244)|Epithelial(262;0.0364)		TTGGGATTTATTTTTTTTCCC	0.284													4	2	---	---	---	---	
TSKS	60385	broad.mit.edu	37	19	50265062	50265062	+	Intron	DEL	A	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50265062delA	uc002ppm.2	-							NM_021733	NP_068379	Q9UJT2	TSKS_HUMAN	testis-specific kinase substrate								protein binding			large_intestine(1)|skin(1)	2		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00153)|GBM - Glioblastoma multiforme(134;0.0145)		ctaaaggaagaaaaaaaaAAG	0.234													5	5	---	---	---	---	
MYH14	79784	broad.mit.edu	37	19	50752588	50752590	+	Intron	DEL	CTT	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50752588_50752590delCTT	uc002prr.1	+						MYH14_uc010enu.1_Intron|MYH14_uc002prq.1_Intron	NM_024729	NP_079005	Q7Z406	MYH14_HUMAN	myosin, heavy chain 14 isoform 2						axon guidance|regulation of cell shape	myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			central_nervous_system(1)	1		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		tctctgtccccttctctctctgg	0.010													4	5	---	---	---	---	
KLK5	25818	broad.mit.edu	37	19	51453036	51453040	+	Intron	DEL	CCCCC	-	-	rs59705989		TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51453036_51453040delCCCCC	uc002pue.2	-						KLK5_uc002puf.2_Intron|KLK5_uc002pug.2_Intron	NM_001077491	NP_001070959	Q9Y337	KLK5_HUMAN	kallikrein-related peptidase 5 preproprotein						epidermis development|positive regulation of G-protein coupled receptor protein signaling pathway|proteolysis	extracellular space	protein binding|serine-type endopeptidase activity				0		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00379)|GBM - Glioblastoma multiforme(134;0.00888)		ctccaTGAcacccccacccccactt	0.229													10	5	---	---	---	---	
KLK5	25818	broad.mit.edu	37	19	51453042	51453056	+	Intron	DEL	CCCCCACTTCCCCAC	-	-	rs112507586	by1000genomes	TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51453042_51453056delCCCCCACTTCCCCAC	uc002pue.2	-						KLK5_uc002puf.2_Intron|KLK5_uc002pug.2_Intron	NM_001077491	NP_001070959	Q9Y337	KLK5_HUMAN	kallikrein-related peptidase 5 preproprotein						epidermis development|positive regulation of G-protein coupled receptor protein signaling pathway|proteolysis	extracellular space	protein binding|serine-type endopeptidase activity				0		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00379)|GBM - Glioblastoma multiforme(134;0.00888)		GAcacccccacccccacttccccacccccaccccc	0.260													10	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	30208382	30208382	+	IGR	DEL	G	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30208382delG								ID1 (14069 upstream) : COX4I2 (17309 downstream)																							atctaccaaaggatgcccaat	0.090													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	20360251	20360256	+	IGR	DEL	GAGTGT	-	-	rs143927554		TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:20360251_20360256delGAGTGT								TMPRSS15 (584281 upstream) : None (None downstream)																							gttgagggcagagtgtgagtgtgagt	0.044													5	3	---	---	---	---	
C21orf62	56245	broad.mit.edu	37	21	34166854	34166854	+	Intron	DEL	A	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34166854delA	uc010glz.2	-						C21orf49_uc002yqs.2_Intron|C21orf49_uc002yqu.3_Intron|C21orf49_uc002yqt.2_Intron|C21orf62_uc011adt.1_Intron|C21orf62_uc011adu.1_Intron	NM_001162495	NP_001155967	Q9NYP8	CU062_HUMAN	hypothetical protein LOC56245											ovary(1)	1		Myeloproliferative disorder(46;0.0255)				CAGCTTATGGAAAAGGAACCC	0.418													4	2	---	---	---	---	
DOPEY2	9980	broad.mit.edu	37	21	37577654	37577654	+	Intron	DEL	T	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37577654delT	uc002yvg.2	+						DOPEY2_uc011aeb.1_Intron	NM_005128	NP_005119	Q9Y3R5	DOP2_HUMAN	pad-1-like						endoplasmic reticulum organization|Golgi to endosome transport|multicellular organismal development|protein transport	Golgi membrane				ovary(1)|central_nervous_system(1)	2						GGAAGTTGGGTTTTTTTTTTT	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	45429012	45429012	+	IGR	DEL	T	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45429012delT								AGPAT3 (21538 upstream) : TRAPPC10 (3194 downstream)																							tgttaactgcttttttttttt	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	16920274	16920275	+	IGR	DEL	AT	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:16920274_16920275delAT								OR11H1 (470470 upstream) : CCT8L2 (151373 downstream)																							TTATAGTGACATGTATGAAAAC	0.267													11	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	16955063	16955065	+	IGR	DEL	ATT	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:16955063_16955065delATT								OR11H1 (505259 upstream) : CCT8L2 (116583 downstream)																							TATGTCTCTCATTATTTTGGTAA	0.187													11	7	---	---	---	---	
P2RX6	9127	broad.mit.edu	37	22	21372024	21372025	+	Intron	DEL	CA	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21372024_21372025delCA	uc010gsu.1	+						P2RX6_uc002ztz.2_Intron|P2RX6_uc010gst.1_Intron|P2RX6_uc002zua.2_Intron|P2RX6_uc002zuc.1_Intron	NM_005446	NP_005437	O15547	P2RX6_HUMAN	purinergic receptor P2X6 isoform 1						muscle contraction|protein homooligomerization	cell junction|cytoplasm|integral to plasma membrane	ATP binding|extracellular ATP-gated cation channel activity|identical protein binding|purinergic nucleotide receptor activity				0						catacacatgcacacacacaca	0.208													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	27282808	27282808	+	IGR	DEL	T	-	-	rs77242810		TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27282808delT								MIAT (167859 upstream) : MN1 (861458 downstream)																							AGTCCCGTTCTTTTTTTTTTG	0.408													7	4	---	---	---	---	
TEX11	56159	broad.mit.edu	37	X	69944900	69944901	+	Intron	INS	-	A	A	rs34205821	by1000genomes	TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69944900_69944901insA	uc004dyl.2	-						TEX11_uc004dyk.2_5'Flank|TEX11_uc004dym.2_Intron	NM_001003811	NP_001003811	Q8IYF3	TEX11_HUMAN	testis expressed sequence 11 isoform 1								protein binding			ovary(3)|breast(1)|skin(1)	5	Renal(35;0.156)					CAGCTTTTTTTAAAAAAAAAAA	0.347													7	6	---	---	---	---	
WDR44	54521	broad.mit.edu	37	X	117519621	117519621	+	Intron	DEL	A	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117519621delA	uc004eqn.2	+						WDR44_uc004eqo.2_Intron|WDR44_uc011mtr.1_Intron|MIR1277_hsa-mir-1277|MI0006419_5'Flank	NM_019045	NP_061918	Q5JSH3	WDR44_HUMAN	WD repeat domain 44 protein							cytosol|endosome membrane|Golgi apparatus|perinuclear region of cytoplasm				lung(2)|upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)	5						acttaaagttaaaaaaaaaaa	0.005													4	4	---	---	---	---	
CUL4B	8450	broad.mit.edu	37	X	119660917	119660917	+	Intron	DEL	C	-	-			TCGA-CJ-4641-01A-02D-1386-10	TCGA-CJ-4641-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:119660917delC	uc004esw.2	-						CUL4B_uc010nqq.2_Intron|CUL4B_uc004esv.2_Intron	NM_003588	NP_003579	Q13620	CUL4B_HUMAN	cullin 4B isoform 1						cell cycle|DNA repair|ubiquitin-dependent protein catabolic process	Cul4B-RING ubiquitin ligase complex|nucleus	protein binding|ubiquitin protein ligase binding			lung(1)|central_nervous_system(1)|pancreas(1)	3						GTTGAAGAttctttttttttt	0.100													5	3	---	---	---	---	
