Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	t_alt_count	t_ref_count	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	filter
WASH7P	653635	broad.mit.edu	37	1	14933	14933	+	Intron	SNP	G	A	A	rs138566748	by1000genomes	TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:14933G>A	uc009vis.2	-						WASH7P_uc009vit.2_Intron|WASH7P_uc001aae.3_Intron|WASH7P_uc009viu.2_Intron|WASH7P_uc001aab.3_Intron|WASH7P_uc001aah.3_Intron|WASH7P_uc009vir.2_Intron|WASH7P_uc009viq.2_Intron|WASH7P_uc001aac.3_Intron|WASH7P_uc009viv.2_RNA|WASH7P_uc009viw.2_RNA					Homo sapiens cDNA FLJ31670 fis, clone NT2RI2004984.												0						GAATTACAAGGTGCTGGCCCA	0.592													3	8	---	---	---	---	PASS
WASH7P	653635	broad.mit.edu	37	1	14976	14976	+	RNA	SNP	G	A	A			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:14976G>A	uc009vis.2	-	3		c.369C>T			WASH7P_uc009vit.2_RNA|WASH7P_uc001aae.3_RNA|WASH7P_uc009viu.2_RNA|WASH7P_uc001aab.3_RNA|WASH7P_uc001aah.3_RNA|WASH7P_uc009vir.2_RNA|WASH7P_uc009viq.2_Intron|WASH7P_uc001aac.3_RNA|WASH7P_uc009viv.2_RNA|WASH7P_uc009viw.2_RNA					Homo sapiens cDNA FLJ31670 fis, clone NT2RI2004984.												0						CTACCCTTGCGCCTCATGACC	0.582													3	6	---	---	---	---	PASS
BMP8B	656	broad.mit.edu	37	1	40225989	40225989	+	3'UTR	SNP	C	A	A			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40225989C>A	uc001cdz.1	-	7					PPIE_uc001cdv.2_Intron|PPIE_uc001cdw.2_Intron	NM_001720	NP_001711	P34820	BMP8B_HUMAN	bone morphogenetic protein 8B preproprotein						cartilage development|cell differentiation|growth|ossification	extracellular space	cytokine activity|growth factor activity				0	all_cancers(7;5.56e-14)|all_lung(5;3.88e-17)|all_epithelial(6;3.78e-16)|Lung NSC(20;7.03e-07)|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;1.87e-18)|Epithelial(16;1.92e-17)|all cancers(16;4.03e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			TCCTCCCTGGCAATGCCCCGG	0.622													5	26	---	---	---	---	PASS
JAK1	3716	broad.mit.edu	37	1	65304164	65304164	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65304164G>A	uc001dbu.1	-	21	3200	c.2951C>T	c.(2950-2952)GCC>GTC	p.A984V	JAK1_uc009wam.1_Missense_Mutation_p.A972V|JAK1_uc009wal.1_Missense_Mutation_p.A161V	NM_002227	NP_002218	P23458	JAK1_HUMAN	janus kinase 1	984	Protein kinase 2.				interferon-gamma-mediated signaling pathway|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|response to antibiotic|type I interferon-mediated signaling pathway	cytoskeleton|cytosol|endomembrane system|membrane|nucleus	ATP binding|growth hormone receptor binding|non-membrane spanning protein tyrosine kinase activity	p.E966_K989del(1)		haematopoietic_and_lymphoid_tissue(34)|prostate(7)|soft_tissue(6)|lung(4)|breast(3)|central_nervous_system(2)|liver(2)|large_intestine(1)|stomach(1)|ovary(1)	61				BRCA - Breast invasive adenocarcinoma(111;0.0485)		AATCTGAACGGCATATTTTAG	0.363			Mis		ALL								5	155	---	---	---	---	PASS
COL11A1	1301	broad.mit.edu	37	1	103483375	103483375	+	Splice_Site	SNP	C	A	A			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:103483375C>A	uc001dul.2	-	11	1731	c.1413_splice	c.e11+1	p.R471_splice	COL11A1_uc001duk.2_Splice_Site|COL11A1_uc001dum.2_Splice_Site_p.R483_splice|COL11A1_uc001dun.2_Splice_Site_p.R432_splice|COL11A1_uc009weh.2_Splice_Site_p.R355_splice	NM_001854	NP_001845	P12107	COBA1_HUMAN	alpha 1 type XI collagen isoform A						collagen fibril organization|detection of mechanical stimulus involved in sensory perception of sound|visual perception	collagen type XI	extracellular matrix binding|extracellular matrix structural constituent|protein binding, bridging			ovary(6)|breast(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	12		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		CATTCACTTACCCTATCGCCA	0.403													63	172	---	---	---	---	PASS
CENPF	1063	broad.mit.edu	37	1	214819699	214819699	+	Silent	SNP	G	A	A			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214819699G>A	uc001hkm.2	+	13	6960	c.6786G>A	c.(6784-6786)CAG>CAA	p.Q2262Q		NM_016343	NP_057427	P49454	CENPF_HUMAN	centromere protein F	2358	Potential.|2-1.|2 X 177 AA tandem repeats.|Interaction with NDE1 and NDEL1.				cell differentiation|cell division|cell proliferation|DNA replication|G2 phase of mitotic cell cycle|kinetochore assembly|metaphase plate congression|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|muscle organ development|negative regulation of transcription, DNA-dependent|protein transport|regulation of G2/M transition of mitotic cell cycle|regulation of striated muscle tissue development|response to drug	condensed chromosome outer kinetochore|cytosol|midbody|nuclear envelope|nuclear matrix|perinuclear region of cytoplasm|spindle pole	chromatin binding|dynein binding|protein C-terminus binding|protein homodimerization activity|transcription factor binding			ovary(6)|central_nervous_system(4)|large_intestine(2)|skin(1)	13				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		AGATGCTTCAGAATCAGTTAA	0.408													38	95	---	---	---	---	PASS
HEATR5B	54497	broad.mit.edu	37	2	37255866	37255866	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37255866G>A	uc002rpp.1	-	23	3655	c.3559C>T	c.(3559-3561)CAT>TAT	p.H1187Y		NM_019024	NP_061897	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	1187							binding			ovary(5)|skin(2)|breast(1)	8		all_hematologic(82;0.21)				ATTAGCCAATGAGAAAGTTTT	0.353													47	132	---	---	---	---	PASS
AFF3	3899	broad.mit.edu	37	2	100199360	100199360	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100199360G>T	uc002tag.2	-	16	2929	c.2693C>A	c.(2692-2694)TCT>TAT	p.S898Y	AFF3_uc002taf.2_Missense_Mutation_p.S923Y|AFF3_uc010fiq.1_Missense_Mutation_p.S898Y|AFF3_uc010yvr.1_Missense_Mutation_p.S1051Y|AFF3_uc002tah.1_Missense_Mutation_p.S923Y	NM_002285	NP_002276	P51826	AFF3_HUMAN	AF4/FMR2 family, member 3 isoform 1	898					multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(2)|pancreas(1)|lung(1)|kidney(1)|skin(1)	6						TCGGCTGGAAGAAGTTAAGTC	0.488													54	120	---	---	---	---	PASS
CCDC148	130940	broad.mit.edu	37	2	159312934	159312934	+	Silent	SNP	A	T	T			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:159312934A>T	uc002tzq.2	-	1	281	c.18T>A	c.(16-18)GCT>GCA	p.A6A	PKP4_uc002tzt.1_5'Flank|PKP4_uc002tzu.2_5'Flank|PKP4_uc002tzv.2_5'Flank|PKP4_uc002tzw.2_5'Flank|PKP4_uc002tzx.2_5'Flank|PKP4_uc002tzy.1_5'Flank|CCDC148_uc002tzr.2_5'UTR|CCDC148_uc010foh.2_5'UTR|CCDC148_uc010foi.1_5'UTR|CCDC148_uc010foj.1_5'UTR|CCDC148_uc010fok.1_5'UTR|CCDC148_uc002tzs.1_Silent_p.A6A	NM_138803	NP_620158	Q8NFR7	CC148_HUMAN	coiled-coil domain containing 148	6										ovary(2)	2						CACCTGGAGAAGCAGAAGCTG	0.552													5	26	---	---	---	---	PASS
IL17RE	132014	broad.mit.edu	37	3	9957050	9957050	+	Silent	SNP	C	T	T			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9957050C>T	uc003btu.2	+	17	1680	c.1563C>T	c.(1561-1563)GAC>GAT	p.D521D	CIDEC_uc003bto.2_Intron|IL17RC_uc010hcr.2_5'Flank|IL17RC_uc011ato.1_5'Flank|IL17RC_uc010hcs.2_5'Flank|IL17RC_uc003btz.2_5'Flank|IL17RC_uc011atp.1_5'Flank|IL17RC_uc003bud.2_5'Flank|IL17RC_uc003bua.2_5'Flank|IL17RC_uc003bub.2_5'Flank|IL17RC_uc010hct.2_5'Flank|IL17RC_uc010hcu.2_5'Flank|IL17RC_uc010hcv.2_5'Flank|IL17RC_uc011atq.1_5'Flank|IL17RC_uc003buc.2_5'Flank|IL17RE_uc003btw.2_Silent_p.D521D|IL17RE_uc003btx.2_Silent_p.D405D|IL17RE_uc010hcq.2_3'UTR|IL17RE_uc003bty.2_RNA	NM_153483	NP_705616	Q8NFR9	I17RE_HUMAN	interleukin 17 receptor E isoform 1	521	SEFIR.|Cytoplasmic (Potential).					cytoplasm|extracellular region|integral to membrane	receptor activity			central_nervous_system(1)	1				OV - Ovarian serous cystadenocarcinoma(96;5.34e-64)		GCGGGCGCGACGTGATCGTGG	0.771													2	2	---	---	---	---	PASS
ZBTB11	27107	broad.mit.edu	37	3	101389965	101389965	+	Intron	SNP	A	C	C			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101389965A>C	uc003dve.3	-						ZBTB11_uc003dvf.2_3'UTR	NM_014415	NP_055230	O95625	ZBT11_HUMAN	zinc finger protein ZNF-U69274						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1						AGTAATACAAAACCCTTACCA	0.398													33	65	---	---	---	---	PASS
C3orf70	285382	broad.mit.edu	37	3	184801263	184801263	+	Missense_Mutation	SNP	A	C	C			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184801263A>C	uc003fpd.2	-	2	476	c.285T>G	c.(283-285)ATT>ATG	p.I95M		NM_001025266	NP_001020437	A6NLC5	CC070_HUMAN	hypothetical protein LOC285382	95											0						CTGAGATCTGAATGGTGTTTG	0.507													54	149	---	---	---	---	PASS
BRPF3	27154	broad.mit.edu	37	6	36198303	36198303	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36198303G>T	uc003olv.3	+	13	3759	c.3535G>T	c.(3535-3537)GTG>TTG	p.V1179L	BRPF3_uc010jwb.2_Missense_Mutation_p.V909L|BRPF3_uc011dtj.1_RNA|BRPF3_uc010jwc.2_RNA|BRPF3_uc011dtk.1_Missense_Mutation_p.V845L|BRPF3_uc010jwd.2_Missense_Mutation_p.V81L	NM_015695	NP_056510	Q9ULD4	BRPF3_HUMAN	bromodomain and PHD finger containing, 3	1179					histone H3 acetylation|platelet activation|platelet degranulation	cytosol|extracellular region|MOZ/MORF histone acetyltransferase complex	protein binding|zinc ion binding			ovary(1)|skin(1)	2						CCGCAAGTCAGTGCAGGTGGC	0.612													24	57	---	---	---	---	PASS
BZW2	28969	broad.mit.edu	37	7	16722403	16722403	+	Splice_Site	SNP	A	T	T			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:16722403A>T	uc003stl.2	+	5	518	c.340_splice	c.e5-2	p.V114_splice	BZW2_uc011jxx.1_Splice_Site|BZW2_uc003stm.2_Splice_Site|BZW2_uc003stj.2_Splice_Site_p.V114_splice|BZW2_uc003stk.2_Splice_Site_p.V38_splice|BZW2_uc003stn.1_Splice_Site_p.V114_splice|BZW2_uc003sto.1_Splice_Site|BZW2_uc003stp.2_Splice_Site|BZW2_uc010kua.2_Splice_Site_p.V114_splice	NM_001159767	NP_001153239	Q9Y6E2	BZW2_HUMAN	basic leucine zipper and W2 domains 2						cell differentiation|nervous system development|RNA metabolic process		protein binding			ovary(2)	2	Lung NSC(10;0.0367)|all_lung(11;0.0837)			UCEC - Uterine corpus endometrioid carcinoma (126;0.199)		TTTTTTTTTTAGGTCTTCAAT	0.274													3	44	---	---	---	---	PASS
C8orf44	56260	broad.mit.edu	37	8	67590120	67590120	+	Silent	SNP	C	A	A			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67590120C>A	uc003xwo.1	+	2	330	c.177C>A	c.(175-177)GTC>GTA	p.V59V	SGK3_uc003xwp.2_Intron|C8orf44_uc003xwq.1_Silent_p.V59V	NM_019607	NP_062553	Q96CB5	CH044_HUMAN	hypothetical protein LOC56260	59											0	Breast(64;0.186)		Epithelial(68;0.000959)|OV - Ovarian serous cystadenocarcinoma(28;0.00318)|all cancers(69;0.00363)|BRCA - Breast invasive adenocarcinoma(89;0.149)			cacctgaggtcaggagttcga	0.075													3	25	---	---	---	---	PASS
RALGPS1	9649	broad.mit.edu	37	9	129931020	129931020	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129931020C>A	uc004bqo.1	+	10	1078	c.811C>A	c.(811-813)CTC>ATC	p.L271I	RALGPS1_uc011mab.1_Missense_Mutation_p.L271I|RALGPS1_uc011mac.1_Missense_Mutation_p.L271I|RALGPS1_uc004bqq.3_Missense_Mutation_p.L271I	NM_014636	NP_055451	Q5JS13	RGPS1_HUMAN	Ral GEF with PH domain and SH3 binding motif 1	271	Ras-GEF.				small GTPase mediated signal transduction	cytoplasm|plasma membrane	guanyl-nucleotide exchange factor activity			ovary(1)	1						CATTGAAGAGCTCCAGAAGTT	0.522													15	227	---	---	---	---	PASS
ODF2	4957	broad.mit.edu	37	9	131258144	131258144	+	Intron	SNP	G	T	T			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131258144G>T	uc011mbd.1	+						ODF2_uc004bvb.2_Intron|ODF2_uc011mbe.1_Intron|ODF2_uc004bvc.2_Intron|ODF2_uc004bvd.3_Intron|ODF2_uc004bvh.2_5'UTR	NM_002540	NP_002531	Q5BJF6	ODFP2_HUMAN	outer dense fiber of sperm tails 2 isoform 1						cell differentiation|G2/M transition of mitotic cell cycle|multicellular organismal development|spermatogenesis	centriole|cilium|cytosol|microtubule|spindle pole	protein binding|structural molecule activity			ovary(1)	1						TTTGTCTTTGGAGTTGGGCCT	0.542													5	7	---	---	---	---	PASS
NOTCH1	4851	broad.mit.edu	37	9	139400096	139400096	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139400096C>T	uc004chz.2	-	25	4252	c.4252G>A	c.(4252-4254)GCC>ACC	p.A1418T	NOTCH1_uc004cia.1_Missense_Mutation_p.A648T	NM_017617	NP_060087	P46531	NOTC1_HUMAN	notch1 preproprotein	1418	Extracellular (Potential).|EGF-like 36.				aortic valve morphogenesis|immune response|negative regulation of BMP signaling pathway|negative regulation of cell-substrate adhesion|negative regulation of myoblast differentiation|negative regulation of osteoblast differentiation|negative regulation of transcription, DNA-dependent|Notch receptor processing	cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane	calcium ion binding|protein binding|receptor activity			haematopoietic_and_lymphoid_tissue(791)|upper_aerodigestive_tract(29)|lung(13)|central_nervous_system(10)|breast(9)|large_intestine(1)|skin(1)|oesophagus(1)|pancreas(1)	856	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		TTGAATTTGGCGGGGCACAGG	0.682			T|Mis|O	TRB@	T-ALL					HNSCC(8;0.001)			3	24	---	---	---	---	PASS
HSD17B7P2	158160	broad.mit.edu	37	10	38645343	38645343	+	5'UTR	SNP	C	T	T	rs75687299	by1000genomes	TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38645343C>T	uc010qex.1	+	1					HSD17B7P2_uc001izq.2_RNA|HSD17B7P2_uc010qew.1_5'UTR|HSD17B7P2_uc001izo.1_RNA|HSD17B7P2_uc001izp.1_5'UTR					SubName: Full=cDNA FLJ60462, highly similar to 3-keto-steroid reductase (EC 1.1.1.270);												0						AAAGCAGCGGCGGCGTTTGCT	0.597													6	13	---	---	---	---	PASS
AGAP6	414189	broad.mit.edu	37	10	51748381	51748381	+	5'UTR	SNP	T	C	C			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:51748381T>C	uc001jix.3	+	1						NM_001077665	NP_001071133	Q5VW22	AGAP6_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH						regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding			skin(1)	1						AGACCATCTCTGCAAGTGCAG	0.706													3	14	---	---	---	---	PASS
WEE1	7465	broad.mit.edu	37	11	9610146	9610146	+	Silent	SNP	C	T	T			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9610146C>T	uc001mhs.2	+	11	2191	c.1938C>T	c.(1936-1938)TAC>TAT	p.Y646Y	WEE1_uc001mht.2_Silent_p.Y432Y	NM_003390	NP_003381	P30291	WEE1_HUMAN	WEE1 tyrosine kinase isoform 1	646					blood coagulation|cell cycle checkpoint|cell division|G1/S transition of mitotic cell cycle|G2/M transition of mitotic cell cycle|mitosis|S phase of mitotic cell cycle	nucleoplasm	ATP binding|magnesium ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding|protein serine/threonine kinase activity			central_nervous_system(2)|ovary(1)|breast(1)|skin(1)	5				all cancers(16;4.59e-09)|Epithelial(150;3.15e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0484)		TTACTATATACTGAGCTACTC	0.453													32	64	---	---	---	---	PASS
OR4A15	81328	broad.mit.edu	37	11	55135466	55135466	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55135466A>G	uc010rif.1	+	1	107	c.107A>G	c.(106-108)AAT>AGT	p.N36S		NM_001005275	NP_001005275	Q8NGL6	O4A15_HUMAN	olfactory receptor, family 4, subfamily A,	36	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2						AATAAGAACAATGTGACTGAA	0.398													5	120	---	---	---	---	PASS
MAP3K11	4296	broad.mit.edu	37	11	65375920	65375920	+	Splice_Site	SNP	C	A	A			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65375920C>A	uc001oew.2	-	2	1233	c.740_splice	c.e2-1	p.I247_splice	MAP3K11_uc001oev.2_5'Flank|MAP3K11_uc010rol.1_Splice_Site|MAP3K11_uc001oex.1_Splice_Site	NM_002419	NP_002410	Q16584	M3K11_HUMAN	mitogen-activated protein kinase kinase kinase						activation of JUN kinase activity|cell proliferation|G1 phase of mitotic cell cycle|microtubule-based process|positive regulation of JNK cascade|protein autophosphorylation	centrosome|microtubule	ATP binding|JUN kinase kinase kinase activity|mitogen-activated protein kinase kinase kinase binding|protein homodimerization activity			breast(3)|lung(1)|central_nervous_system(1)|skin(1)	6						AGCAGCAAAACTAGAGAAGAG	0.557													13	33	---	---	---	---	PASS
H2AFJ	55766	broad.mit.edu	37	12	14927825	14927825	+	3'UTR	SNP	C	G	G	rs6645	by1000genomes	TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14927825C>G	uc009zia.2	+	1					H2AFJ_uc001rch.3_RNA	NM_177925	NP_808760	Q9BTM1	H2AJ_HUMAN	H2A histone family, member J						nucleosome assembly	nucleosome|nucleus	DNA binding			ovary(1)	1						AGCTGGCTCCCCCAGCAAAGG	0.617													3	41	---	---	---	---	PASS
KRT2	3849	broad.mit.edu	37	12	53045802	53045802	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53045802C>T	uc001sat.2	-	1	158	c.125G>A	c.(124-126)TGC>TAC	p.C42Y		NM_000423	NP_000414	P35908	K22E_HUMAN	keratin 2	42	Head.				keratinization|keratinocyte activation|keratinocyte migration|keratinocyte proliferation	Golgi apparatus|keratin filament	protein binding|structural constituent of cytoskeleton			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(357;0.19)		GCGGCTCAAGCAGGAGAAGCT	0.532													7	37	---	---	---	---	PASS
RNF10	9921	broad.mit.edu	37	12	121004766	121004766	+	Missense_Mutation	SNP	G	C	C			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121004766G>C	uc001typ.3	+	13	2507	c.2024G>C	c.(2023-2025)AGT>ACT	p.S675T	RNF10_uc010szk.1_RNA|RNF10_uc001tyq.3_Missense_Mutation_p.S586T	NM_014868	NP_055683	Q8N5U6	RNF10_HUMAN	ring finger protein 10	675					negative regulation of Schwann cell proliferation|positive regulation of myelination|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus	protein binding|transcription regulatory region DNA binding|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)	2	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CTCAGCAGAAGTCCAGGTTCC	0.498													57	189	---	---	---	---	PASS
SACS	26278	broad.mit.edu	37	13	23904337	23904337	+	Missense_Mutation	SNP	C	G	G			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23904337C>G	uc001uon.2	-	10	14267	c.13678G>C	c.(13678-13680)GTG>CTG	p.V4560L	SACS_uc001uoo.2_Missense_Mutation_p.V4413L|SACS_uc001uop.1_Intron|SACS_uc001uoq.1_Intron	NM_014363	NP_055178	Q9NZJ4	SACS_HUMAN	sacsin	4560	HEPN.				cell death|negative regulation of inclusion body assembly|protein folding	axon|cell body fiber|dendrite|mitochondrion|nucleus	ATP binding|chaperone binding|Hsp70 protein binding|proteasome binding			ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	12		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		CATTCCATCACCCTCATAGCA	0.358													9	186	---	---	---	---	PASS
RGS6	9628	broad.mit.edu	37	14	72925078	72925078	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:72925078G>A	uc001xna.3	+	5	858	c.335G>A	c.(334-336)CGT>CAT	p.R112H	RGS6_uc010ttn.1_Missense_Mutation_p.R112H|RGS6_uc001xmx.3_Missense_Mutation_p.R112H|RGS6_uc010tto.1_RNA|RGS6_uc001xmy.3_Missense_Mutation_p.R112H|RGS6_uc010ttp.1_Missense_Mutation_p.R43H|RGS6_uc001xmz.1_5'Flank|RGS6_uc010arg.2_RNA	NM_004296	NP_004287	P49758	RGS6_HUMAN	regulator of G-protein signalling 6	112	DEP.				G-protein coupled receptor protein signaling pathway|intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|signal transducer activity			upper_aerodigestive_tract(1)|lung(1)|skin(1)	3				all cancers(60;0.00309)|BRCA - Breast invasive adenocarcinoma(234;0.0281)|STAD - Stomach adenocarcinoma(64;0.0302)|OV - Ovarian serous cystadenocarcinoma(108;0.0476)		ACCTTTTATCGTTTCCAGGTA	0.458													41	109	---	---	---	---	PASS
CCDC88C	440193	broad.mit.edu	37	14	91755525	91755525	+	Silent	SNP	G	A	A			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91755525G>A	uc010aty.2	-	25	4464	c.4365C>T	c.(4363-4365)GCC>GCT	p.A1455A		NM_001080414	NP_001073883	Q9P219	DAPLE_HUMAN	DVL-binding protein DAPLE	1455					microtubule cytoskeleton organization|protein destabilization|protein homooligomerization|regulation of protein phosphorylation|Wnt receptor signaling pathway	cytoplasm|insoluble fraction	microtubule binding|PDZ domain binding|protein self-association			ovary(3)	3		all_cancers(154;0.0468)				CGGGGTTCTCGGCCTGTGATC	0.682													50	88	---	---	---	---	PASS
B2M	567	broad.mit.edu	37	15	45003781	45003781	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45003781C>T	uc001zuc.2	+	1	97	c.37C>T	c.(37-39)CTC>TTC	p.L13F	B2M_uc010uek.1_Missense_Mutation_p.L13F|B2M_uc010bdx.1_Missense_Mutation_p.L13F	NM_004048	NP_004039	P61769	B2MG_HUMAN	beta-2-microglobulin precursor	13					antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|regulation of defense response to virus by virus|viral reproduction	early endosome membrane|Golgi membrane|MHC class I protein complex	protein binding			ovary(2)|skin(1)	3		all_cancers(109;1.88e-13)|all_epithelial(112;2.13e-11)|Lung NSC(122;2.22e-07)|all_lung(180;1.81e-06)|Melanoma(134;0.0122)		all cancers(107;4.16e-21)|GBM - Glioblastoma multiforme(94;8.97e-07)|COAD - Colon adenocarcinoma(120;0.0357)|Colorectal(105;0.0377)|Lung(196;0.0903)|LUSC - Lung squamous cell carcinoma(244;0.192)		GCTCGCGCTACTCTCTCTTTC	0.612													5	87	---	---	---	---	PASS
SLC28A2	9153	broad.mit.edu	37	15	45559673	45559673	+	Silent	SNP	C	A	A			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45559673C>A	uc001zva.2	+	11	1028	c.963C>A	c.(961-963)ATC>ATA	p.I321I		NM_004212	NP_004203	O43868	S28A2_HUMAN	solute carrier family 28 (sodium-coupled	321					nucleobase, nucleoside and nucleotide metabolic process	integral to plasma membrane|membrane fraction	nucleoside binding|nucleoside:sodium symporter activity|purine nucleoside transmembrane transporter activity			ovary(4)	4		all_cancers(109;8.53e-07)|all_epithelial(112;1.39e-05)|Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;3.77e-16)|GBM - Glioblastoma multiforme(94;2.71e-06)		CTCTGCTCATCCGTCCCTACC	0.557													94	173	---	---	---	---	PASS
SRL	6345	broad.mit.edu	37	16	4247843	4247843	+	Silent	SNP	G	A	A			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4247843G>A	uc002cvz.3	-	4	346	c.333C>T	c.(331-333)AAC>AAT	p.N111N	SRL_uc002cvy.3_RNA	NM_001098814	NP_001092284	Q86TD4	SRCA_HUMAN	sarcalumenin	570						sarcoplasmic reticulum lumen	GTP binding|GTPase activity			ovary(3)|skin(2)	5						CAAGGAGGTAGTTTATCATGG	0.428													41	98	---	---	---	---	PASS
VPS35	55737	broad.mit.edu	37	16	46717480	46717480	+	Missense_Mutation	SNP	C	G	G			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46717480C>G	uc002eef.3	-	2	141	c.42G>C	c.(40-42)AAG>AAC	p.K14N	VPS35_uc002eee.2_5'UTR	NM_018206	NP_060676	Q96QK1	VPS35_HUMAN	vacuolar protein sorting 35	14					protein transport|retrograde transport, endosome to Golgi	cytosol|endosome|membrane	protein binding				0		all_cancers(37;7.65e-05)|all_epithelial(9;0.000154)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116)				CATCCAAGAGCTTTTCCTGCT	0.448													32	79	---	---	---	---	PASS
POLR2C	5432	broad.mit.edu	37	16	57503112	57503112	+	Silent	SNP	G	A	A			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57503112G>A	uc002elt.1	+	5	380	c.294G>A	c.(292-294)TCG>TCA	p.S98S	POLR2C_uc010vhq.1_Silent_p.S98S	NM_032940	NP_116558	P19387	RPB3_HUMAN	DNA directed RNA polymerase II polypeptide C	98					mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of viral transcription|protein phosphorylation|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	DNA-directed RNA polymerase II, core complex	DNA binding|DNA-directed RNA polymerase activity|protein dimerization activity				0						CCGAGTGCTCGGTGGAGTTCA	0.577													52	105	---	---	---	---	PASS
RABEP1	9135	broad.mit.edu	37	17	5265015	5265015	+	Intron	SNP	A	T	T			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5265015A>T	uc002gbm.3	+						RABEP1_uc010clc.1_Intron|RABEP1_uc010cld.1_Intron|RABEP1_uc010vsw.1_Intron|RABEP1_uc002gbl.3_Intron|NUP88_uc002gbn.2_RNA	NM_004703	NP_004694	Q15276	RABE1_HUMAN	rabaptin, RAB GTPase binding effector protein 1						apoptosis|cellular membrane fusion|endocytosis|protein transport	centrosome|early endosome|endocytic vesicle|recycling endosome	growth factor activity|GTPase activator activity|protein homodimerization activity			large_intestine(1)|ovary(1)	2						ACGCTGAGGCACACTGGGAAG	0.478													4	21	---	---	---	---	PASS
RCVRN	5957	broad.mit.edu	37	17	9801384	9801384	+	3'UTR	SNP	T	G	G			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9801384T>G	uc002gme.1	-	3						NM_002903	NP_002894	P35243	RECO_HUMAN	recoverin						visual perception		calcium ion binding|calcium sensitive guanylate cyclase activator activity				0						GAGTGGTAGGTGGAGGGAGGA	0.398													23	98	---	---	---	---	PASS
DNAH9	1770	broad.mit.edu	37	17	11784599	11784599	+	Missense_Mutation	SNP	A	T	T			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11784599A>T	uc002gne.2	+	55	10743	c.10675A>T	c.(10675-10677)AAT>TAT	p.N3559Y	DNAH9_uc010coo.2_Missense_Mutation_p.N2853Y|DNAH9_uc002gnf.2_5'Flank	NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9 isoform 2	3559	AAA 5 (By similarity).				cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			skin(10)|ovary(4)|breast(3)|central_nervous_system(2)|pancreas(1)	20		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		CAAGCTGGCTAATCCTCACTA	0.522													35	116	---	---	---	---	PASS
TMEM132E	124842	broad.mit.edu	37	17	32953491	32953491	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:32953491C>T	uc002hif.2	+	2	741	c.413C>T	c.(412-414)TCG>TTG	p.S138L		NM_207313	NP_997196	Q6IEE7	T132E_HUMAN	transmembrane protein 132E precursor	138	Extracellular (Potential).					integral to membrane				central_nervous_system(1)	1				BRCA - Breast invasive adenocarcinoma(366;0.231)		GTGCCCGCCTCGCAGCCCGTG	0.701													12	19	---	---	---	---	PASS
HOXB1	3211	broad.mit.edu	37	17	46607033	46607033	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46607033C>T	uc002ink.1	-	2	788	c.782G>A	c.(781-783)CGC>CAC	p.R261H		NM_002144	NP_002135	P14653	HXB1_HUMAN	homeobox B1	261	Homeobox.					nucleus	protein domain specific binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1						CTCTCGCTCGCGCTTCTTCTG	0.632													73	193	---	---	---	---	PASS
TBCD	6904	broad.mit.edu	37	17	80863900	80863900	+	Silent	SNP	C	A	A			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80863900C>A	uc002kfz.2	+	20	2023	c.1893C>A	c.(1891-1893)GCC>GCA	p.A631A	TBCD_uc002kfx.1_Silent_p.A614A|TBCD_uc002kfy.1_Silent_p.A631A|TBCD_uc002kgb.1_5'UTR	NM_005993	NP_005984	Q9BTW9	TBCD_HUMAN	beta-tubulin cofactor D	631	HEAT 3.				'de novo' posttranslational protein folding|adherens junction assembly|negative regulation of cell-substrate adhesion|negative regulation of microtubule polymerization|post-chaperonin tubulin folding pathway|tight junction assembly	adherens junction|cytoplasm|lateral plasma membrane|microtubule|tight junction	beta-tubulin binding|chaperone binding|GTPase activator activity				0	Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0266)|all_epithelial(8;0.0696)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.18)			TTGCTTACGCCTTGTACAAAC	0.542													3	18	---	---	---	---	PASS
VN1R2	317701	broad.mit.edu	37	19	53762110	53762110	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53762110G>A	uc002qbi.2	+	1	566	c.482G>A	c.(481-483)GGA>GAA	p.G161E		NM_173856	NP_776255	Q8NFZ6	VN1R2_HUMAN	vomeronasal 1 receptor 2	161	Extracellular (Potential).				response to pheromone	integral to membrane|plasma membrane	pheromone receptor activity				0				GBM - Glioblastoma multiforme(134;0.00301)		AATTATTTTGGATGCAAATTT	0.458													41	110	---	---	---	---	PASS
VN1R2	317701	broad.mit.edu	37	19	53762116	53762116	+	Missense_Mutation	SNP	A	T	T			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53762116A>T	uc002qbi.2	+	1	572	c.488A>T	c.(487-489)AAA>ATA	p.K163I		NM_173856	NP_776255	Q8NFZ6	VN1R2_HUMAN	vomeronasal 1 receptor 2	163	Extracellular (Potential).				response to pheromone	integral to membrane|plasma membrane	pheromone receptor activity				0				GBM - Glioblastoma multiforme(134;0.00301)		TTTGGATGCAAATTTCTTTTG	0.453													36	99	---	---	---	---	PASS
ZNF552	79818	broad.mit.edu	37	19	58319823	58319823	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58319823C>T	uc002qqg.2	-	3	979	c.809G>A	c.(808-810)TGT>TAT	p.C270Y	ZNF587_uc002qqb.2_Intron|ZNF552_uc010yhg.1_Missense_Mutation_p.C266Y	NM_024762	NP_079038	Q9H707	ZN552_HUMAN	zinc finger protein 552	270	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0259)		ACATATCCCACACGTATAAGG	0.413													5	81	---	---	---	---	PASS
RBM39	9584	broad.mit.edu	37	20	34322841	34322841	+	Intron	SNP	T	C	C			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34322841T>C	uc002xeb.2	-						RBM39_uc002xdz.2_5'Flank|RBM39_uc002xea.2_Intron|RBM39_uc010gfn.2_Intron|RBM39_uc010zvm.1_Intron|RBM39_uc002xeg.2_Intron|RBM39_uc002xec.2_Intron|RBM39_uc002xed.2_Intron|RBM39_uc002xee.2_Intron|RBM39_uc002xef.2_Intron|RBM39_uc010zvn.1_Intron	NM_184234	NP_909122	Q14498	RBM39_HUMAN	RNA binding motif protein 39 isoform a						mRNA processing|regulation of transcription, DNA-dependent|RNA splicing|transcription, DNA-dependent	centrosome|nuclear speck	nucleotide binding|protein binding|RNA binding			ovary(1)|central_nervous_system(1)	2	all_epithelial(2;0.00295)|Lung NSC(9;0.00453)|Breast(12;0.00544)|all_lung(11;0.00676)					CCAAAGTCTTTAATGGCAGTG	0.378													16	29	---	---	---	---	PASS
CCDC22	28952	broad.mit.edu	37	X	49105114	49105114	+	Silent	SNP	G	A	A	rs138555929	byFrequency	TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49105114G>A	uc004dnd.1	+	12	1506	c.1350G>A	c.(1348-1350)CTG>CTA	p.L450L	CCDC22_uc004dnc.1_RNA	NM_014008	NP_054727	O60826	CCD22_HUMAN	coiled-coil domain containing 22	450	Potential.									central_nervous_system(1)	1						CTCGACGGCTGGCAGAGATCC	0.617													3	3	---	---	---	---	PASS
CXorf66	347487	broad.mit.edu	37	X	139040297	139040297	+	Silent	SNP	G	A	A			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:139040297G>A	uc004fbb.2	-	2	190	c.168C>T	c.(166-168)ATC>ATT	p.I56I		NM_001013403	NP_001013421	Q5JRM2	CX066_HUMAN	hypothetical protein LOC347487 precursor	56	Helical; (Potential).					integral to membrane					0						CAAAAACCATGATGATAATAC	0.318													146	84	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	36586349	36586349	+	IGR	DEL	A	-	-	rs146743730		TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36586349delA								COL8A2 (20499 upstream) : TRAPPC3 (15826 downstream)																							actccgtctcaaaaaaaaaaa	0.005													4	2	---	---	---	---	
TM2D1	83941	broad.mit.edu	37	1	62160525	62160526	+	Intron	INS	-	TA	TA	rs149200386	by1000genomes	TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62160525_62160526insTA	uc001czz.1	-							NM_032027	NP_114416	Q9BX74	TM2D1_HUMAN	beta-amyloid binding protein precursor						apoptosis					ovary(1)	1						TAAACCATTATTATATATATAT	0.272													6	4	---	---	---	---	
STXBP3	6814	broad.mit.edu	37	1	109349880	109349892	+	Intron	DEL	AAAAAAAAAAAAA	-	-	rs71913282		TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109349880_109349892delAAAAAAAAAAAAA	uc001dvy.2	+						STXBP3_uc001dvz.2_Intron	NM_007269	NP_009200	O00186	STXB3_HUMAN	syntaxin binding protein 3						negative regulation of calcium ion-dependent exocytosis|neutrophil degranulation|platelet aggregation|protein transport|vesicle docking involved in exocytosis	cytosol|nucleus|platelet alpha granule|specific granule|tertiary granule	syntaxin-2 binding			ovary(3)|central_nervous_system(1)	4		all_epithelial(167;0.000154)|all_lung(203;0.00026)|Lung NSC(277;0.000508)		Colorectal(144;0.0386)|Lung(183;0.104)|COAD - Colon adenocarcinoma(174;0.137)|Epithelial(280;0.231)		actccacctcaaaaaaaaaaaaaaaaaaaaaaa	0.136													4	2	---	---	---	---	
SIKE1	80143	broad.mit.edu	37	1	115319269	115319270	+	Intron	INS	-	T	T	rs34656268		TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115319269_115319270insT	uc001efo.3	-						SIKE1_uc001efp.3_Intron	NM_025073	NP_079349	Q9BRV8	SIKE1_HUMAN	suppressor of IKK epsilon isoform 2							cytosol	protein binding				0						ATTCACGGATATTTTTTTTTTT	0.188													5	3	---	---	---	---	
KLHL20	27252	broad.mit.edu	37	1	173735619	173735619	+	Intron	DEL	A	-	-			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173735619delA	uc001gjc.2	+						KLHL20_uc010pmr.1_Intron|KLHL20_uc009wwf.2_Intron	NM_014458	NP_055273	Q9Y2M5	KLH20_HUMAN	kelch-like 20						cytoskeleton organization|negative regulation of apoptosis|proteasomal ubiquitin-dependent protein catabolic process|response to interferon-alpha	actin cytoskeleton|cell surface|Cul3-RING ubiquitin ligase complex|Golgi apparatus|perinuclear region of cytoplasm|PML body	actin binding|interferon-gamma binding|ubiquitin-protein ligase activity			ovary(1)	1						taaaaaatacaaaaaaaaaaa	0.000													3	4	---	---	---	---	
SFRS7	6432	broad.mit.edu	37	2	38975943	38975943	+	Intron	DEL	T	-	-			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38975943delT	uc002rqz.2	-						SFRS7_uc002rra.2_Intron|SFRS7_uc010ynp.1_Intron|GEMIN6_uc002rrb.2_5'Flank	NM_001031684	NP_001026854	Q16629	SRSF7_HUMAN	splicing factor, arginine/serine-rich 7						mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	nucleoplasm	nucleotide binding|protein binding|RNA binding|zinc ion binding				0		all_hematologic(82;0.248)				TTGTTGAGTATTTTTTTTTTT	0.264													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	72353291	72353292	+	IGR	DEL	CA	-	-	rs138553487		TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72353291_72353292delCA								DYSF (439399 upstream) : CYP26B1 (3075 downstream)																							gtacacacaccacacacacaca	0.129													1	5	---	---	---	---	
RGPD1	400966	broad.mit.edu	37	2	87204958	87204958	+	Intron	DEL	T	-	-			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87204958delT	uc010fgv.2	+						RMND5A_uc002srs.3_Intron|RGPD1_uc002ssb.2_Intron|RGPD1_uc002ssc.2_Intron	NM_001024457	NP_001019628	Q68DN6	RGPD1_HUMAN	RANBP2-like and GRIP domain containing 1						intracellular transport		binding				0						Gttatttttattttttttttt	0.318													6	3	---	---	---	---	
GPR155	151556	broad.mit.edu	37	2	175306646	175306646	+	Intron	DEL	T	-	-	rs113036023		TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175306646delT	uc002uit.2	-						GPR155_uc002uiu.2_Intron|GPR155_uc002uiv.2_Intron|GPR155_uc010fqs.2_Intron	NM_001033045	NP_001028217	Q7Z3F1	GP155_HUMAN	G protein-coupled receptor 155 isoform 9						intracellular signal transduction|transmembrane transport	integral to membrane				ovary(1)	1						aatttttgtattttttttttt	0.000													7	4	---	---	---	---	
CYP20A1	57404	broad.mit.edu	37	2	204137273	204137274	+	Intron	INS	-	A	A	rs72103565		TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204137273_204137274insA	uc002uzv.3	+						CYP20A1_uc002uzx.3_Intron|CYP20A1_uc010zif.1_Intron|CYP20A1_uc002uzy.3_Intron|CYP20A1_uc002uzw.3_Intron|CYP20A1_uc010ftw.2_Intron	NM_177538	NP_803882	Q6UW02	CP20A_HUMAN	cytochrome P450, family 20, subfamily A,							integral to membrane	electron carrier activity|heme binding|monooxygenase activity|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen				0						aaccctgactcaaaaaaaaaaa	0.104													5	4	---	---	---	---	
CHRND	1144	broad.mit.edu	37	2	233396194	233396198	+	Intron	DEL	GCCTC	-	-			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233396194_233396198delGCCTC	uc002vsw.2	+						CHRND_uc010zmg.1_Intron|CHRND_uc010fyc.2_Intron|CHRND_uc010zmh.1_Intron	NM_000751	NP_000742	Q07001	ACHD_HUMAN	nicotinic acetylcholine receptor delta						muscle contraction|musculoskeletal movement|neuromuscular process|skeletal muscle tissue growth|synaptic transmission	cell junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	nicotinic acetylcholine-activated cation-selective channel activity|receptor activity			ovary(1)|breast(1)|skin(1)	3		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;1.89e-16)|BRCA - Breast invasive adenocarcinoma(100;0.00078)|Lung(119;0.00579)|LUSC - Lung squamous cell carcinoma(224;0.00754)		CTCAAGCCCGGCCTCACCCTGCTTG	0.605													134	58	---	---	---	---	
VHL	7428	broad.mit.edu	37	3	10191642	10191643	+	Frame_Shift_Del	DEL	GA	-	-			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10191642_10191643delGA	uc003bvc.2	+	3	848_849	c.635_636delGA	c.(634-636)GGAfs	p.G212fs	VHL_uc003bvd.2_Frame_Shift_Del_p.G171fs	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	212					anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.D213fs*8(1)|p.D213fs*>2(1)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		CAACGGATGGGAGATTGAAGAT	0.465		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				12	6	---	---	---	---	
SLC6A6	6533	broad.mit.edu	37	3	14507773	14507774	+	Intron	INS	-	AA	AA	rs11310077		TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14507773_14507774insAA	uc010heg.2	+						SLC6A6_uc003byq.2_Intron|SLC6A6_uc003byr.2_Intron	NM_001134367	NP_001127839	P31641	SC6A6_HUMAN	solute carrier family 6 (neurotransmitter						cellular amino acid metabolic process	integral to plasma membrane	amino acid transmembrane transporter activity|neurotransmitter:sodium symporter activity|taurine:sodium symporter activity			ovary(1)	1						gtctcaaatttaaaaaaaaaaa	0.000													4	2	---	---	---	---	
GLB1	2720	broad.mit.edu	37	3	33075271	33075271	+	Intron	DEL	A	-	-	rs71687294		TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33075271delA	uc003cfi.1	-						GLB1_uc003cfh.1_Intron|GLB1_uc003cfj.1_Intron|GLB1_uc011axk.1_Intron	NM_000404	NP_000395	P16278	BGAL_HUMAN	galactosidase, beta 1 isoform a preproprotein						carbohydrate metabolic process	lysosome|perinuclear region of cytoplasm	beta-galactosidase activity|cation binding|protein binding			large_intestine(1)	1		Melanoma(143;0.104)				agactgtctcaaaaaaaaaaa	0.224													2	5	---	---	---	---	
SLMAP	7871	broad.mit.edu	37	3	57850102	57850103	+	Intron	INS	-	A	A			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57850102_57850103insA	uc003dje.1	+						SLMAP_uc003djc.1_Intron|SLMAP_uc003djd.1_Intron|SLMAP_uc003djf.1_Intron|SLMAP_uc003djg.1_5'Flank	NM_007159	NP_009090	Q14BN4	SLMAP_HUMAN	sarcolemma associated protein						muscle contraction|protein folding	integral to plasma membrane|microtubule organizing center|prefoldin complex|sarcolemma|smooth endoplasmic reticulum	unfolded protein binding				0				BRCA - Breast invasive adenocarcinoma(55;0.000271)|KIRC - Kidney renal clear cell carcinoma(284;0.0602)|Kidney(284;0.0754)|OV - Ovarian serous cystadenocarcinoma(275;0.182)		aactccatctcaaaaaaaaaaa	0.109													6	4	---	---	---	---	
FRMD4B	23150	broad.mit.edu	37	3	69245689	69245690	+	Intron	INS	-	AAAAC	AAAAC	rs144990660	by1000genomes	TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69245689_69245690insAAAAC	uc003dnv.2	-						FRMD4B_uc003dnw.2_Intron|FRMD4B_uc003dnu.2_Intron|FRMD4B_uc011bga.1_Intron	NM_015123	NP_055938	Q9Y2L6	FRM4B_HUMAN	FERM domain containing 4B							cytoplasm|cytoskeleton	binding			ovary(3)|central_nervous_system(1)	4		Lung NSC(201;0.0138)|Prostate(884;0.11)		BRCA - Breast invasive adenocarcinoma(55;0.000201)|Epithelial(33;0.00141)|LUSC - Lung squamous cell carcinoma(21;0.00999)|Lung(16;0.0182)		CTTCAGACCAAAAAACAAAACA	0.287													4	6	---	---	---	---	
KALRN	8997	broad.mit.edu	37	3	124158048	124158049	+	Intron	DEL	CA	-	-	rs34895768		TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124158048_124158049delCA	uc003ehg.2	+						KALRN_uc010hrv.1_Intron|KALRN_uc003ehf.1_Intron|KALRN_uc011bjy.1_Intron|KALRN_uc003ehh.1_Intron	NM_001024660	NP_001019831	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase isoform 1						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|vesicle-mediated transport	actin cytoskeleton|cytosol	ATP binding|GTPase activator activity|metal ion binding|protein binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			large_intestine(2)|ovary(2)|central_nervous_system(1)|skin(1)	6						ctctctctctcacacacacaca	0.144													4	2	---	---	---	---	
KIAA0226	9711	broad.mit.edu	37	3	197431787	197431787	+	Intron	DEL	T	-	-	rs80272519		TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197431787delT	uc003fyc.2	-						KIAA0226_uc003fyd.3_Intron|KIAA0226_uc003fyf.2_Intron|KIAA0226_uc003fyg.2_Intron	NM_014687	NP_055502	Q92622	RUBIC_HUMAN	hypothetical protein LOC9711 isoform 2.						autophagy|endocytosis|negative regulation of autophagy|negative regulation of endocytosis	early endosome|late endosome|lysosome	protein binding				0	all_cancers(143;8.26e-10)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;2.19e-23)|all cancers(36;1.39e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.21e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(93;0.0446)		GGTTTGCATGTTTTTTTTTTT	0.423													5	3	---	---	---	---	
UBE2D3	7323	broad.mit.edu	37	4	103718308	103718308	+	3'UTR	DEL	T	-	-			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103718308delT	uc003hwk.2	-	8					UBE2D3_uc003hwh.2_5'Flank|UBE2D3_uc003hwi.2_3'UTR|UBE2D3_uc003hwj.2_RNA|UBE2D3_uc003hwl.2_3'UTR|UBE2D3_uc011cet.1_3'UTR|UBE2D3_uc011ceu.1_3'UTR|UBE2D3_uc003hwo.2_3'UTR|UBE2D3_uc003hwp.2_3'UTR|UBE2D3_uc003hwq.2_3'UTR|UBE2D3_uc003hwr.2_3'UTR	NM_181887	NP_871616	P61077	UB2D3_HUMAN	ubiquitin-conjugating enzyme E2D 3 isoform 1						apoptosis|BMP signaling pathway|DNA repair|negative regulation of type I interferon production|proteasomal ubiquitin-dependent protein catabolic process|protein K11-linked ubiquitination|protein K48-linked ubiquitination|protein monoubiquitination|transforming growth factor beta receptor signaling pathway	endosome membrane|plasma membrane	ATP binding|protein binding|ubiquitin-protein ligase activity				0		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.13e-08)		ACATGCTCCATTTTTTTTTTT	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	122671349	122671349	+	IGR	DEL	A	-	-			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:122671349delA								ANXA5 (53202 upstream) : TMEM155 (8736 downstream)																							ctgggcaaATaaggaccttat	0.005													4	2	---	---	---	---	
HAVCR1	26762	broad.mit.edu	37	5	156471440	156471446	+	Intron	DEL	AAGAAAG	-	-	rs60316649		TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156471440_156471446delAAGAAAG	uc010jij.1	-						HAVCR1_uc011ddl.1_Intron|HAVCR1_uc003lwi.2_Intron	NM_001099414	NP_001092884	Q96D42	HAVR1_HUMAN	hepatitis A virus cellular receptor 1						interspecies interaction between organisms	integral to membrane	receptor activity			ovary(1)|skin(1)	2	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			aggagaaagaaagaaagaaagaaagaa	0.000													4	2	---	---	---	---	
NOP16	51491	broad.mit.edu	37	5	175814066	175814069	+	Intron	DEL	TCTC	-	-	rs145796794		TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175814066_175814069delTCTC	uc011dfl.1	-						NOP16_uc003med.2_Intron|NOP16_uc003mee.2_Intron|NOP16_uc011dfm.1_Intron|HIGD2A_uc003meg.2_5'Flank	NM_016391	NP_057475	Q9Y3C1	NOP16_HUMAN	NOP16 nucleolar protein homolog							nucleolus				ovary(1)|central_nervous_system(1)	2						GGAGGCTTTTTCTCTCTCtctctc	0.245													4	4	---	---	---	---	
C6orf218	221718	broad.mit.edu	37	6	10430699	10430701	+	Intron	DEL	TTT	-	-	rs139837855		TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10430699_10430701delTTT	uc003myz.2	-							NR_027793				Homo sapiens chromosome 6 open reading frame 218, mRNA (cDNA clone IMAGE:3917693).												0	Breast(50;0.0427)|Ovarian(93;0.0991)	all_hematologic(90;0.124)				CTCTGACTAGttttttttttttt	0.202													6	3	---	---	---	---	
BTN2A3	54718	broad.mit.edu	37	6	26430816	26430817	+	Intron	INS	-	A	A	rs34293101		TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26430816_26430817insA	uc011dkl.1	+						BTN2A3_uc011dkm.1_Intron					RecName: Full=Butyrophilin subfamily 2 member A3; Flags: Precursor;												0						agctcagtctcaaaaaaaaaaa	0.252													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	64722027	64722028	+	IGR	INS	-	A	A	rs34277183		TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64722027_64722028insA								INTS4L1 (27428 upstream) : ZNF92 (116740 downstream)																							agactctgtctaaaaaaaaaaa	0.178													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	53358414	53358415	+	IGR	INS	-	A	A			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53358414_53358415insA								ST18 (35975 upstream) : FAM150A (88183 downstream)																							CTTTTCATTTCAAAAAAAAAAA	0.366													4	3	---	---	---	---	
ARMC1	55156	broad.mit.edu	37	8	66539259	66539259	+	Intron	DEL	A	-	-	rs144015307		TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66539259delA	uc003xvl.2	-						ARMC1_uc011leo.1_Intron	NM_018120	NP_060590	Q9NVT9	ARMC1_HUMAN	armadillo repeat-containing protein						metal ion transport		metal ion binding			skin(1)	1			Epithelial(68;0.103)|OV - Ovarian serous cystadenocarcinoma(28;0.235)			aataaagaataaaaaCAATGT	0.179													4	2	---	---	---	---	
AQP7	364	broad.mit.edu	37	9	33386780	33386781	+	Intron	INS	-	A	A	rs144468472	by1000genomes	TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33386780_33386781insA	uc003zst.2	-						SUGT1P1_uc010mjq.1_Intron|AQP7_uc003zsu.1_Intron|AQP7_uc010mjs.2_Intron|AQP7_uc010mjt.2_Intron|AQP7_uc011lnx.1_Intron|AQP7_uc011lny.1_Intron|AQP7_uc003zss.3_Intron|AQP7_uc011lnz.1_Intron|AQP7_uc011loa.1_Intron	NM_001170	NP_001161	O14520	AQP7_HUMAN	aquaporin 7						excretion|generation of precursor metabolites and energy	cell-cell junction|cytoplasm|integral to plasma membrane	glycerol channel activity|water channel activity				0			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.191)		aatggtaggtcggggggcccag	0.257													10	5	---	---	---	---	
UGCG	7357	broad.mit.edu	37	9	114685398	114685398	+	Intron	DEL	T	-	-			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114685398delT	uc004bft.2	+							NM_003358	NP_003349	Q16739	CEGT_HUMAN	ceramide glucosyltransferase						epidermis development|glucosylceramide biosynthetic process	Golgi membrane|integral to membrane|membrane fraction	ceramide glucosyltransferase activity			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(323;0.0433)	Miglustat(DB00419)	AAAACAAAGGTTTTTTTTTTT	0.294													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	133376666	133376679	+	IGR	DEL	GTGTGTGTGTGTGT	-	-	rs36233815		TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133376666_133376679delGTGTGTGTGTGTGT								ASS1 (6 upstream) : LOC100272217 (76060 downstream)																							TTTCTAgtgagtgtgtgtgtgtgtgtgtgtgtgt	0.350													5	3	---	---	---	---	
PFKP	5214	broad.mit.edu	37	10	3174816	3174819	+	Intron	DEL	AACT	-	-	rs72145058		TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3174816_3174819delAACT	uc001igp.2	+						PFKP_uc001igq.2_Intron|PFKP_uc009xhr.2_Intron|PFKP_uc009xht.2_Intron|PFKP_uc009xhu.2_Intron	NM_002627	NP_002618	Q01813	K6PP_HUMAN	phosphofructokinase, platelet						glycolysis	6-phosphofructokinase complex	6-phosphofructokinase activity|ATP binding|metal ion binding|protein binding			upper_aerodigestive_tract(1)|ovary(1)|lung(1)	3				GBM - Glioblastoma multiforme(1;0.000975)|all cancers(11;0.00351)|Epithelial(11;0.142)		GCATTTAGACAACTAATATTTTTG	0.387													5	3	---	---	---	---	
MAP3K8	1326	broad.mit.edu	37	10	30728362	30728362	+	Intron	DEL	A	-	-			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30728362delA	uc001ivi.1	+						MAP3K8_uc009xlf.1_Intron|MAP3K8_uc001ivj.1_Intron	NM_005204	NP_005195	P41279	M3K8_HUMAN	mitogen-activated protein kinase kinase kinase						cell cycle|T cell costimulation	cytosol	ATP binding|magnesium ion binding|MAP kinase kinase kinase activity|protein binding			breast(3)|central_nervous_system(1)	4		Prostate(175;0.151)				TTAAAGATGCAAAAAAAAAAG	0.264													6	3	---	---	---	---	
ZCCHC24	219654	broad.mit.edu	37	10	81190443	81190444	+	Intron	DEL	CA	-	-	rs68024462		TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81190443_81190444delCA	uc001kak.2	-						ZCCHC24_uc010qlr.1_Intron|ZCCHC24_uc009xrw.2_Intron	NM_153367	NP_699198	Q8N2G6	ZCH24_HUMAN	zinc finger, CCHC domain containing 24								nucleic acid binding|zinc ion binding			breast(1)	1						acacacacaccacacacacaca	0.455													4	2	---	---	---	---	
C10orf58	84293	broad.mit.edu	37	10	82182420	82182420	+	Intron	DEL	T	-	-	rs145616854		TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:82182420delT	uc001kcc.3	+						C10orf58_uc001kcd.3_Intron|C10orf58_uc001kce.3_Intron|C10orf58_uc001kcf.3_Intron	NM_032333	NP_115709	Q9BRX8	CJ058_HUMAN	hypothetical protein LOC84293 precursor							extracellular region					0			Colorectal(32;0.229)			ATTTGTGCTCTTTTTTTTTTT	0.433													4	2	---	---	---	---	
KIF11	3832	broad.mit.edu	37	10	94388745	94388745	+	Intron	DEL	T	-	-			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94388745delT	uc001kic.2	+						KIF11_uc010qnq.1_Intron	NM_004523	NP_004514	P52732	KIF11_HUMAN	kinesin family member 11						blood coagulation|cell division|microtubule-based movement|spindle assembly involved in mitosis	chromatin remodeling complex|cytosol|kinesin complex|microtubule|spindle pole	ATP binding|microtubule motor activity|protein kinase binding			skin(1)	1						TCCTTCAAGAttttttttttt	0.119													4	2	---	---	---	---	
OSBPL5	114879	broad.mit.edu	37	11	3109284	3109285	+	3'UTR	INS	-	C	C	rs138510089	by1000genomes	TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3109284_3109285insC	uc001lxk.2	-	22					OSBPL5_uc010qxq.1_3'UTR|OSBPL5_uc009ydw.2_3'UTR|OSBPL5_uc001lxl.2_3'UTR|OSBPL5_uc001lxj.2_3'UTR	NM_020896	NP_065947	Q9H0X9	OSBL5_HUMAN	oxysterol-binding protein-like protein 5 isoform						cholesterol metabolic process|cholesterol transport|Golgi to plasma membrane transport	cytosol	oxysterol binding|protein binding			large_intestine(2)|central_nervous_system(1)	3		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00607)|LUSC - Lung squamous cell carcinoma(625;0.207)		GGCCCGCAGCGCCTTGTGGCCC	0.668													3	3	---	---	---	---	
KIF18A	81930	broad.mit.edu	37	11	28098482	28098483	+	Intron	INS	-	A	A			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:28098482_28098483insA	uc001msc.2	-							NM_031217	NP_112494	Q8NI77	KI18A_HUMAN	kinesin family member 18A						blood coagulation|microtubule depolymerization|microtubule-based movement|mitotic metaphase plate congression|mitotic prometaphase|protein transport	caveola|cytosol|kinetochore microtubule|microtubule organizing center|nucleus|ruffle	actin binding|ATP binding|microtubule plus-end binding|plus-end-directed microtubule motor activity|tubulin-dependent ATPase activity|ubiquitin binding			ovary(2)	2						gactccttctgaaaaaaaaaaa	0.099													5	3	---	---	---	---	
FBXO3	26273	broad.mit.edu	37	11	33769061	33769061	+	Intron	DEL	T	-	-			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33769061delT	uc001muz.2	-						FBXO3_uc010rej.1_Intron|FBXO3_uc001muy.2_Intron|FBXO3_uc009ykb.2_Intron|FBXO3_uc001mva.1_Intron|FBXO3_uc001mvb.1_Intron|FBXO3_uc010rek.1_Intron	NM_012175	NP_036307	Q9UK99	FBX3_HUMAN	F-box only protein 3 isoform 1						proteolysis	nucleus	ubiquitin-protein ligase activity			pancreas(1)	1		Lung NSC(402;0.0804)		BRCA - Breast invasive adenocarcinoma(625;0.00315)|Lung(977;0.00488)|LUSC - Lung squamous cell carcinoma(625;0.008)		TCCTCTTGACttttttttttt	0.134													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	96221820	96221823	+	IGR	DEL	AGGA	-	-			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96221820_96221823delAGGA								NTN4 (36890 upstream) : SNRPF (30886 downstream)																							agagaaagagaggaaggaaggaag	0.005													4	2	---	---	---	---	
SLC17A8	246213	broad.mit.edu	37	12	100806371	100806371	+	Intron	DEL	A	-	-			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100806371delA	uc010svi.1	+						SLC17A8_uc009ztx.2_Intron	NM_139319	NP_647480	Q8NDX2	VGLU3_HUMAN	solute carrier family 17 (sodium-dependent						neurotransmitter transport|sensory perception of sound|sodium ion transport	cell junction|integral to membrane|synaptic vesicle membrane|synaptosome	L-glutamate transmembrane transporter activity|symporter activity			ovary(3)	3						aagtaaagttaaaaaaaaaaa	0.109													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	108972363	108972365	+	IGR	DEL	ATC	-	-			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108972363_108972365delATC								ISCU (9205 upstream) : TMEM119 (11259 downstream)																							cagccccattatcatcaccacca	0.000													4	2	---	---	---	---	
RSRC2	65117	broad.mit.edu	37	12	123003139	123003140	+	Intron	INS	-	A	A	rs139622590		TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123003139_123003140insA	uc001ucr.2	-						RSRC2_uc001uco.2_Intron|RSRC2_uc001ucp.2_Intron|RSRC2_uc001ucq.2_Intron|RSRC2_uc001ucs.2_Intron|RSRC2_uc001uct.2_Intron|RSRC2_uc001ucu.2_Intron	NM_023012	NP_075388	Q7L4I2	RSRC2_HUMAN	arginine/serine-rich coiled-coil 2 isoform a											ovary(1)	1	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;5.14e-05)|Epithelial(86;0.000183)|BRCA - Breast invasive adenocarcinoma(302;0.201)		gactccgtgtcaaaaaaaaaaa	0.163													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	19609025	19609026	+	Intron	DEL	TG	-	-			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19609025_19609026delTG	uc001vvi.2	+											Homo sapiens prostate-specific P775P mRNA sequence.																		cctctctaactgtagaacatca	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	22467591	22467594	+	5'Flank	DEL	ACAC	-	-			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22467591_22467594delACAC	uc001yui.1	-											Homo sapiens clone IgA5728-2 immunoglobulin A heavy chain mRNA, partial cds.																		AACTCCTAATacacacacacacac	0.201													4	2	---	---	---	---	
DECR2	26063	broad.mit.edu	37	16	460579	460579	+	Intron	DEL	T	-	-	rs11315123		TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:460579delT	uc002chb.2	+						DECR2_uc002chc.2_Intron|DECR2_uc010bqv.2_Intron|DECR2_uc002chd.2_Intron|DECR2_uc002che.1_Intron	NM_020664	NP_065715	Q9NUI1	DECR2_HUMAN	2,4-dienoyl CoA reductase 2							peroxisome	2,4-dienoyl-CoA reductase (NADPH) activity|binding				0		Hepatocellular(16;0.00015)				GGCCTCCCCCTGACGGCCGCC	0.781													9	7	---	---	---	---	
ABCA17P	650655	broad.mit.edu	37	16	2475097	2475098	+	Intron	DEL	TC	-	-			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2475097_2475098delTC	uc002cqc.1	+							NR_003574				Homo sapiens cDNA FLJ37881 fis, clone BRSTN2000367.												0						GGTAActctgtctctctctctc	0.465													4	2	---	---	---	---	
SNX29	92017	broad.mit.edu	37	16	12662161	12662162	+	Intron	INS	-	AA	AA	rs71388727	byFrequency	TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12662161_12662162insAA	uc002dby.3	+							NM_001080530	NP_001073999	Q8TEQ0	SNX29_HUMAN	sorting nexin 29						cell communication		phosphatidylinositol binding			ovary(1)	1						GGAGTGCTGTTAAAAAAAAAAA	0.450													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32126700	32126726	+	IGR	DEL	AATGTGAACATACAAAAAACAAATCAG	-	-			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32126700_32126726delAATGTGAACATACAAAAAACAAATCAG								ZNF267 (198074 upstream) : HERC2P4 (35884 downstream)																							ATGCCTGCCAAATGTGAACATACAAAAAACAAATCAGAATGTGCCAT	0.352													4	3	---	---	---	---	
ABCC12	94160	broad.mit.edu	37	16	48167439	48167439	+	Intron	DEL	A	-	-			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48167439delA	uc002efc.1	-						ABCC12_uc002eey.1_Intron|ABCC12_uc002eez.1_Intron|ABCC12_uc002efa.1_Intron|ABCC12_uc002efb.1_Intron|ABCC12_uc002efd.1_Intron|ABCC12_uc002efe.1_Intron	NM_033226	NP_150229	Q96J65	MRP9_HUMAN	ATP-binding cassette protein C12							integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(2)|skin(1)	3		all_cancers(37;0.0474)|all_lung(18;0.047)				cctgtctcagaaaaaaaaaaa	0.219													4	3	---	---	---	---	
NFAT5	10725	broad.mit.edu	37	16	69602248	69602253	+	Intron	DEL	TATGTG	-	-	rs9937747	by1000genomes	TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69602248_69602253delTATGTG	uc002exm.1	+						NFAT5_uc002exh.1_Intron|NFAT5_uc002exi.2_Intron|NFAT5_uc002exj.1_Intron|NFAT5_uc002exk.1_Intron|NFAT5_uc002exl.1_Intron|NFAT5_uc002exn.1_Intron|MIR1538_hsa-mir-1538|MI0007259_5'Flank	NM_006599	NP_006590	O94916	NFAT5_HUMAN	nuclear factor of activated T-cells 5 isoform c						excretion|signal transduction|transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity				0						tatatatatatatgtgtgtgtgtgtg	0.097													4	2	---	---	---	---	
LOC283922	283922	broad.mit.edu	37	16	74375977	74375978	+	Intron	DEL	CA	-	-			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74375977_74375978delCA	uc002fcr.2	-						LOC283922_uc010vms.1_Intron					Homo sapiens cDNA FLJ39449 fis, clone PROST2008360, highly similar to Homo sapiens pyruvate dehydrogenase phosphatase regulatory subunit (PDPR), mRNA.												0						CAACACGGGCCACCGAGAAGAT	0.495													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	20632409	20632410	+	IGR	DEL	TG	-	-	rs34406877		TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20632409_20632410delTG								LGALS9B (261561 upstream) : CCDC144NL (134300 downstream)																							atgtgtagtttgtgtgtgtgtg	0.035													4	2	---	---	---	---	
BPTF	2186	broad.mit.edu	37	17	65905565	65905565	+	Intron	DEL	T	-	-			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65905565delT	uc002jgf.2	+						BPTF_uc002jge.2_Intron	NM_182641	NP_872579	Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor						brain development|chromatin remodeling|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|NURF complex	sequence-specific DNA binding|transcription factor binding|zinc ion binding			ovary(2)|skin(2)	4	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			GACCTTTGTCTTTTTTTTTTT	0.299													10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	66830811	66830812	+	IGR	INS	-	TTTC	TTTC			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66830811_66830812insTTTC								FAM20A (233716 upstream) : ABCA8 (32621 downstream)																							tatttatctaatttccttcctt	0.005													4	2	---	---	---	---	
PPFIA3	8541	broad.mit.edu	37	19	49641825	49641826	+	Intron	DEL	AA	-	-	rs3032696		TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49641825_49641826delAA	uc002pmr.2	+						PPFIA3_uc010yai.1_Intron|PPFIA3_uc010yaj.1_Intron|PPFIA3_uc002pms.2_Intron	NM_003660	NP_003651	O75145	LIPA3_HUMAN	PTPRF interacting protein alpha 3							cell surface|cytoplasm	protein binding			lung(1)	1		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.36e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000203)|GBM - Glioblastoma multiforme(486;0.00307)|Epithelial(262;0.00677)		GTTCAAACTCAAAGGGCAAAGG	0.475													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	12061138	12061139	+	IGR	INS	-	AT	AT			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:12061138_12061139insAT								BTBD3 (153896 upstream) : SPTLC3 (928488 downstream)																							CCAacacacacacacacacaca	0.371													4	2	---	---	---	---	
FAM182B	728882	broad.mit.edu	37	20	25838735	25838738	+	Intron	DEL	ACCC	-	-			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25838735_25838738delACCC	uc002wvd.1	-						FAM182B_uc002wve.2_Intron					Homo sapiens cDNA FLJ30282 fis, clone BRACE2002803.												0						actcaccccaacccacaccgtcat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	31819036	31819037	+	IGR	INS	-	A	A			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31819036_31819037insA								C20orf71 (3479 upstream) : PLUNC (4765 downstream)																							aagaaagaaagaaagaaagaaa	0.000													4	2	---	---	---	---	
RPRD1B	58490	broad.mit.edu	37	20	36668650	36668650	+	Intron	DEL	T	-	-	rs72441703		TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36668650delT	uc002xho.3	+							NM_021215	NP_067038	Q9NQG5	RPR1B_HUMAN	Regulation of nuclear pre-mRNA domain containing											pancreas(1)	1						tttctttttcttttttttttt	0.303													6	5	---	---	---	---	
C20orf166	128826	broad.mit.edu	37	20	61150006	61150008	+	Intron	DEL	CCT	-	-			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61150006_61150008delCCT	uc011aaj.1	+						C20orf200_uc002ycy.2_5'Flank|C20orf200_uc002ycz.1_5'Flank|uc011aak.1_5'Flank|MIR1-1_hsa-mir-1-1|MI0000651_5'Flank	NM_178463	NP_848558	Q9H1L0	CT166_HUMAN	hypothetical protein LOC128826												0	Breast(26;1.04e-08)		BRCA - Breast invasive adenocarcinoma(19;7.17e-06)			ACCCTGCAGGcctcctcctcctc	0.586													4	3	---	---	---	---	
RTEL1	51750	broad.mit.edu	37	20	62324809	62324810	+	Intron	INS	-	CCA	CCA	rs77223947		TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62324809_62324810insCCA	uc002yfu.1	+						RTEL1_uc011abc.1_Intron|RTEL1_uc002yft.1_Intron|RTEL1_uc011abd.1_Intron|RTEL1_uc011abe.1_Intron|RTEL1_uc002yfw.2_Intron|RTEL1_uc002yfx.1_Intron|TNFRSF6B_uc002yfy.2_5'Flank	NM_016434	NP_057518	Q9NZ71	RTEL1_HUMAN	regulator of telomere elongation helicase 1						DNA repair|regulation of double-strand break repair via homologous recombination|telomere maintenance	nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding|iron-sulfur cluster binding|metal ion binding				0	all_cancers(38;6.47e-12)|all_epithelial(29;3.75e-13)		Epithelial(9;1.25e-09)|all cancers(9;5.13e-09)|BRCA - Breast invasive adenocarcinoma(10;7.26e-05)|OV - Ovarian serous cystadenocarcinoma(5;0.00223)|Colorectal(105;0.107)			cagcaccacctccacctccacc	0.233													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	30274437	30274444	+	IGR	DEL	CCATCTCG	-	-	rs2776223	by1000genomes	TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30274437_30274444delCCATCTCG								N6AMT1 (16744 upstream) : RNF160 (26022 downstream)																							tgcaatggcaccatctcgccatctcagc	0.087													4	2	---	---	---	---	
DMC1	11144	broad.mit.edu	37	22	38964457	38964458	+	Intron	DEL	TG	-	-	rs11570378		TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38964457_38964458delTG	uc003avz.1	-						DMC1_uc011anv.1_5'Flank|DMC1_uc003awa.1_Intron	NM_007068	NP_008999	Q14565	DMC1_HUMAN	DMC1 dosage suppressor of mck1 homolog						reciprocal meiotic recombination	condensed nuclear chromosome	ATP binding|DNA binding|DNA-dependent ATPase activity|protein binding			ovary(1)	1	Melanoma(58;0.0286)					CATTATTTCTtgtgtgtgtgtg	0.366								Homologous_recombination					2	4	---	---	---	---	
TTLL1	25809	broad.mit.edu	37	22	43435575	43435576	+	3'UTR	INS	-	A	A	rs143546633	by1000genomes	TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43435575_43435576insA	uc003bdi.2	-	11					TTLL1_uc010gzh.2_3'UTR|TTLL1_uc003bdj.2_3'UTR|TTLL1_uc003bdh.2_3'UTR	NM_012263	NP_036395	O95922	TTLL1_HUMAN	tubulin tyrosine ligase-like family, member 1						protein polyglutamylation	cytoplasm|microtubule	ATP binding|tubulin-glutamic acid ligase activity|tubulin-tyrosine ligase activity			skin(1)	1		Ovarian(80;0.0694)		BRCA - Breast invasive adenocarcinoma(115;0.00461)		GGTTAAAAATTAAAAAAAAAAG	0.312													4	3	---	---	---	---	
APOO	79135	broad.mit.edu	37	X	23874672	23874672	+	Intron	DEL	T	-	-			TCGA-BP-5194-01A-02D-1429-08	TCGA-BP-5194-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:23874672delT	uc004dax.2	-						APOO_uc004daw.2_Intron|APOO_uc004day.3_Intron	NM_024122	NP_077027	Q9BUR5	APOO_HUMAN	apolipoprotein O precursor						lipid transport	high-density lipoprotein particle|integral to membrane|low-density lipoprotein particle|very-low-density lipoprotein particle					0						caatggtagattttttttttt	0.000													4	2	---	---	---	---	
