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
SLFNL1	200172	broad.mit.edu	37	1	41483497	41483497	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41483497C>T	uc001cgm.1	-	3	987	c.767G>A	c.(766-768)GGC>GAC	p.G256D	SLFNL1_uc009vwf.1_Missense_Mutation_p.G256D|SLFNL1_uc001cgn.1_Missense_Mutation_p.G197D|SLFNL1_uc009vwg.1_Missense_Mutation_p.G256D	NM_144990	NP_659427	Q499Z3	SLNL1_HUMAN	schlafen-like 1	256							ATP binding			skin(1)	1	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Breast(333;0.1)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0393)				GAGCAGGCTGCCGCCCTCGCT	0.667													3	50	---	---	---	---	PASS
NASP	4678	broad.mit.edu	37	1	46073597	46073597	+	Silent	SNP	A	G	G	rs76379164	byFrequency	TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46073597A>G	uc001coi.1	+	6	1116	c.1014A>G	c.(1012-1014)GTA>GTG	p.V338V	NASP_uc010olq.1_Silent_p.V301V|NASP_uc001coh.1_Silent_p.V340V|NASP_uc001coj.1_Intron|NASP_uc010olr.1_Silent_p.V274V|NASP_uc001cok.1_Silent_p.V221V	NM_002482	NP_002473	P49321	NASP_HUMAN	nuclear autoantigenic sperm protein isoform 2	338	Glu-rich (acidic).				blastocyst development|cell cycle|cell proliferation|DNA replication|histone exchange|protein transport	cytoplasm|nucleus	Hsp90 protein binding			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.211)					GTCAAGAAGTACCACCTGCTG	0.552													5	82	---	---	---	---	PASS
SYT11	23208	broad.mit.edu	37	1	155838359	155838359	+	Missense_Mutation	SNP	G	C	C			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155838359G>C	uc001fmg.2	+	2	901	c.638G>C	c.(637-639)AGA>ACA	p.R213T	SYT11_uc010pgq.1_Intron	NM_152280	NP_689493	Q9BT88	SYT11_HUMAN	synaptotagmin XI	213	Cytoplasmic (Potential).|C2 1.					cell junction|synaptic vesicle membrane	protein binding|transporter activity			ovary(1)|skin(1)	2	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)		OV - Ovarian serous cystadenocarcinoma(3;0.000162)			GTGAAGACCAGAGTGCTGCGG	0.572													3	76	---	---	---	---	PASS
KIRREL	55243	broad.mit.edu	37	1	158063224	158063224	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158063224C>A	uc001frn.3	+	12	1971	c.1567C>A	c.(1567-1569)CGC>AGC	p.R523S	KIRREL_uc010pib.1_Missense_Mutation_p.R423S|KIRREL_uc009wsq.2_Missense_Mutation_p.R359S|KIRREL_uc001fro.3_Missense_Mutation_p.R337S	NM_018240	NP_060710	Q96J84	KIRR1_HUMAN	kin of IRRE like precursor	523	Cytoplasmic (Potential).					integral to membrane				ovary(1)	1	all_hematologic(112;0.0378)					CCTCTACCGGCGCCGCAAAGG	0.602													3	92	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	90139453	90139453	+	RNA	SNP	G	C	C			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90139453G>C	uc010fhm.2	+	18		c.2246G>C								Parts of antibodies, mostly variable regions.																		GCTGCATCCAGTTTGCAAAGT	0.512													4	170	---	---	---	---	PASS
EIF5B	9669	broad.mit.edu	37	2	99985894	99985894	+	Missense_Mutation	SNP	T	C	C			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99985894T>C	uc002tab.2	+	8	1611	c.1427T>C	c.(1426-1428)ATG>ACG	p.M476T		NM_015904	NP_056988	O60841	IF2P_HUMAN	eukaryotic translation initiation factor 5B	476					regulation of translational initiation	cytosol	GTP binding|GTPase activity|protein binding|translation initiation factor activity			ovary(2)|pancreas(1)	3						GTAGAAGTTATGGAACAAGGA	0.353													7	62	---	---	---	---	PASS
LY75	4065	broad.mit.edu	37	2	160737621	160737621	+	Silent	SNP	C	T	T	rs11675155	byFrequency	TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160737621C>T	uc002ubc.3	-	8	1446	c.1377G>A	c.(1375-1377)ACG>ACA	p.T459T	LY75_uc002ubb.3_Silent_p.T459T|LY75_uc010fos.2_Silent_p.T459T|LY75_uc010fot.1_Silent_p.T459T	NM_002349	NP_002340	O60449	LY75_HUMAN	lymphocyte antigen 75 precursor	459	C-type lectin 2.|Extracellular (Potential).				endocytosis|immune response|inflammatory response	integral to plasma membrane	receptor activity|sugar binding				0				COAD - Colon adenocarcinoma(177;0.132)		CACAGTTGGGCGTCTTATTGT	0.368													5	165	---	---	---	---	PASS
RPS23	6228	broad.mit.edu	37	5	81574182	81574182	+	5'UTR	SNP	C	T	T	rs6880209	by1000genomes	TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:81574182C>T	uc003khu.2	-	1					ATP6AP1L_uc003khv.2_5'Flank	NM_001025	NP_001016	P62266	RS23_HUMAN	ribosomal protein S23						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic small ribosomal subunit	protein binding|structural constituent of ribosome				0		Lung NSC(167;0.0025)|all_lung(232;0.00278)|Ovarian(174;0.0336)		OV - Ovarian serous cystadenocarcinoma(54;1.94e-42)|Epithelial(54;8.38e-37)|all cancers(79;1.42e-31)		AGAGAAGCACCGCAGGAAGGA	0.687													2	3	---	---	---	---	PASS
LOC202181	202181	broad.mit.edu	37	5	177054546	177054546	+	Missense_Mutation	SNP	T	A	A			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177054546T>A	uc011dgc.1	-	2	327	c.199A>T	c.(199-201)AAT>TAT	p.N67Y	LOC202181_uc011dgb.1_RNA	NM_198567	NP_940969			hypothetical protein LOC375484												0						AGGGGAAAATTCTCTTCAATG	0.413													5	56	---	---	---	---	PASS
FZD9	8326	broad.mit.edu	37	7	72849476	72849476	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72849476C>T	uc003tyb.2	+	1	1368	c.1139C>T	c.(1138-1140)GCG>GTG	p.A380V		NM_003508	NP_003499	O00144	FZD9_HUMAN	frizzled 9 precursor	380	Extracellular (Potential).				B cell differentiation|brain development|canonical Wnt receptor signaling pathway|embryo development|gonad development|neuroblast proliferation|vasculature development	cell surface|filopodium membrane|integral to membrane|perinuclear region of cytoplasm	G-protein coupled receptor activity|PDZ domain binding|protein heterodimerization activity|protein homodimerization activity|Wnt receptor activity|Wnt-protein binding			central_nervous_system(1)	1		Lung NSC(55;0.0659)|all_lung(88;0.152)				CGCAAGGTGGCGGGTGATGAG	0.667													4	71	---	---	---	---	PASS
HGF	3082	broad.mit.edu	37	7	81359036	81359036	+	Missense_Mutation	SNP	G	T	T			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:81359036G>T	uc003uhl.2	-	8	1090	c.925C>A	c.(925-927)CAA>AAA	p.Q309K	HGF_uc003uhm.2_Missense_Mutation_p.Q304K	NM_000601	NP_000592	P14210	HGF_HUMAN	hepatocyte growth factor isoform 1	309	Kringle 3.				epithelial to mesenchymal transition|mitosis|platelet activation|platelet degranulation|proteolysis|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling	platelet alpha granule lumen	growth factor activity|serine-type endopeptidase activity			ovary(2)|central_nervous_system(2)	4						CCTTCTCCTTGACCTTGGATG	0.398													10	130	---	---	---	---	PASS
PCLO	27445	broad.mit.edu	37	7	82474612	82474612	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82474612C>T	uc003uhx.2	-	13	14310	c.14021G>A	c.(14020-14022)AGC>AAC	p.S4674N	PCLO_uc003uhv.2_Missense_Mutation_p.S4674N|PCLO_uc003uht.1_Missense_Mutation_p.S125N|PCLO_uc003uhu.1_Missense_Mutation_p.S104N	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	4562					cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity			ovary(7)	7						CTTCTTTTTGCTCACTGAGGG	0.468													3	29	---	---	---	---	PASS
LOC442421	442421	broad.mit.edu	37	9	66500933	66500933	+	RNA	SNP	G	C	C			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66500933G>C	uc004aed.1	+	3		c.1026G>C								Homo sapiens similar to prostaglandin E receptor 4, subtype EP4; PGE receptor, EP4 subtype; prostaglandin E2 receptor, mRNA (cDNA clone IMAGE:5288780).												0						CAGCAAGAGCGCCGCGGAGCG	0.607													2	11	---	---	---	---	PASS
RNF20	56254	broad.mit.edu	37	9	104314514	104314514	+	Missense_Mutation	SNP	A	T	T			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104314514A>T	uc004bbn.2	+	12	1590	c.1500A>T	c.(1498-1500)AAA>AAT	p.K500N		NM_019592	NP_062538	Q5VTR2	BRE1A_HUMAN	ring finger protein 20	500	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)		ATAAGCGGAAATTGAGAGAAG	0.448													7	105	---	---	---	---	PASS
OR13C2	392376	broad.mit.edu	37	9	107367082	107367082	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107367082G>A	uc011lvq.1	-	1	827	c.827C>T	c.(826-828)ACC>ATC	p.T276I		NM_001004481	NP_001004481	Q8NGS9	O13C2_HUMAN	olfactory receptor, family 13, subfamily C,	276	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1						AATTTTGTCGGTAGCATCCAA	0.408													8	154	---	---	---	---	PASS
RC3H2	54542	broad.mit.edu	37	9	125613481	125613481	+	Missense_Mutation	SNP	T	C	C			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125613481T>C	uc010mwc.1	-	20	3500	c.3259A>G	c.(3259-3261)AGT>GGT	p.S1087G	uc004bnb.1_5'Flank|RC3H2_uc004bnc.2_RNA	NM_001100588	NP_001094058	Q9HBD1	RC3H2_HUMAN	ring finger and CCCH-type zinc finger domains 2	1087						cell surface|endomembrane system|membrane|membrane fraction|perinuclear region of cytoplasm	DNA binding|zinc ion binding			ovary(2)|lung(2)	4						TTTTGAGAACTGATACCAAGC	0.363													7	129	---	---	---	---	PASS
ARHGAP22	58504	broad.mit.edu	37	10	49654442	49654442	+	Missense_Mutation	SNP	G	T	T			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:49654442G>T	uc001jgt.2	-	10	2386	c.2089C>A	c.(2089-2091)CCA>ACA	p.P697T	ARHGAP22_uc001jgs.2_Missense_Mutation_p.P607T|ARHGAP22_uc001jgu.2_Missense_Mutation_p.P713T|ARHGAP22_uc010qgl.1_Missense_Mutation_p.P654T|ARHGAP22_uc010qgm.1_Missense_Mutation_p.P703T|ARHGAP22_uc001jgv.2_Missense_Mutation_p.P395T|ARHGAP22_uc001jgr.2_Missense_Mutation_p.P414T	NM_021226	NP_067049	Q7Z5H3	RHG22_HUMAN	Rho GTPase activating protein 2	697					angiogenesis|cell differentiation|regulation of small GTPase mediated signal transduction|regulation of transcription, DNA-dependent|small GTPase mediated signal transduction|transcription, DNA-dependent	cytosol|nucleus	GTPase activator activity			ovary(1)	1						TTTTACTTTGGGGCCCTGGCA	0.542													3	43	---	---	---	---	PASS
LOC650368	650368	broad.mit.edu	37	11	3427845	3427845	+	RNA	SNP	C	T	T			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3427845C>T	uc010qxs.1	+	9		c.838C>T			LOC650368_uc001lxx.2_RNA|LOC650368_uc001lxy.2_RNA	NR_024248				Homo sapiens cDNA FLJ41654 fis, clone FEBRA2025463, weakly  similar to Homo sapiens HMT-1 mRNA for beta-1,4 mannosyltransferase.												0						CTTCAAGTGGCAGGAGCAGAA	0.587													4	45	---	---	---	---	PASS
CD248	57124	broad.mit.edu	37	11	66082756	66082756	+	Silent	SNP	C	T	T			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66082756C>T	uc001ohm.1	-	1	1760	c.1743G>A	c.(1741-1743)CAG>CAA	p.Q581Q		NM_020404	NP_065137	Q9HCU0	CD248_HUMAN	tumor endothelial marker 1 precursor	581	Pro-rich.|Extracellular (Potential).					integral to membrane|proteinaceous extracellular matrix	calcium ion binding|sugar binding			large_intestine(3)	3					Cefalotin(DB00456)	TAATGGGAAGCTGGGTGGCCT	0.632													10	177	---	---	---	---	PASS
ACAT1	38	broad.mit.edu	37	11	108002646	108002646	+	Missense_Mutation	SNP	G	T	T			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108002646G>T	uc001pjy.2	+	2	161	c.85G>T	c.(85-87)GTG>TTG	p.V29L	ACAT1_uc001pjw.1_Missense_Mutation_p.V29L|ACAT1_uc001pjx.2_5'UTR	NM_000019	NP_000010	P24752	THIL_HUMAN	acetyl-Coenzyme A acetyltransferase 1 precursor	29					acetoacetic acid biosynthetic process|branched chain family amino acid catabolic process|ketone body biosynthetic process|ketone body catabolic process	mitochondrial matrix	acetyl-CoA C-acetyltransferase activity|metal ion binding			ovary(3)	3		all_cancers(61;6.41e-10)|all_epithelial(67;2.83e-06)|Melanoma(852;1.46e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;2.96e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.00108)|OV - Ovarian serous cystadenocarcinoma(223;0.192)	Sulfasalazine(DB00795)	AATAAGATATGTGGAACGGAG	0.209													3	55	---	---	---	---	PASS
ROBO4	54538	broad.mit.edu	37	11	124766108	124766108	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124766108C>T	uc001qbg.2	-	4	805	c.665G>A	c.(664-666)CGG>CAG	p.R222Q	ROBO4_uc010sas.1_Missense_Mutation_p.R77Q|ROBO4_uc001qbh.2_Missense_Mutation_p.R112Q|ROBO4_uc001qbi.2_5'Flank|ROBO4_uc010sat.1_5'Flank	NM_019055	NP_061928	Q8WZ75	ROBO4_HUMAN	roundabout homolog 4, magic roundabout	222	Ig-like C2-type 2.				angiogenesis|cell differentiation	integral to membrane	receptor activity			ovary(1)|skin(1)	2	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0301)		GATGGAAACCCGGGCTGCGCG	0.607													3	73	---	---	---	---	PASS
SLC25A3	5250	broad.mit.edu	37	12	98993848	98993848	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:98993848C>A	uc001tfo.2	+	6	880	c.760C>A	c.(760-762)CGC>AGC	p.R254S	SLC25A3_uc001tfm.2_Missense_Mutation_p.R253S|SLC25A3_uc001tfn.2_Missense_Mutation_p.R253S|SLC25A3_uc001tfp.2_Missense_Mutation_p.R253S|SLC25A3_uc001tfq.2_Missense_Mutation_p.R123S|SLC25A3_uc001tfr.2_Missense_Mutation_p.R254S|SLC25A3_uc001tfs.2_Missense_Mutation_p.R210S|SLC25A3_uc009ztn.2_Missense_Mutation_p.R253S|SLC25A3_uc001tft.2_Missense_Mutation_p.R253S	NM_005888	NP_005879	Q00325	MPCP_HUMAN	solute carrier family 25 member 3 isoform a	254	Mitochondrial intermembrane (Potential).				generation of precursor metabolites and energy	integral to plasma membrane|mitochondrial inner membrane	phosphate carrier activity|symporter activity				0		Lung NSC(355;4.08e-05)|Breast(359;0.00191)|Colorectal(145;0.00205)|Myeloproliferative disorder(1001;0.0255)		GBM - Glioblastoma multiforme(134;1.36e-23)|BRCA - Breast invasive adenocarcinoma(302;0.000115)		TCCTAAGCCCCGCAGTGAATG	0.428													3	63	---	---	---	---	PASS
EP400	57634	broad.mit.edu	37	12	132547087	132547087	+	Silent	SNP	G	A	A	rs12366766		TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132547087G>A	uc001ujn.2	+	46	8210	c.8175G>A	c.(8173-8175)CAG>CAA	p.Q2725Q	EP400_uc001ujl.2_Silent_p.Q2724Q|EP400_uc001ujm.2_Silent_p.Q2644Q|EP400_uc001ujp.2_5'UTR	NM_015409	NP_056224	Q96L91	EP400_HUMAN	E1A binding protein p400	2761	Poly-Gln.|Interaction with ZNF42 (By similarity).				histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent	NuA4 histone acetyltransferase complex|nuclear speck	ATP binding|DNA binding|helicase activity			central_nervous_system(4)|ovary(3)|breast(3)|skin(2)	12	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		agcagcagcagcaacaacagc	0.289													4	19	---	---	---	---	PASS
RTL1	388015	broad.mit.edu	37	14	101348187	101348187	+	Missense_Mutation	SNP	T	C	C			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101348187T>C	uc010txj.1	-	1	2998	c.2939A>G	c.(2938-2940)GAC>GGC	p.D980G	MIR433_hsa-mir-433|MI0001723_5'Flank|uc001yig.3_5'Flank|MIR127_hsa-mir-127|MI0000472_5'Flank|MIR432_hsa-mir-432|MI0003133_5'Flank|uc010txk.1_5'Flank|MIR136_hsa-mir-136|MI0000475_5'Flank	NM_001134888	NP_001128360	A6NKG5	RTL1_HUMAN	retrotransposon-like 1	980										pancreas(1)	1						CTCCATGACGTCAAAGTTGAA	0.557													3	101	---	---	---	---	PASS
TUBGCP4	27229	broad.mit.edu	37	15	43663575	43663575	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43663575C>A	uc001zro.2	+	1	263	c.23C>A	c.(22-24)GCT>GAT	p.A8D	ZSCAN29_uc001zrj.1_5'Flank|ZSCAN29_uc001zrk.1_5'Flank|ZSCAN29_uc010bdf.1_5'Flank|ZSCAN29_uc001zrl.1_5'Flank|ZSCAN29_uc010bdg.1_5'Flank|ZSCAN29_uc001zrm.2_5'Flank|TUBGCP4_uc001zrn.2_Missense_Mutation_p.A8D	NM_014444	NP_055259	Q9UGJ1	GCP4_HUMAN	tubulin, gamma complex associated protein 4	8					G2/M transition of mitotic cell cycle|microtubule nucleation|protein complex assembly	centrosome|cytosol|gamma-tubulin ring complex|microtubule|spindle pole	structural constituent of cytoskeleton			ovary(3)	3		all_cancers(109;1.27e-10)|all_epithelial(112;4.82e-09)|Lung NSC(122;1.72e-06)|all_lung(180;1.59e-05)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;3.53e-07)		CTGCTCTTGGCTCTGAGCGGG	0.652											OREG0023087	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	5	21	---	---	---	---	PASS
CLK3	1198	broad.mit.edu	37	15	74914890	74914890	+	Missense_Mutation	SNP	G	C	C			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74914890G>C	uc010uln.1	+	5	1427	c.966G>C	c.(964-966)TTG>TTC	p.L322F	CLK3_uc002ayg.3_Missense_Mutation_p.L174F|CLK3_uc002ayh.3_5'UTR|CLK3_uc002ayj.3_Intron|CLK3_uc002ayk.3_Missense_Mutation_p.L101F|CLK3_uc002ayl.3_5'Flank	NM_001130028	NP_001123500	P49761	CLK3_HUMAN	CDC-like kinase 3 isoform a	322	Protein kinase.					acrosomal vesicle|nucleus	ATP binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			stomach(2)	2						TGGAGTGCTTGGACCATGCCA	0.567													5	114	---	---	---	---	PASS
ACAN	176	broad.mit.edu	37	15	89400137	89400137	+	Missense_Mutation	SNP	A	G	G			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89400137A>G	uc010upo.1	+	12	4695	c.4321A>G	c.(4321-4323)ACT>GCT	p.T1441A	ACAN_uc010upp.1_Missense_Mutation_p.T1441A|ACAN_uc002bna.2_RNA	NM_013227	NP_037359	E7EX88	E7EX88_HUMAN	aggrecan isoform 2 precursor	1441					cell adhesion		hyaluronic acid binding|sugar binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			TCTAGAGACTACTGCCCCTGG	0.537													5	189	---	---	---	---	PASS
PKD1	5310	broad.mit.edu	37	16	2155909	2155909	+	Missense_Mutation	SNP	T	A	A			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2155909T>A	uc002cos.1	-	20	8029	c.7820A>T	c.(7819-7821)CAC>CTC	p.H2607L	PKD1_uc002cot.1_Missense_Mutation_p.H2607L|PKD1_uc010bse.1_5'Flank	NM_001009944	NP_001009944	P98161	PKD1_HUMAN	polycystin 1 isoform 1 precursor	2607	Extracellular (Potential).|REJ.				calcium-independent cell-matrix adhesion|homophilic cell adhesion|neuropeptide signaling pathway	basolateral plasma membrane|integral to plasma membrane	protein domain specific binding|sugar binding			central_nervous_system(2)|skin(1)	3						CTCGATGACGTGCTGGGGATC	0.657													4	45	---	---	---	---	PASS
TOX3	27324	broad.mit.edu	37	16	52484402	52484402	+	Silent	SNP	C	T	T			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:52484402C>T	uc002egw.2	-	4	636	c.465G>A	c.(463-465)CGG>CGA	p.R155R	TOX3_uc010vgt.1_Silent_p.R150R|TOX3_uc010vgu.1_Silent_p.R155R	NM_001080430	NP_001073899	O15405	TOX3_HUMAN	TOX high mobility group box family member 3	155					apoptosis|negative regulation of neuron apoptosis|positive regulation of anti-apoptosis|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	chromatin binding|estrogen response element binding|phosphoprotein binding|protein homodimerization activity				0						GGACGATGGACCGCATGATCA	0.562													5	102	---	---	---	---	PASS
EPN2	22905	broad.mit.edu	37	17	19235303	19235303	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19235303G>A	uc002gvd.3	+	10	1997	c.1549G>A	c.(1549-1551)GCG>ACG	p.A517T	EPN2_uc010cql.1_Missense_Mutation_p.A226T|EPN2_uc002gve.3_Missense_Mutation_p.A460T|EPN2_uc002gvf.3_Missense_Mutation_p.A232T|EPN2_uc010vyo.1_Missense_Mutation_p.A225T|EPN2_uc010vyp.1_Missense_Mutation_p.A453T|EPN2_uc010vyq.1_Missense_Mutation_p.A454T|EPN2_uc002gvh.1_Intron|EPN2_uc002gvj.3_Missense_Mutation_p.A180T	NM_014964	NP_055779	O95208	EPN2_HUMAN	epsin 2 isoform b	517	6 X 3 AA repeats of [DE]-P-W.				endocytosis		lipid binding			skin(1)	1	all_cancers(12;3.11e-05)|all_epithelial(12;0.00121)|Hepatocellular(7;0.00345)|Breast(13;0.143)					GGGCCCCAACGCGGCCCTGGT	0.627													4	134	---	---	---	---	PASS
SLFN11	91607	broad.mit.edu	37	17	33690215	33690215	+	Silent	SNP	G	T	T			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33690215G>T	uc010ctp.2	-	4	1054	c.612C>A	c.(610-612)ATC>ATA	p.I204I	SLFN11_uc010ctq.2_Silent_p.I204I|SLFN11_uc002hjh.3_Silent_p.I204I|SLFN11_uc002hjg.3_Silent_p.I204I|SLFN11_uc010ctr.2_Silent_p.I204I	NM_001104588	NP_001098058	Q7Z7L1	SLN11_HUMAN	schlafen family member 11	204						nucleus	ATP binding			large_intestine(1)|ovary(1)|skin(1)	3		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		GAAAAGGCAGGATTTCACCAT	0.413													7	171	---	---	---	---	PASS
TRIM37	4591	broad.mit.edu	37	17	57076695	57076695	+	Intron	SNP	C	A	A			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57076695C>A	uc002iwy.3	-						TRIM37_uc002iwz.3_3'UTR|TRIM37_uc002ixa.3_3'UTR|TRIM37_uc010woc.1_3'UTR	NM_001005207	NP_001005207	O94972	TRI37_HUMAN	tripartite motif-containing 37 protein							perinuclear region of cytoplasm|peroxisome	ligase activity|protein binding|zinc ion binding			lung(2)|pancreas(2)|ovary(1)|skin(1)|breast(1)	7	Medulloblastoma(34;0.0922)|all_neural(34;0.101)					CAGCAAAATTCAGGGTCAAGG	0.373									Mulibrey_Nanism				5	107	---	---	---	---	PASS
RAB12	201475	broad.mit.edu	37	18	8609872	8609872	+	Silent	SNP	C	A	A			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8609872C>A	uc002knp.2	+	1	430	c.147C>A	c.(145-147)GGC>GGA	p.G49G	RAB12_uc002kno.1_Silent_p.G145G	NM_001025300	NP_001020471	Q6IQ22	RAB12_HUMAN	RAB12, member RAS oncogene family	49	GTP.				protein transport|small GTPase mediated signal transduction	Golgi membrane	GTP binding				0						TCATTATCGGCTCCCGCGGCG	0.652													4	20	---	---	---	---	PASS
SETBP1	26040	broad.mit.edu	37	18	42532845	42532845	+	Silent	SNP	C	A	A			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:42532845C>A	uc010dni.2	+	4	3836	c.3540C>A	c.(3538-3540)GGC>GGA	p.G1180G		NM_015559	NP_056374	Q9Y6X0	SETBP_HUMAN	SET binding protein 1 isoform a	1180						nucleus	DNA binding			upper_aerodigestive_tract(2)|large_intestine(1)	3				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)		AAGCCACAGGCTTCTCCAGCC	0.522									Schinzel-Giedion_syndrome				9	77	---	---	---	---	PASS
ALPK2	115701	broad.mit.edu	37	18	56246150	56246150	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56246150C>A	uc002lhj.3	-	4	2072	c.1858G>T	c.(1858-1860)GAC>TAC	p.D620Y		NM_052947	NP_443179	Q86TB3	ALPK2_HUMAN	heart alpha-kinase	620							ATP binding|protein serine/threonine kinase activity			ovary(7)|skin(5)|lung(1)|central_nervous_system(1)	14						GAGACTGAGTCTGTTGAAGTT	0.473											OREG0025011	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	5	160	---	---	---	---	PASS
RTBDN	83546	broad.mit.edu	37	19	12940772	12940772	+	Nonsense_Mutation	SNP	G	A	A			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12940772G>A	uc002mvi.2	-	2	152	c.22C>T	c.(22-24)CGA>TGA	p.R8*	RTBDN_uc002mvh.1_Nonsense_Mutation_p.R40*|RTBDN_uc002mvj.2_Nonsense_Mutation_p.R40*	NM_001080997	NP_001074466	Q9BSG5	RTBDN_HUMAN	retbindin isoform 1	8						extracellular region					0						CCGATGGGTCGCATGTGGACC	0.612													3	47	---	---	---	---	PASS
RHPN2	85415	broad.mit.edu	37	19	33490564	33490564	+	Missense_Mutation	SNP	G	T	T	rs147870656	byFrequency	TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33490564G>T	uc002nuf.2	-	10	1219	c.1153C>A	c.(1153-1155)CTC>ATC	p.L385I	RHPN2_uc010xro.1_Missense_Mutation_p.L234I|RHPN2_uc002nue.2_Missense_Mutation_p.L115I	NM_033103	NP_149094	Q8IUC4	RHPN2_HUMAN	rhophilin, Rho GTPase binding protein 2	385	BRO1.				signal transduction	perinuclear region of cytoplasm	protein binding			central_nervous_system(5)|ovary(1)	6	Esophageal squamous(110;0.137)					TGGTCGTAGAGCTGGGACAGG	0.602													8	44	---	---	---	---	PASS
LIG1	3978	broad.mit.edu	37	19	48622427	48622427	+	Silent	SNP	A	G	G	rs20581	byFrequency	TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48622427A>G	uc002pia.1	-	25	2526	c.2406T>C	c.(2404-2406)GAT>GAC	p.D802D	LIG1_uc010xze.1_Silent_p.D495D|LIG1_uc002phz.1_RNA|LIG1_uc002pib.1_RNA|LIG1_uc010xzf.1_Silent_p.D734D|LIG1_uc010xzg.1_Silent_p.D771D	NM_000234	NP_000225	P18858	DNLI1_HUMAN	DNA ligase I	802					anatomical structure morphogenesis|base-excision repair|cell division|DNA ligation involved in DNA repair|DNA strand elongation involved in DNA replication|double-strand break repair via homologous recombination|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	nucleoplasm	ATP binding|DNA binding|DNA ligase (ATP) activity|metal ion binding			large_intestine(2)|lung(1)	3		all_epithelial(76;3.1e-06)|all_lung(116;4.39e-06)|Lung NSC(112;8.96e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;8.45e-05)|all cancers(93;0.000423)|Epithelial(262;0.0177)|GBM - Glioblastoma multiforme(486;0.0329)	Bleomycin(DB00290)	CCAGCTCCTCATCACTGAAGC	0.627								NER					4	8	---	---	---	---	PASS
ZNF813	126017	broad.mit.edu	37	19	53993763	53993763	+	Missense_Mutation	SNP	G	C	C			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53993763G>C	uc002qbu.2	+	4	405	c.277G>C	c.(277-279)GAT>CAT	p.D93H	ZNF813_uc010eqq.1_Intron	NM_001004301	NP_001004301	Q6ZN06	ZN813_HUMAN	zinc finger protein 813	93					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)	1				GBM - Glioblastoma multiforme(134;0.00619)		AATTGATAAAGATATTCATAA	0.398													11	145	---	---	---	---	PASS
ENTPD6	955	broad.mit.edu	37	20	25188018	25188018	+	Missense_Mutation	SNP	A	C	C			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25188018A>C	uc002wuj.2	+	3	541	c.361A>C	c.(361-363)ACC>CCC	p.T121P	ENTPD6_uc010zsy.1_Missense_Mutation_p.T121P|ENTPD6_uc010gdj.1_Missense_Mutation_p.T93P|ENTPD6_uc010zsz.1_Intron|ENTPD6_uc002wum.2_Missense_Mutation_p.T104P|ENTPD6_uc010zta.1_Missense_Mutation_p.T121P|ENTPD6_uc002wun.2_Missense_Mutation_p.T121P|ENTPD6_uc002wuk.2_Missense_Mutation_p.T120P|ENTPD6_uc002wul.2_Missense_Mutation_p.T120P|ENTPD6_uc010ztb.1_Missense_Mutation_p.T93P|ENTPD6_uc010ztc.1_Missense_Mutation_p.T93P|ENTPD6_uc002wuo.2_Intron|ENTPD6_uc010ztd.1_5'Flank	NM_001247	NP_001238	O75354	ENTP6_HUMAN	ectonucleoside triphosphate diphosphohydrolase 6	121	Lumenal (Potential).					Golgi membrane|integral to membrane	nucleoside-diphosphatase activity				0						CTTCCAGTTCACCCGGCCCCC	0.587													4	31	---	---	---	---	PASS
KCNG1	3755	broad.mit.edu	37	20	49620863	49620863	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49620863C>A	uc002xwa.3	-	3	1550	c.1255G>T	c.(1255-1257)GTC>TTC	p.V419F		NM_002237	NP_002228	Q9UIX4	KCNG1_HUMAN	potassium voltage-gated channel, subfamily G,	419						voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(1)|central_nervous_system(1)	2						ATGGTGATGACAGCCCACCAG	0.647													5	81	---	---	---	---	PASS
MAGEB3	4114	broad.mit.edu	37	X	30254530	30254530	+	Silent	SNP	A	G	G	rs2071310	byFrequency	TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:30254530A>G	uc004dca.1	+	5	1226	c.489A>G	c.(487-489)GTA>GTG	p.V163V		NM_002365	NP_002356	O15480	MAGB3_HUMAN	melanoma antigen family B, 3	163	MAGE.										0						TGGAGGTGGTATTTGGTGTTG	0.408													3	43	---	---	---	---	PASS
DDX3X	1654	broad.mit.edu	37	X	41196665	41196665	+	Missense_Mutation	SNP	C	G	G			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41196665C>G	uc004dfe.2	+	2	905	c.50C>G	c.(49-51)GCT>GGT	p.A17G	DDX3X_uc004dfd.1_RNA|DDX3X_uc010nhf.1_Missense_Mutation_p.A17G|DDX3X_uc004dff.2_Missense_Mutation_p.A17G|DDX3X_uc011mkq.1_Missense_Mutation_p.A17G|DDX3X_uc011mkr.1_Missense_Mutation_p.A17G|DDX3X_uc011mks.1_Missense_Mutation_p.A17G|DDX3X_uc004dfg.2_RNA|DDX3X_uc011mkt.1_RNA	NM_001356	NP_001347	O00571	DDX3X_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 3	17					interspecies interaction between organisms	cytoplasm|nuclear speck	ATP binding|ATP-dependent RNA helicase activity|DNA binding|protein binding|RNA binding			ovary(2)|breast(2)|central_nervous_system(1)|skin(1)	6						TTCTAGTTTGCTGGCCTAGAC	0.418										HNSCC(61;0.18)			3	38	---	---	---	---	PASS
IGBP1	3476	broad.mit.edu	37	X	69366563	69366563	+	Missense_Mutation	SNP	G	A	A	rs141927060		TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69366563G>A	uc004dxv.2	+	3	1062	c.563G>A	c.(562-564)CGT>CAT	p.R188H	IGBP1_uc004dxw.2_Missense_Mutation_p.R188H	NM_001551	NP_001542	P78318	IGBP1_HUMAN	immunoglobulin binding protein 1	188					B cell activation|negative regulation of caspase activity|negative regulation of stress-activated MAPK cascade|negative regulation of transcription from RNA polymerase II promoter|regulation of microtubule-based movement|response to interleukin-1|response to tumor necrosis factor|signal transduction	cytoplasm	protein phosphatase type 2A regulator activity			kidney(1)|pancreas(1)	2						GATGATGAGCGTGTTCGTGAA	0.413													3	27	---	---	---	---	PASS
IGBP1	3476	broad.mit.edu	37	X	69366608	69366608	+	Missense_Mutation	SNP	T	C	C	rs61755732	byFrequency	TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69366608T>C	uc004dxv.2	+	3	1107	c.608T>C	c.(607-609)ATC>ACC	p.I203T	IGBP1_uc004dxw.2_Missense_Mutation_p.I203T	NM_001551	NP_001542	P78318	IGBP1_HUMAN	immunoglobulin binding protein 1	203					B cell activation|negative regulation of caspase activity|negative regulation of stress-activated MAPK cascade|negative regulation of transcription from RNA polymerase II promoter|regulation of microtubule-based movement|response to interleukin-1|response to tumor necrosis factor|signal transduction	cytoplasm	protein phosphatase type 2A regulator activity			kidney(1)|pancreas(1)	2						TGGATTGATATCAGCTTAGAA	0.433													3	16	---	---	---	---	PASS
DKC1	1736	broad.mit.edu	37	X	153994551	153994551	+	Missense_Mutation	SNP	G	C	C			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153994551G>C	uc004fmm.2	+	5	534	c.324G>C	c.(322-324)TGG>TGC	p.W108C	DKC1_uc010nvf.2_Missense_Mutation_p.W108C|SNORA36A_uc004fmn.2_5'Flank	NM_001363	NP_001354	O60832	DKC1_HUMAN	dyskerin isoform 1	108					cell proliferation|pseudouridine synthesis|rRNA processing|telomere maintenance via telomerase	Cajal body|nucleolus|telomerase holoenzyme complex	protein binding|pseudouridine synthase activity|RNA binding|telomerase activity				0	all_cancers(53;8.15e-17)|all_epithelial(53;1.1e-10)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					TGGTAGCCTGGATTCGACGGA	0.478									Congenital_Dyskeratosis				5	59	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	99474094	99474094	+	Intron	DEL	A	-	-			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:99474094delA	uc001dsd.1	+											Homo sapiens cDNA FLJ38225 fis, clone FCBBF2003528.																		AACAGCAACTAAAAAAAAAAA	0.353													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	121485344	121485347	+	IGR	DEL	TGTT	-	-	rs7415636		TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:121485344_121485347delTGTT								LOC647121 (171658 upstream) : None (None downstream)																							ggaaacactctgtttgtaaagtct	0.005													1495	7	---	---	---	---	
LGTN	1939	broad.mit.edu	37	1	206766826	206766827	+	Intron	DEL	GA	-	-	rs113332386		TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206766826_206766827delGA	uc001heh.2	-						LGTN_uc009xbw.2_Intron	NM_006893	NP_008824	P41214	EIF2D_HUMAN	ligatin						intracellular protein transport	cytoplasm	protein binding|receptor activity|translation initiation factor activity				0	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.166)			gagagagcgcgagagagagaga	0.213													5	3	---	---	---	---	
USH2A	7399	broad.mit.edu	37	1	215812335	215812336	+	Intron	INS	-	A	A	rs146300382	by1000genomes	TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215812335_215812336insA	uc001hku.1	-							NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B						maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		aaaacaacaacaaaaaaaaaac	0.129										HNSCC(13;0.011)			8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	64602739	64602741	+	IGR	DEL	CAC	-	-			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64602739_64602741delCAC								PELI1 (231134 upstream) : HSPC159 (78586 downstream)																							ccaccaccatcaccaccatcacc	0.163													6	3	---	---	---	---	
CYP20A1	57404	broad.mit.edu	37	2	204137575	204137575	+	Intron	DEL	T	-	-			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204137575delT	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						ttatattttcttttttttttt	0.035													5	3	---	---	---	---	
TMCC1	23023	broad.mit.edu	37	3	129547382	129547382	+	Intron	DEL	A	-	-			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129547382delA	uc003emz.3	-						TMCC1_uc010htg.2_Intron	NM_001017395	NP_001017395	O94876	TMCC1_HUMAN	transmembrane and coiled-coil domain family 1							integral to membrane				skin(1)	1						acaaaaaaacaaaaaaaaaaC	0.318													4	2	---	---	---	---	
CXCL9	4283	broad.mit.edu	37	4	76926198	76926198	+	Intron	DEL	T	-	-			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76926198delT	uc003hjh.1	-							NM_002416	NP_002407	Q07325	CXCL9_HUMAN	small inducible cytokine B9 precursor						cell-cell signaling|cellular defense response|chemotaxis|G-protein coupled receptor protein signaling pathway|immune response|inflammatory response	extracellular space	chemokine activity			ovary(1)	1			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			ACTGGTTGAAttttttttttt	0.149													6	3	---	---	---	---	
POU4F2	5458	broad.mit.edu	37	4	147560458	147560466	+	In_Frame_Del	DEL	GGCGGCGGC	-	-	rs72269802		TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:147560458_147560466delGGCGGCGGC	uc003ikv.2	+	1	414_422	c.166_174delGGCGGCGGC	c.(166-174)GGCGGCGGCdel	p.GGG65del		NM_004575	NP_004566	Q12837	PO4F2_HUMAN	Brn3b POU domain transcription factor	65_67	Poly-Gly.				estrogen receptor signaling pathway|MAPKKK cascade|negative regulation of transcription from RNA polymerase II promoter	nuclear speck	RNA polymerase II core promoter proximal region sequence-specific DNA binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription			breast(1)	1	all_hematologic(180;0.151)					CGCTggtggtggcggcggcggcggcggcg	0.397													8	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	90475765	90475772	+	IGR	DEL	GAAGGAAG	-	-			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90475765_90475772delGAAGGAAG								GPR98 (15733 upstream) : ARRDC3 (188769 downstream)																							aaggaaggaagaaggaaggaaggaagga	0.029													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	165455504	165455505	+	IGR	DEL	TA	-	-	rs71282177		TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:165455504_165455505delTA								None (None upstream) : None (None downstream)																							TTTTTTTTTTTATTTCAATCTG	0.272													4	2	---	---	---	---	
RHAG	6005	broad.mit.edu	37	6	49604649	49604650	+	5'Flank	INS	-	A	A			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49604649_49604650insA	uc003ozk.3	-						RHAG_uc010jzl.2_5'Flank|RHAG_uc010jzm.2_5'Flank	NM_000324	NP_000315	Q02094	RHAG_HUMAN	Rh-associated glycoprotein						carbon dioxide transport|cellular ion homeostasis	integral to plasma membrane	ammonia transmembrane transporter activity|ammonium transmembrane transporter activity|ankyrin binding			breast(1)|skin(1)	2	Lung NSC(77;0.0255)					GACATCACAAGAAAAAAAAAAT	0.406													4	2	---	---	---	---	
SYNCRIP	10492	broad.mit.edu	37	6	86346559	86346559	+	Intron	DEL	A	-	-	rs116240890	by1000genomes	TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86346559delA	uc003pla.2	-						SYNCRIP_uc003pku.2_Intron|SYNCRIP_uc003pkw.2_Intron|SYNCRIP_uc003pky.2_Intron|SYNCRIP_uc003pkv.2_Intron|SYNCRIP_uc003pkx.2_Intron|SYNCRIP_uc003pkz.2_Intron	NM_006372	NP_006363	O60506	HNRPQ_HUMAN	synaptotagmin binding, cytoplasmic RNA						CRD-mediated mRNA stabilization|interspecies interaction between organisms	catalytic step 2 spliceosome|CRD-mediated mRNA stability complex|endoplasmic reticulum|histone pre-mRNA 3'end processing complex|microsome|nucleoplasm	nucleotide binding|protein binding			ovary(2)	2		all_cancers(76;0.000137)|Acute lymphoblastic leukemia(125;3.66e-08)|Prostate(29;8.2e-07)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0297)		BRCA - Breast invasive adenocarcinoma(108;0.0389)		GTGATGTGGGAAAAAAAAAAC	0.353													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	105890907	105890910	+	IGR	DEL	TCCT	-	-			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:105890907_105890910delTCCT								PREP (39938 upstream) : PRDM1 (643285 downstream)																							cctccctccctccttccttccttc	0.108													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	160133097	160133113	+	IGR	DEL	CTCGGCTGCTCAGACCT	-	-	rs71551146		TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160133097_160133113delCTCGGCTGCTCAGACCT								SOD2 (18744 upstream) : WTAP (15016 downstream)																							ataaccaccacTCGGCTGCTCAGacctccataaccac	0.074													8	5	---	---	---	---	
CTSB	1508	broad.mit.edu	37	8	11711114	11711114	+	Intron	DEL	T	-	-	rs34504234		TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11711114delT	uc003wum.2	-						CTSB_uc011kxl.1_Intron|CTSB_uc003wun.2_Intron|CTSB_uc003wuo.2_Intron|CTSB_uc003wup.2_Intron|CTSB_uc003wuq.2_Intron|CTSB_uc010lsc.2_Intron|CTSB_uc003wur.2_Intron|CTSB_uc003wus.1_Intron|CTSB_uc003wut.1_Intron	NM_147780	NP_680090	P07858	CATB_HUMAN	cathepsin B preproprotein						proteolysis|regulation of apoptosis|regulation of catalytic activity	lysosome|melanosome	cysteine-type endopeptidase activity				0	all_epithelial(15;0.205)		STAD - Stomach adenocarcinoma(15;0.00546)	COAD - Colon adenocarcinoma(149;0.184)		CGGAGAACTCTTAAGGAGCTG	0.667													3	4	---	---	---	---	
C9orf150	286343	broad.mit.edu	37	9	12775861	12775862	+	In_Frame_Ins	INS	-	GGCGGCGGC	GGCGGCGGC	rs139315731	by1000genomes	TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:12775861_12775862insGGCGGCGGC	uc003zkw.2	+	1	850_851	c.147_148insGGCGGCGGC	c.(145-150)insGGCGGCGGC	p.55_56insGGG		NM_203403	NP_981948	Q8IV03	CI150_HUMAN	hypothetical protein LOC286343	58_59	Gly-rich.										0				GBM - Glioblastoma multiforme(1;1.64e-13)		gcggtggtggtggcggcggcgg	0.505													7	5	---	---	---	---	
FAM154A	158297	broad.mit.edu	37	9	19028208	19028209	+	Intron	INS	-	A	A			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19028208_19028209insA	uc003zni.1	-						FAM154A_uc010mip.1_Intron	NM_153707	NP_714918	Q8IYX7	F154A_HUMAN	hypothetical protein LOC158297											pancreas(1)	1				GBM - Glioblastoma multiforme(50;6.53e-16)		TAAAACAAAACAAAaaaaatac	0.262													4	4	---	---	---	---	
TET1	80312	broad.mit.edu	37	10	70371619	70371620	+	Intron	DEL	GA	-	-			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70371619_70371620delGA	uc001jok.3	+							NM_030625	NP_085128	Q8NFU7	TET1_HUMAN	CXXC finger 6						DNA demethylation|inner cell mass cell differentiation|negative regulation of methylation-dependent chromatin silencing|stem cell maintenance		iron ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|structure-specific DNA binding|zinc ion binding			ovary(5)|lung(2)|prostate(1)|breast(1)	9						gggagagagggagagagagaga	0.084													4	2	---	---	---	---	
KIAA0913	23053	broad.mit.edu	37	10	75550606	75550607	+	Intron	INS	-	A	A			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75550606_75550607insA	uc009xrl.2	+						KIAA0913_uc001jve.2_Intron|KIAA0913_uc001jvf.2_Intron|KIAA0913_uc001jvh.2_5'Flank|KIAA0913_uc001jvi.2_5'Flank|KIAA0913_uc010qkr.1_5'Flank|KIAA0913_uc001jvj.2_5'Flank	NM_015037	NP_055852	A7E2V4	K0913_HUMAN	hypothetical protein LOC23053								zinc ion binding			breast(1)	1	Prostate(51;0.0112)					gacttggtctcaaaaaaaaaaa	0.193													4	2	---	---	---	---	
C11orf9	745	broad.mit.edu	37	11	61538036	61538036	+	Intron	DEL	G	-	-			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61538036delG	uc001nsc.1	+						C11orf9_uc001nse.1_Intron	NM_001127392	NP_001120864	Q9Y2G1	MRF_HUMAN	myelin gene regulatory factor isoform 2						central nervous system myelination|positive regulation of myelination|positive regulation of transcription, DNA-dependent	integral to membrane|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			breast(1)	1						GTGGGAAGGTGGGGTACAGGG	0.667													4	2	---	---	---	---	
ACVR1B	91	broad.mit.edu	37	12	52345498	52345500	+	5'UTR	DEL	GCG	-	-	rs10540557		TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52345498_52345500delGCG	uc001rzn.2	+	1					ACVR1B_uc001rzl.2_5'UTR|ACVR1B_uc001rzm.2_5'UTR|ACVR1B_uc010snn.1_5'UTR	NM_004302	NP_004293	P36896	ACV1B_HUMAN	activin A receptor, type IB isoform a precursor						G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|peptidyl-threonine phosphorylation|positive regulation of activin receptor signaling pathway|positive regulation of erythrocyte differentiation|protein autophosphorylation|transmembrane receptor protein serine/threonine kinase signaling pathway	cell surface	activin receptor activity, type I|ATP binding|metal ion binding|SMAD binding|transforming growth factor beta receptor activity|ubiquitin protein ligase binding			pancreas(4)|breast(2)|ovary(1)|lung(1)|kidney(1)	9				BRCA - Breast invasive adenocarcinoma(357;0.104)	Adenosine triphosphate(DB00171)	CTGCTGggctgcggcggcggcgg	0.310													3	3	---	---	---	---	
MYL6B	140465	broad.mit.edu	37	12	56551173	56551174	+	Intron	INS	-	A	A			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56551173_56551174insA	uc001sjs.2	+						MYL6B_uc001sjt.2_Intron|MYL6B_uc001sju.1_Intron|MYL6_uc001sjv.2_5'Flank|MYL6_uc001sjw.1_5'Flank|MYL6_uc001sjx.1_5'Flank|MYL6_uc010sqd.1_5'Flank|MYL6_uc001sjz.2_5'Flank|MYL6_uc010sqe.1_5'Flank	NM_002475	NP_002466	P14649	MYL6B_HUMAN	smooth muscle and non-muscle myosin alkali light						muscle filament sliding|skeletal muscle tissue development	cytosol|muscle myosin complex|unconventional myosin complex	calcium ion binding|motor activity|protein binding|structural constituent of muscle				0			OV - Ovarian serous cystadenocarcinoma(18;0.0979)			aactccgtctcaaaaaaaaaaa	0.243													7	4	---	---	---	---	
KNTC1	9735	broad.mit.edu	37	12	123036452	123036453	+	Intron	INS	-	T	T			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123036452_123036453insT	uc001ucv.2	+						KNTC1_uc010taf.1_Intron	NM_014708	NP_055523	P50748	KNTC1_HUMAN	Rough Deal homolog, centromere/kinetochore						cell division|mitotic cell cycle checkpoint|mitotic prometaphase|protein complex assembly|regulation of exit from mitosis	condensed chromosome kinetochore|cytosol|kinetochore microtubule|nucleus|spindle pole	protein binding			ovary(5)|kidney(3)|lung(1)|central_nervous_system(1)	10	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.21e-05)|Epithelial(86;0.000178)|BRCA - Breast invasive adenocarcinoma(302;0.217)		CAGGTCAGGTCttttttttttc	0.208													4	2	---	---	---	---	
TMED2	10959	broad.mit.edu	37	12	124069112	124069114	+	5'UTR	DEL	GGC	-	-	rs63022462		TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124069112_124069114delGGC	uc001ufg.2	+	1						NM_006815	NP_006806	Q15363	TMED2_HUMAN	coated vesicle membrane protein precursor						protein transport|vesicle-mediated transport	COPI coated vesicle membrane|ER-Golgi intermediate compartment|integral to membrane|microsome|zymogen granule membrane	protein binding				0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000138)|Epithelial(86;0.000613)|all cancers(50;0.00745)		aaggcagcggggcggcggcggcg	0.512													4	6	---	---	---	---	
SDCCAG1	9147	broad.mit.edu	37	14	50269013	50269013	+	Intron	DEL	A	-	-			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50269013delA	uc001wxc.2	-						SDCCAG1_uc010anj.1_Intron|SDCCAG1_uc001wwz.2_5'Flank|SDCCAG1_uc001wxa.2_5'Flank|SDCCAG1_uc010tqi.1_Intron|SDCCAG1_uc001wxe.2_Intron|SDCCAG1_uc001wxd.1_Intron	NM_004713	NP_004704	O60524	NEMF_HUMAN	serologically defined colon cancer antigen 1							cytoplasm|nucleus					0	all_epithelial(31;0.000822)|Breast(41;0.0117)	all_lung(585;1.02e-05)		OV - Ovarian serous cystadenocarcinoma(311;5.99e-34)		TAGCATTTCCAAAAAAAAAAA	0.204													4	2	---	---	---	---	
WDR72	256764	broad.mit.edu	37	15	54004802	54004803	+	Intron	INS	-	A	A	rs112182674		TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:54004802_54004803insA	uc002acj.2	-						WDR72_uc010bfi.1_Intron	NM_182758	NP_877435	Q3MJ13	WDR72_HUMAN	WD repeat domain 72											lung(1)|skin(1)	2				all cancers(107;0.0511)		ACCCCACCGCCAAAAAAAAAAA	0.188													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	102292874	102292876	+	Intron	DEL	CTC	-	-			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102292874_102292876delCTC	uc010usj.1	+						uc002bxo.2_5'Flank|uc002bxp.3_5'Flank|uc002bxt.2_5'Flank|uc002bxz.3_5'Flank|uc002byd.2_5'Flank|uc002bye.2_5'Flank|uc002byf.1_5'Flank|uc002byg.2_5'Flank|uc002byi.2_5'Flank|uc002byk.2_5'Flank|uc002bym.2_5'Flank|uc002byn.2_5'Flank|uc010usm.1_5'Flank|uc002byr.2_5'Flank					RecName: Full=Uncharacterized protein C15orf51.; Flags: Fragment;																		AGTTCATCTTCTCAGAGCTGCTG	0.581													4	2	---	---	---	---	
MAF	4094	broad.mit.edu	37	16	79633806	79633808	+	5'UTR	DEL	GCC	-	-	rs5818251		TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:79633806_79633808delGCC	uc002ffn.2	-	1					MAF_uc002ffm.2_5'UTR	NM_001031804	NP_001026974	O75444	MAF_HUMAN	v-maf musculoaponeurotic fibrosarcoma oncogene						transcription from RNA polymerase II promoter	chromatin|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			lung(1)	1		all_epithelial(2;0.139)|Lung NSC(2;0.186)|Melanoma(2;0.211)		UCEC - Uterine corpus endometrioid carcinoma (2;0.0178)		CCATTCTCCTgccgccgccgccg	0.522			T	IGH@	MM								30	22	---	---	---	---	
KRBA2	124751	broad.mit.edu	37	17	8274486	8274486	+	Intron	DEL	A	-	-			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8274486delA	uc002glf.1	-						KRBA2_uc002glg.1_Intron	NM_213597	NP_998762	Q6ZNG9	KRBA2_HUMAN	KRAB-A domain containing 2						DNA integration|regulation of transcription, DNA-dependent	intracellular	DNA binding				0						agactgtttcaaaaaaaaaaa	0.189													4	2	---	---	---	---	
CYTSB	92521	broad.mit.edu	37	17	20139988	20139988	+	Intron	DEL	A	-	-			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20139988delA	uc002gwq.2	+						CYTSB_uc010cqx.2_Intron|CYTSB_uc002gwr.2_Intron|CYTSB_uc002gws.2_Intron|CYTSB_uc002gwv.2_Intron|CYTSB_uc010vzf.1_Intron|CYTSB_uc002gww.2_Intron|CYTSB_uc002gwt.2_Intron|CYTSB_uc002gwu.2_Intron	NM_001033553	NP_001028725	Q5M775	CYTSB_HUMAN	spectrin domain with coiled-coils 1 NSP5b3b							nucleus					0						ttttttttttatGTCTGAAAA	0.418													5	3	---	---	---	---	
CCDC144C	348254	broad.mit.edu	37	17	20254234	20254235	+	Intron	INS	-	T	T			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20254234_20254235insT	uc010cqy.1	+							NR_023380				Homo sapiens cDNA FLJ59693 complete cds, moderately similar to Ankyrin repeat domain-containing protein 26.												0						AAGAGGAATTGTTTTTTTTTTT	0.248													4	2	---	---	---	---	
NFE2L1	4779	broad.mit.edu	37	17	46137413	46137413	+	3'UTR	DEL	A	-	-			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46137413delA	uc002imz.3	+	6					NFE2L1_uc002ina.3_3'UTR|NFE2L1_uc002inb.3_3'UTR|NFE2L1_uc010wle.1_3'UTR|NFE2L1_uc010wlf.1_3'UTR	NM_003204	NP_003195	Q14494	NF2L1_HUMAN	nuclear factor erythroid 2-like 1						anatomical structure morphogenesis|heme biosynthetic process|inflammatory response|transcription from RNA polymerase II promoter	nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription cofactor activity			skin(1)	1						CCCCCCCCCGAAAAAAAAATC	0.458													4	2	---	---	---	---	
RNF138	51444	broad.mit.edu	37	18	29693911	29693912	+	Intron	DEL	TG	-	-			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29693911_29693912delTG	uc002kxg.2	+						RNF138_uc002kxh.2_Intron	NM_016271	NP_057355	Q8WVD3	RN138_HUMAN	ring finger protein 138 isoform 1						Wnt receptor signaling pathway	intracellular	ligase activity|protein kinase binding|zinc ion binding				0						TTTGGGGGGATGTGTGTGTGTG	0.361													6	3	---	---	---	---	
CALR3	125972	broad.mit.edu	37	19	16601575	16601575	+	Intron	DEL	T	-	-	rs67790241		TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16601575delT	uc002ned.2	-						MED26_uc002nee.2_Intron	NM_145046	NP_659483	Q96L12	CALR3_HUMAN	calreticulin 3 precursor						protein folding	endoplasmic reticulum lumen	calcium ion binding|sugar binding|unfolded protein binding				0						TTCTATATAAttttttttttt	0.189													4	4	---	---	---	---	
PAK4	10298	broad.mit.edu	37	19	39614513	39614530	+	5'Flank	DEL	GAAGGAAAGAAAGAGAAA	-	-	rs72010258	by1000genomes	TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39614513_39614530delGAAGGAAAGAAAGAGAAA	uc002okj.1	+						PAK4_uc002okl.1_5'Flank|PAK4_uc002okn.1_5'Flank|PAK4_uc002okm.1_5'Flank|PAK4_uc002oko.1_5'Flank|PAK4_uc002okp.1_5'Flank	NM_001014831	NP_001014831	O96013	PAK4_HUMAN	p21-activated kinase 4 isoform 1						cellular component movement|signal transduction	Golgi apparatus	ATP binding|protein binding|protein serine/threonine kinase activity			lung(3)|ovary(1)	4	all_cancers(60;1.03e-07)|all_epithelial(25;9.66e-08)|all_lung(34;1.58e-07)|Lung NSC(34;1.88e-07)|Ovarian(47;0.0454)		Epithelial(26;4.82e-25)|all cancers(26;2.94e-22)|Lung(45;0.000797)|LUSC - Lung squamous cell carcinoma(53;0.00113)			aggaaggaaggaaggaaagaaagagaaagaaagaaaga	0.000													4	2	---	---	---	---	
JAG1	182	broad.mit.edu	37	20	10653815	10653815	+	Intron	DEL	A	-	-	rs33929314		TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10653815delA	uc002wnw.2	-							NM_000214	NP_000205	P78504	JAG1_HUMAN	jagged 1 precursor						angiogenesis|cell communication|cell fate determination|endothelial cell differentiation|hemopoiesis|keratinocyte differentiation|myoblast differentiation|Notch receptor processing|Notch signaling pathway|regulation of cell migration|regulation of cell proliferation	extracellular region|integral to plasma membrane	calcium ion binding|growth factor activity|Notch binding|structural molecule activity			lung(3)|ovary(2)|central_nervous_system(2)|breast(1)|pancreas(1)	9						ATTCCGGGGCAAAAAAAAAAA	0.587									Alagille_Syndrome				4	2	---	---	---	---	
VSTM2L	128434	broad.mit.edu	37	20	36572310	36572311	+	Intron	INS	-	C	C	rs33961791		TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36572310_36572311insC	uc002xhk.3	+							NM_080607	NP_542174	Q96N03	VTM2L_HUMAN	V-set and transmembrane domain containing 2 like											ovary(1)|central_nervous_system(1)	2		Myeloproliferative disorder(115;0.00878)				CGATCTTGGGACCCCCCCCCCC	0.416													4	2	---	---	---	---	
TRPM2	7226	broad.mit.edu	37	21	45839713	45839714	+	Intron	INS	-	TGG	TGG			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45839713_45839714insTGG	uc002zet.1	+						TRPM2_uc002zeu.1_Intron|TRPM2_uc002zew.1_Intron|TRPM2_uc010gpt.1_Intron|TRPM2_uc002zex.1_Intron|TRPM2_uc002zey.1_Intron|uc011afe.1_Intron	NM_003307	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel,							integral to plasma membrane	ADP-ribose diphosphatase activity|calcium channel activity|sodium channel activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3						ggtggtggtgatggtggtgatg	0.000													4	2	---	---	---	---	
MED15	51586	broad.mit.edu	37	22	20920813	20920814	+	In_Frame_Ins	INS	-	CAG	CAG			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20920813_20920814insCAG	uc002zsp.2	+	7	830_831	c.750_751insCAG	c.(748-753)insCAG	p.262_263insQ	MED15_uc002zso.2_In_Frame_Ins_p.191_192insQ|MED15_uc002zsq.2_In_Frame_Ins_p.262_263insQ|MED15_uc010gso.2_In_Frame_Ins_p.262_263insQ|MED15_uc002zsr.2_In_Frame_Ins_p.236_237insQ|MED15_uc011ahs.1_In_Frame_Ins_p.236_237insQ|MED15_uc002zss.2_In_Frame_Ins_p.181_182insQ|MED15_uc011ahu.1_5'UTR	NM_001003891	NP_001003891	Q96RN5	MED15_HUMAN	mediator complex subunit 15 isoform a	262_263				Missing (in Ref. 3; BAB85034).	regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	Golgi apparatus|mediator complex	protein binding			skin(1)	1	all_cancers(11;2.07e-24)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)|Epithelial(17;0.209)			aacaacagcaacagcagcagca	0.312													34	12	---	---	---	---	
MTMR3	8897	broad.mit.edu	37	22	30384736	30384736	+	Intron	DEL	T	-	-			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30384736delT	uc003agv.3	+						MTMR3_uc003agu.3_Intron|MTMR3_uc003agw.3_Intron	NM_021090	NP_066576	Q13615	MTMR3_HUMAN	myotubularin-related protein 3 isoform c						phosphatidylinositol dephosphorylation	cytoplasm|membrane|membrane fraction|nucleus	metal ion binding|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity			breast(3)|ovary(1)|skin(1)	5			OV - Ovarian serous cystadenocarcinoma(5;0.00204)|Epithelial(10;0.06)|all cancers(5;0.107)			TTGAAAGATGTTTTTTTTttt	0.154													3	3	---	---	---	---	
USP9X	8239	broad.mit.edu	37	X	41043077	41043078	+	Intron	INS	-	T	T			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41043077_41043078insT	uc004dfb.2	+						USP9X_uc004dfc.2_Intron	NM_001039590	NP_001034679	Q93008	USP9X_HUMAN	ubiquitin specific protease 9, X-linked isoform						BMP signaling pathway|cell division|chromosome segregation|female gamete generation|mitosis|protein deubiquitination|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent protein catabolic process	cytoplasm	co-SMAD binding|cysteine-type endopeptidase activity|ubiquitin thiolesterase activity			lung(3)|breast(2)|ovary(1)	6						gtttttgtttattttttttttc	0.332													4	2	---	---	---	---	
SEPT6	23157	broad.mit.edu	37	X	118759508	118759508	+	Intron	DEL	T	-	-			TCGA-EJ-5515-01A-01D-1576-08	TCGA-EJ-5515-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118759508delT	uc004erv.2	-						SEPT6_uc010nqk.2_Intron|SEPT6_uc004ers.2_Intron|SEPT6_uc004ert.2_Intron|SEPT6_uc004eru.2_Intron|SEPT6_uc004erw.2_Intron	NM_015129	NP_055944	Q14141	SEPT6_HUMAN	septin 6 isoform B						cell cycle|cytokinesis|interspecies interaction between organisms	cleavage furrow|condensed chromosome kinetochore|midbody|septin complex|spindle	GTP binding|protein binding			lung(1)|ovary(1)|prostate(1)|kidney(1)	4						ACTGATACTCttttttttttt	0.244													4	2	---	---	---	---	
