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	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	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	pox	qox	pox_cutoff	isArtifactMode	oxoGCut
MST1P2	11209	broad.mit.edu	37	1	16974592	16974592	+	RNA	SNP	C	T	T	rs150466841	by1000genomes	TCGA-EM-A1CS-01A-11D-A13W-08	TCGA-EM-A1CS-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	645f8020-f9c7-407b-b3d4-149b956964a7	f1a11253-4f1b-42db-a81c-3979b7791777	g.chr1:16974592C>T	uc010och.1	+	7		c.1052C>T			MST1P2_uc001azk.2_RNA|MST1P2_uc001azl.3_RNA|MST1P2_uc009vox.2_RNA|MST1P2_uc001azm.3_RNA	NR_027504				Homo sapiens cDNA FLJ43241 fis, clone HEART1000010, weakly  similar to Hepatocyte growth factor-like protein precursor.												0						TGCCGGAACCCCGACGGCTCA	0.667000													4	56	---	---	---	---	0	0	0.029380	0	0
SYNPO2L	79933	broad.mit.edu	37	10	75406952	75406952	+	Missense_Mutation	SNP	A	G	G			TCGA-EM-A1CS-01A-11D-A13W-08	TCGA-EM-A1CS-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	645f8020-f9c7-407b-b3d4-149b956964a7	f1a11253-4f1b-42db-a81c-3979b7791777	g.chr10:75406952A>G	uc001jut.3	-	4	2610	c.2458T>C	c.(2458-2460)TTT>CTT	p.F820L	SYNPO2L_uc001jus.3_Missense_Mutation_p.F596L	NM_001114133	NP_001107605	Q9H987	SYP2L_HUMAN	synaptopodin 2-like isoform a	820	Pro-rich.					cytoplasm|cytoskeleton	actin binding			ovary(1)	1	Prostate(51;0.0112)					TGGGGGAAAAAGGGAGAGAGC	0.577000													3	147	---	---	---	---	0	0	0.115264	0	0
DMBT1	1755	broad.mit.edu	37	10	124336139	124336139	+	Missense_Mutation	SNP	C	T	T			TCGA-EM-A1CS-01A-11D-A13W-08	TCGA-EM-A1CS-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	645f8020-f9c7-407b-b3d4-149b956964a7	f1a11253-4f1b-42db-a81c-3979b7791777	g.chr10:124336139C>T	uc001lgk.1	+	7	614	c.508C>T	c.(508-510)CGC>TGC	p.R170C	DMBT1_uc001lgl.1_Missense_Mutation_p.R170C|DMBT1_uc001lgm.1_Missense_Mutation_p.R170C|DMBT1_uc009xzz.1_Missense_Mutation_p.R170C|DMBT1_uc010qtx.1_Missense_Mutation_p.R170C|DMBT1_uc009yaa.1_Missense_Mutation_p.R22C	NM_007329	NP_015568	Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1 isoform b	170	SRCR 1.				epithelial cell differentiation|induction of bacterial agglutination|innate immune response|interspecies interaction between organisms|protein transport|response to virus	extrinsic to membrane|phagocytic vesicle membrane|zymogen granule membrane	calcium-dependent protein binding|Gram-negative bacterial cell surface binding|Gram-positive bacterial cell surface binding|pattern recognition receptor activity|scavenger receptor activity|zymogen binding			central_nervous_system(7)	7		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				GGATGATGTGCGCTGCTCAGG	0.587000													5	217	---	---	---	---	0	0	0.014758	0	0
FRY	10129	broad.mit.edu	37	13	32698958	32698958	+	Missense_Mutation	SNP	T	C	C			TCGA-EM-A1CS-01A-11D-A13W-08	TCGA-EM-A1CS-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	645f8020-f9c7-407b-b3d4-149b956964a7	f1a11253-4f1b-42db-a81c-3979b7791777	g.chr13:32698958T>C	uc001utx.2	+	7	1158	c.662T>C	c.(661-663)ATG>ACG	p.M221T	FRY_uc010tdw.1_RNA	NM_023037	NP_075463	Q5TBA9	FRY_HUMAN	furry homolog	221					regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane				ovary(5)|large_intestine(1)|skin(1)	7		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		ACTGGCAATATGCATATTGTG	0.438000													5	201	---	---	---	---	0	0	0.029380	0	0
ARHGEF7	8874	broad.mit.edu	37	13	111870032	111870032	+	Missense_Mutation	SNP	A	G	G			TCGA-EM-A1CS-01A-11D-A13W-08	TCGA-EM-A1CS-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	645f8020-f9c7-407b-b3d4-149b956964a7	f1a11253-4f1b-42db-a81c-3979b7791777	g.chr13:111870032A>G	uc001vrs.2	+	6	788	c.538A>G	c.(538-540)ACC>GCC	p.T180A	ARHGEF7_uc001vrr.2_Missense_Mutation_p.T159A|ARHGEF7_uc001vrt.2_Missense_Mutation_p.T130A|ARHGEF7_uc010tjn.1_RNA|ARHGEF7_uc001vru.1_Missense_Mutation_p.T2A|ARHGEF7_uc001vrv.3_Missense_Mutation_p.T2A|ARHGEF7_uc001vrw.3_Missense_Mutation_p.T2A|ARHGEF7_uc001vrx.3_Missense_Mutation_p.T2A|ARHGEF7_uc010tjo.1_Missense_Mutation_p.T77A	NM_001113511	NP_001106983	Q14155	ARHG7_HUMAN	PAK-interacting exchange factor beta isoform c	180					apoptosis|epidermal growth factor receptor signaling pathway|induction of apoptosis by extracellular signals|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1)	7	all_lung(23;3.96e-05)|Lung NSC(43;0.00156)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.188)			TTAGGACATGACCGATAATAG	0.378000													3	63	---	---	---	---	0	0	0.115264	0	0
LOC645752	645752	broad.mit.edu	37	15	78211517	78211517	+	Missense_Mutation	SNP	C	G	G			TCGA-EM-A1CS-01A-11D-A13W-08	TCGA-EM-A1CS-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	645f8020-f9c7-407b-b3d4-149b956964a7	f1a11253-4f1b-42db-a81c-3979b7791777	g.chr15:78211517C>G	uc010bky.2	-	11	1014	c.250G>C	c.(250-252)GTC>CTC	p.V84L		NR_027024				SubName: Full=GOLGA6 protein; Flags: Fragment;												0						TTGCTCAGGACACTCAAGGCC	0.557000													6	284	---	---	---	---	0	0	0.021553	0	0
Unknown	0	broad.mit.edu	37	15	102305084	102305084	+	5'Flank	SNP	T	C	C			TCGA-EM-A1CS-01A-11D-A13W-08	TCGA-EM-A1CS-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	645f8020-f9c7-407b-b3d4-149b956964a7	f1a11253-4f1b-42db-a81c-3979b7791777	g.chr15:102305084T>C	uc002cbx.1	-						uc002ccc.1_5'Flank|uc010uth.1_RNA|uc002cci.2_5'Flank|uc002ccj.2_5'Flank|uc002cck.2_5'Flank|uc002ccl.1_5'Flank|uc002ccm.1_5'Flank					DQ582460																		GACATCAACATGAACACCATC	0.632000													3	27	---	---	---	---	0	0	0.115264	0	0
DDX11L2	84771	broad.mit.edu	37	2	114357557	114357557	+	Nonstop_Mutation	SNP	A	G	G	rs115341812	by1000genomes	TCGA-EM-A1CS-01A-11D-A13W-08	TCGA-EM-A1CS-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	645f8020-f9c7-407b-b3d4-149b956964a7	f1a11253-4f1b-42db-a81c-3979b7791777	g.chr2:114357557A>G	uc010yxx.1	-	3	709	c.382T>C	c.(382-384)TAG>CAG	p.*128Q						SubName: Full=DEAD/H box polypeptide 11 like 2;												0						GCCTACTTCTAGTGAAACTGG	0.567000													7	30	---	---	---	---	0	0	0.029380	0	0
GLI2	2736	broad.mit.edu	37	2	121708835	121708835	+	Missense_Mutation	SNP	G	A	A			TCGA-EM-A1CS-01A-11D-A13W-08	TCGA-EM-A1CS-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	645f8020-f9c7-407b-b3d4-149b956964a7	f1a11253-4f1b-42db-a81c-3979b7791777	g.chr2:121708835G>A	uc010flp.2	+	3	301	c.271G>A	c.(271-273)GGC>AGC	p.G91S	GLI2_uc010yyu.1_Missense_Mutation_p.G91S|GLI2_uc002tmq.1_Intron|GLI2_uc002tmr.1_Intron|GLI2_uc002tmt.3_Intron|GLI2_uc002tmu.3_Intron|GLI2_uc002tmv.1_Intron|GLI2_uc010flo.1_5'UTR|GLI2_uc002tmw.1_Missense_Mutation_p.G91S	NM_005270	NP_005261	P10070	GLI2_HUMAN	GLI-Kruppel family member GLI2	91					axon guidance|branching morphogenesis of a tube|cell proliferation|cerebellar cortex morphogenesis|developmental growth|embryonic digestive tract development|epidermal cell differentiation|floor plate formation|heart development|hindgut morphogenesis|kidney development|lung development|negative regulation of transcription from RNA polymerase II promoter|odontogenesis of dentine-containing tooth|osteoblast development|osteoblast differentiation|pituitary gland development|positive regulation of DNA replication|positive regulation of T cell differentiation in thymus|positive regulation of transcription from RNA polymerase II promoter|proximal/distal pattern formation|skeletal system development|smoothened signaling pathway involved in ventral spinal cord interneuron specification|spinal cord ventral commissure morphogenesis	nucleus|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|lung(2)|breast(1)|central_nervous_system(1)|pancreas(1)	13	Renal(3;0.0496)	Prostate(154;0.0623)				TGCCCTCAGCGGCAGCCCTGT	0.632000													6	194	---	---	---	---	0	0	0.021553	0	0
LBP	3929	broad.mit.edu	37	20	37002620	37002620	+	Missense_Mutation	SNP	G	A	A			TCGA-EM-A1CS-01A-11D-A13W-08	TCGA-EM-A1CS-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	645f8020-f9c7-407b-b3d4-149b956964a7	f1a11253-4f1b-42db-a81c-3979b7791777	g.chr20:37002620G>A	uc002xic.1	+	14	1399	c.1364G>A	c.(1363-1365)CGT>CAT	p.R455H		NM_004139	NP_004130	P18428	LBP_HUMAN	lipopolysaccharide-binding protein precursor	455					acute-phase response|cellular defense response|cellular response to lipoteichoic acid|defense response to Gram-negative bacterium|defense response to Gram-positive bacterium|detection of molecule of bacterial origin|innate immune response|lipid transport|lipopolysaccharide transport|lipopolysaccharide-mediated signaling pathway|macrophage activation involved in immune response|negative regulation of tumor necrosis factor production|opsonization|positive regulation of interleukin-6 production|positive regulation of interleukin-8 production|positive regulation of macrophage activation|positive regulation of respiratory burst involved in inflammatory response|positive regulation of toll-like receptor 4 signaling pathway|positive regulation of tumor necrosis factor production|Toll signaling pathway	extracellular space	Gram-negative bacterial cell surface binding|Gram-positive bacterial cell surface binding|lipid binding|lipopolysaccharide binding|lipoteichoic acid binding|receptor binding			ovary(1)|central_nervous_system(1)	2		Myeloproliferative disorder(115;0.00878)				CTGCTGAAGCGTGTTCAGCTC	0.488000													28	79	---	---	---	---	0	0	0.144211	0	0
LOC96610	96610	broad.mit.edu	37	22	22664606	22664606	+	RNA	SNP	A	G	G			TCGA-EM-A1CS-01A-11D-A13W-08	TCGA-EM-A1CS-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	645f8020-f9c7-407b-b3d4-149b956964a7	f1a11253-4f1b-42db-a81c-3979b7791777	g.chr22:22664606A>G	uc011aim.1	+	31		c.2121A>G			LOC96610_uc011aiq.1_RNA					Parts of antibodies, mostly variable regions.												0						GTCTTCATGCAAACTTGGTAT	0.398000													2	8	---	---	---	---	0	0	0.115264	0	0
GGT1	2678	broad.mit.edu	37	22	25023483	25023483	+	Missense_Mutation	SNP	T	G	G			TCGA-EM-A1CS-01A-11D-A13W-08	TCGA-EM-A1CS-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	645f8020-f9c7-407b-b3d4-149b956964a7	f1a11253-4f1b-42db-a81c-3979b7791777	g.chr22:25023483T>G	uc003aan.1	+	12	1592	c.1105T>G	c.(1105-1107)TAC>GAC	p.Y369D	GGT1_uc003aas.1_Missense_Mutation_p.Y369D|GGT1_uc003aat.1_Missense_Mutation_p.Y369D|GGT1_uc003aau.1_Missense_Mutation_p.Y369D|GGT1_uc003aav.1_Missense_Mutation_p.Y369D|GGT1_uc003aaw.1_Missense_Mutation_p.Y369D|GGT1_uc003aax.1_Missense_Mutation_p.Y369D|GGT1_uc003aay.1_Missense_Mutation_p.Y25D	NM_013430	NP_038347	P19440	GGT1_HUMAN	gamma-glutamyltransferase 1 precursor	369	Extracellular (Potential).				glutathione biosynthetic process	integral to membrane	acyltransferase activity|gamma-glutamyltransferase activity|protein binding				0					Glutathione(DB00143)	GATCTCCTACTACAAGCCCGA	0.627000													3	35	---	---	---	---	0	0	0.009096	0	0
MIR1324	100302212	broad.mit.edu	37	3	75679970	75679970	+	RNA	SNP	G	T	T			TCGA-EM-A1CS-01A-11D-A13W-08	TCGA-EM-A1CS-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	645f8020-f9c7-407b-b3d4-149b956964a7	f1a11253-4f1b-42db-a81c-3979b7791777	g.chr3:75679970G>T	hsa-mir-1324|MI0006657	+			c.57G>T																				0						CTTCCCTCTGGGTACCAGACA	0.507000													7	120	---	---	---	---	0.00448238	0.00500972	0.047766	1	0
ADAMTS19	171019	broad.mit.edu	37	5	128863519	128863519	+	Missense_Mutation	SNP	A	T	T			TCGA-EM-A1CS-01A-11D-A13W-08	TCGA-EM-A1CS-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	645f8020-f9c7-407b-b3d4-149b956964a7	f1a11253-4f1b-42db-a81c-3979b7791777	g.chr5:128863519A>T	uc003kvb.1	+	5	1147	c.1147A>T	c.(1147-1149)ACT>TCT	p.T383S	ADAMTS19_uc003kvc.1_RNA	NM_133638	NP_598377	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1	383	Peptidase M12B.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(5)|breast(2)|lung(1)|skin(1)	9		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.222)		GCTCCATGAAACTCCAGTAAG	0.308000													48	79	---	---	---	---	0	0	0.139131	0	0
MUC17	140453	broad.mit.edu	37	7	100681033	100681033	+	Silent	SNP	G	A	A			TCGA-EM-A1CS-01A-11D-A13W-08	TCGA-EM-A1CS-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	645f8020-f9c7-407b-b3d4-149b956964a7	f1a11253-4f1b-42db-a81c-3979b7791777	g.chr7:100681033G>A	uc003uxp.1	+	3	6389	c.6336G>A	c.(6334-6336)ACG>ACA	p.T2112T	MUC17_uc010lho.1_RNA	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17 precursor	2112	Extracellular (Potential).|33.|59 X approximate tandem repeats.|Ser-rich.					extracellular region|integral to membrane|plasma membrane	extracellular matrix constituent, lubricant activity			ovary(14)|skin(8)|breast(3)|lung(2)	27	Lung NSC(181;0.136)|all_lung(186;0.182)					TCAGCACCACGCCGGTGGCCA	0.498000													6	436	---	---	---	---	0	0	0.047766	0	0
RPL23AP53	644128	broad.mit.edu	37	8	163401	163401	+	RNA	SNP	G	C	C			TCGA-EM-A1CS-01A-11D-A13W-08	TCGA-EM-A1CS-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	645f8020-f9c7-407b-b3d4-149b956964a7	f1a11253-4f1b-42db-a81c-3979b7791777	g.chr8:163401G>C	uc010lra.2	-	4		c.732C>G			RPL23AP53_uc003woq.3_RNA|RPL23AP53_uc010lrb.2_RNA	NR_003572				Homo sapiens cDNA FLJ45055 fis, clone BRAWH3022900.												0						TCTGGTGCTTGTTGGCTTTAA	0.463000													4	22	---	---	---	---	0	0	0.021553	0	0
AMBP	259	broad.mit.edu	37	9	116839008	116839008	+	Missense_Mutation	SNP	A	C	C			TCGA-EM-A1CS-01A-11D-A13W-08	TCGA-EM-A1CS-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	645f8020-f9c7-407b-b3d4-149b956964a7	f1a11253-4f1b-42db-a81c-3979b7791777	g.chr9:116839008A>C	uc004bie.3	-	2	393	c.130T>G	c.(130-132)TGG>GGG	p.W44G	AMBP_uc011lxk.1_5'UTR|AMBP_uc010mvc.1_RNA	NM_001633	NP_001624	P02760	AMBP_HUMAN	alpha-1-microglobulin/bikunin preproprotein	44					cell adhesion|female pregnancy|heme catabolic process|interspecies interaction between organisms|negative regulation of immune response|negative regulation of JNK cascade|protein-chromophore linkage	extracellular region|plasma membrane	calcium channel inhibitor activity|calcium oxalate binding|heme binding|IgA binding|protein homodimerization activity|serine-type endopeptidase inhibitor activity|transporter activity			skin(1)	1					Human Serum Albumin(DB00062)|Serum albumin iodonated(DB00064)	AGGTTGTACCACTTCCCATAG	0.557000													19	49	---	---	---	---	0	0	0.062417	0	0
Unknown	0	broad.mit.edu	37	MT	9040	9040	+	RNA	SNP	C	T	T			TCGA-EM-A1CS-01A-11D-A13W-08	TCGA-EM-A1CS-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	645f8020-f9c7-407b-b3d4-149b956964a7	f1a11253-4f1b-42db-a81c-3979b7791777	g.chrM:9040C>T	uc011mfi.1	+	1		c.378C>T			uc004cov.3_5'Flank					Homo sapiens mRNA for OK/SW-CL.16, complete cds.																		ACCTACTCATGCACCTAATTG	0.443000													2	1	---	---	---	---	0	0	0.115264	0	0
YY2	404281	broad.mit.edu	37	X	21875408	21875408	+	Missense_Mutation	SNP	C	T	T			TCGA-EM-A1CS-01A-11D-A13W-08	TCGA-EM-A1CS-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	645f8020-f9c7-407b-b3d4-149b956964a7	f1a11253-4f1b-42db-a81c-3979b7791777	g.chrX:21875408C>T	uc011mjp.1	+	1	806	c.806C>T	c.(805-807)GCC>GTC	p.A269V	MBTPS2_uc004dae.2_Intron|MBTPS2_uc010nfr.2_Intron|YY2_uc010nfq.2_Missense_Mutation_p.A487V|MBTPS2_uc004dab.2_Intron	NM_206923	NP_996806	O15391	TYY2_HUMAN	YY2 transcription factor	269	Mediates transcriptional repression.|C2H2-type 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|plasma membrane	DNA binding|zinc ion binding			breast(1)|skin(1)	2						CGGGATTACGCCGCCATGAGA	0.498000													5	310	---	---	---	---	0	0	0.014758	0	0
ARMCX3	51566	broad.mit.edu	37	X	100880307	100880307	+	Nonsense_Mutation	SNP	C	A	A			TCGA-EM-A1CS-01A-11D-A13W-08	TCGA-EM-A1CS-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	645f8020-f9c7-407b-b3d4-149b956964a7	f1a11253-4f1b-42db-a81c-3979b7791777	g.chrX:100880307C>A	uc004ehz.1	+	5	871	c.338C>A	c.(337-339)TCA>TAA	p.S113*	ARMCX3_uc004eia.1_Nonsense_Mutation_p.S113*|ARMCX3_uc004eib.1_Nonsense_Mutation_p.S113*|ARMCX3_uc004eic.1_Nonsense_Mutation_p.S113*	NM_016607	NP_057691	Q9UH62	ARMX3_HUMAN	armadillo repeat containing, X-linked 3	113	ARM 1.					integral to membrane	binding			ovary(1)|lung(1)	2						TCCCCCAATTCAGATGATACC	0.423000													13	108	---	---	---	---	5.50884e-06	6.54174e-06	0.093190	1	0
Unknown	0	broad.mit.edu	37	1	243251423	243251423	+	RNA	DEL	A	-	-			TCGA-EM-A1CS-01A-11D-A13W-08	TCGA-EM-A1CS-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	645f8020-f9c7-407b-b3d4-149b956964a7	f1a11253-4f1b-42db-a81c-3979b7791777	g.chr1:243251423delA	uc001hzq.1	-	8		c.1209delT								Homo sapiens cDNA FLJ52610 complete cds.																		actccatctcaaaaaaaaaaa	0.179													3	5	---	---	---	---					
Unknown	0	broad.mit.edu	37	12	77054687	77054687	+	IGR	DEL	T	-	-	rs2369296	by1000genomes	TCGA-EM-A1CS-01A-11D-A13W-08	TCGA-EM-A1CS-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	645f8020-f9c7-407b-b3d4-149b956964a7	f1a11253-4f1b-42db-a81c-3979b7791777	g.chr12:77054687delT								OSBPL8 (101098 upstream) : ZDHHC17 (103167 downstream)																							aaaaaaaaaataaataaaGGA	0.358													4	9	---	---	---	---					
EP400	57634	broad.mit.edu	37	12	132547093	132547094	+	In_Frame_Ins	INS	-	CAG	CAG	rs28513925	by1000genomes	TCGA-EM-A1CS-01A-11D-A13W-08	TCGA-EM-A1CS-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	645f8020-f9c7-407b-b3d4-149b956964a7	f1a11253-4f1b-42db-a81c-3979b7791777	g.chr12:132547093_132547094insCAG	uc001ujn.2	+	46	8216_8217	c.8181_8182insCAG	c.(8179-8184)insCAG	p.2748_2749insQ	EP400_uc001ujl.2_In_Frame_Ins_p.2747_2748insQ|EP400_uc001ujm.2_In_Frame_Ins_p.2667_2668insQ|EP400_uc001ujp.2_5'UTR	NM_015409	NP_056224	Q96L91	EP400_HUMAN	E1A binding protein p400	2784_2785	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)		agcagcaacaacagcagcagca	0.292													8	69	---	---	---	---					
FAM155A	728215	broad.mit.edu	37	13	108518687	108518689	+	In_Frame_Del	DEL	CTG	-	-			TCGA-EM-A1CS-01A-11D-A13W-08	TCGA-EM-A1CS-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	645f8020-f9c7-407b-b3d4-149b956964a7	f1a11253-4f1b-42db-a81c-3979b7791777	g.chr13:108518687_108518689delCTG	uc001vql.2	-	1	772_774	c.256_258delCAG	c.(256-258)CAGdel	p.Q86del		NM_001080396	NP_001073865	B1AL88	F155A_HUMAN	family with sequence similarity 155, member A	86	Poly-Gln.					integral to membrane	binding			skin(1)	1						gccgctgcctctgctgctgctgc	0.404													7	66	---	---	---	---					
POLG	5428	broad.mit.edu	37	15	89876827	89876828	+	In_Frame_Ins	INS	-	TGCTGC	TGCTGC	rs41550117		TCGA-EM-A1CS-01A-11D-A13W-08	TCGA-EM-A1CS-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	645f8020-f9c7-407b-b3d4-149b956964a7	f1a11253-4f1b-42db-a81c-3979b7791777	g.chr15:89876827_89876828insTGCTGC	uc002bns.3	-	2	440_441	c.158_159insGCAGCA	c.(157-159)CAA>CAGCAGCAA	p.53_53Q>QQQ	POLG_uc002bnr.3_In_Frame_Ins_p.53_53Q>QQQ	NM_002693	NP_002684	P54098	DPOG1_HUMAN	DNA-directed DNA polymerase gamma	53	Poly-Gln.				base-excision repair, gap-filling|cell death|DNA-dependent DNA replication	mitochondrial nucleoid	DNA binding|DNA-directed DNA polymerase activity|protease binding			ovary(1)|lung(1)	2	Lung NSC(78;0.0472)|all_lung(78;0.089)		STAD - Stomach adenocarcinoma(125;0.165)			gaggctgctgttgctgctgctg	0.460								DNA_polymerases_(catalytic_subunits)					9	25	---	---	---	---					
ATAD5	79915	broad.mit.edu	37	17	29157882	29157882	+	5'Flank	DEL	A	-	-			TCGA-EM-A1CS-01A-11D-A13W-08	TCGA-EM-A1CS-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	645f8020-f9c7-407b-b3d4-149b956964a7	f1a11253-4f1b-42db-a81c-3979b7791777	g.chr17:29157882delA	uc002hfs.1	+							NM_024857	NP_079133	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5						response to DNA damage stimulus	nucleus	ATP binding|nucleoside-triphosphatase activity			ovary(3)	3		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				ACTTTAACGTAAAAAAAAAAG	0.323													7	27	---	---	---	---					
Unknown	0	broad.mit.edu	37	17	43675430	43675431	+	IGR	INS	-	A	A	rs1724389		TCGA-EM-A1CS-01A-11D-A13W-08	TCGA-EM-A1CS-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	645f8020-f9c7-407b-b3d4-149b956964a7	f1a11253-4f1b-42db-a81c-3979b7791777	g.chr17:43675430_43675431insA								LRRC37A4 (79914 upstream) : LOC644172 (2060 downstream)																							TACACTGTTTTTTTTTTTTTTT	0.277													3	6	---	---	---	---					
ARRDC2	27106	broad.mit.edu	37	19	18118931	18118931	+	5'Flank	DEL	C	-	-			TCGA-EM-A1CS-01A-11D-A13W-08	TCGA-EM-A1CS-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	645f8020-f9c7-407b-b3d4-149b956964a7	f1a11253-4f1b-42db-a81c-3979b7791777	g.chr19:18118931delC	uc002nhv.2	+						ARRDC2_uc002nhu.2_Intron	NM_015683	NP_056498	Q8TBH0	ARRD2_HUMAN	arrestin domain containing 2 isoform 1											pancreas(1)	1						GGTGACCCCACCCCCCCCCGC	0.672													2	4	---	---	---	---					
SFRS15	57466	broad.mit.edu	37	21	33044257	33044259	+	In_Frame_Del	DEL	GCT	-	-			TCGA-EM-A1CS-01A-11D-A13W-08	TCGA-EM-A1CS-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	645f8020-f9c7-407b-b3d4-149b956964a7	f1a11253-4f1b-42db-a81c-3979b7791777	g.chr21:33044257_33044259delGCT	uc002ypd.2	-	20	3323_3325	c.2897_2899delAGC	c.(2896-2901)CAGCCA>CCA	p.Q966del	SFRS15_uc002ype.2_In_Frame_Del_p.Q944del|SFRS15_uc010glu.2_In_Frame_Del_p.Q951del	NM_020706	NP_065757	O95104	SFR15_HUMAN	splicing factor, arginine/serine-rich 15 isoform	966	Poly-Gln.					nucleus	nucleotide binding|RNA binding				0						GATGGTGgtggctgctgctgctg	0.291													9	215	---	---	---	---					
Unknown	0	broad.mit.edu	37	6	160132814	160132831	+	IGR	DEL	CACTCACATTGCTCTGAT	-	-	rs62437333	by1000genomes	TCGA-EM-A1CS-01A-11D-A13W-08	TCGA-EM-A1CS-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	645f8020-f9c7-407b-b3d4-149b956964a7	f1a11253-4f1b-42db-a81c-3979b7791777	g.chr6:160132814_160132831delCACTCACATTGCTCTGAT								SOD2 (18461 upstream) : WTAP (15298 downstream)																							ccataaccaccactcacattgctctgatcaccataacc	0.050													10	198	---	---	---	---					
Unknown	0	broad.mit.edu	37	6	160133471	160133488	+	IGR	DEL	CTCACACTGCTCAGACCT	-	-	rs71296993		TCGA-EM-A1CS-01A-11D-A13W-08	TCGA-EM-A1CS-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	645f8020-f9c7-407b-b3d4-149b956964a7	f1a11253-4f1b-42db-a81c-3979b7791777	g.chr6:160133471_160133488delCTCACACTGCTCAGACCT								SOD2 (19118 upstream) : WTAP (14641 downstream)																							ataaccaccactcacactgctcagacctccataaccac	0.078													7	49	---	---	---	---					
SGK223	157285	broad.mit.edu	37	8	8234868	8234869	+	In_Frame_Ins	INS	-	GCCGCT	GCCGCT	rs150979349	by1000genomes	TCGA-EM-A1CS-01A-11D-A13W-08	TCGA-EM-A1CS-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	645f8020-f9c7-407b-b3d4-149b956964a7	f1a11253-4f1b-42db-a81c-3979b7791777	g.chr8:8234868_8234869insGCCGCT	uc003wsh.3	-	2	1050_1051	c.1050_1051insAGCGGC	c.(1048-1053)insAGCGGC	p.350_351insSG		NM_001080826	NP_001074295	Q86YV5	SG223_HUMAN	pragmin	350_351							ATP binding|non-membrane spanning protein tyrosine kinase activity				0						GGGCTACTGGCGCCGCTGCCGC	0.653													11	43	---	---	---	---					
PRKDC	5591	broad.mit.edu	37	8	48866910	48866910	+	Frame_Shift_Del	DEL	T	-	-			TCGA-EM-A1CS-01A-11D-A13W-08	TCGA-EM-A1CS-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	645f8020-f9c7-407b-b3d4-149b956964a7	f1a11253-4f1b-42db-a81c-3979b7791777	g.chr8:48866910delT	uc003xqi.2	-	5	553	c.496delA	c.(496-498)ATAfs	p.I166fs	PRKDC_uc003xqj.2_Frame_Shift_Del_p.I166fs|PRKDC_uc011ldh.1_Frame_Shift_Del_p.I166fs	NM_006904	NP_008835	P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic	166					cellular response to insulin stimulus|double-strand break repair via nonhomologous end joining|peptidyl-serine phosphorylation|positive regulation of transcription from RNA polymerase II promoter	DNA-dependent protein kinase-DNA ligase 4 complex|transcription factor complex	ATP binding|DNA binding|DNA-dependent protein kinase activity|transcription factor binding			lung(12)|central_nervous_system(9)|ovary(6)|skin(4)|large_intestine(3)	34		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)				GTATCTGGTATTTTTTTTTTC	0.264								NHEJ					2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	9	81651253	81651253	+	IGR	DEL	T	-	-			TCGA-EM-A1CS-01A-11D-A13W-08	TCGA-EM-A1CS-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	645f8020-f9c7-407b-b3d4-149b956964a7	f1a11253-4f1b-42db-a81c-3979b7791777	g.chr9:81651253delT								PSAT1 (706246 upstream) : TLE4 (535625 downstream)																							tacaCTAGACTTTTTTTTTTT	0.264													4	4	---	---	---	---					
SNAPC4	6621	broad.mit.edu	37	9	139277995	139277997	+	In_Frame_Del	DEL	GCT	-	-	rs35266724		TCGA-EM-A1CS-01A-11D-A13W-08	TCGA-EM-A1CS-10A-01D-A13W-08									Somatic	Phase_I	Capture				Illumina GAIIx	645f8020-f9c7-407b-b3d4-149b956964a7	f1a11253-4f1b-42db-a81c-3979b7791777	g.chr9:139277995_139277997delGCT	uc004chh.2	-	15	1633_1635	c.1624_1626delAGC	c.(1624-1626)AGCdel	p.S542del		NM_003086	NP_003077	Q5SXM2	SNPC4_HUMAN	small nuclear RNA activating complex,	542					snRNA transcription from RNA polymerase II promoter|snRNA transcription from RNA polymerase III promoter	snRNA-activating protein complex	DNA binding|sequence-specific DNA binding transcription factor activity				0		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.31e-06)|Epithelial(140;7.13e-06)		CGTCCTCCTCgctgctgctgctg	0.473													9	13	---	---	---	---					
