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
EIF4G3	8672	broad.mit.edu	37	1	21268202	21268202	+	Missense_Mutation	SNP	G	A	A			TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr1:21268202G>A	uc001bec.2	-	9	1533	c.1277C>T	c.(1276-1278)CCT>CTT	p.P426L	EIF4G3_uc010odi.1_Missense_Mutation_p.P30L|EIF4G3_uc010odj.1_Missense_Mutation_p.P425L|EIF4G3_uc009vpz.2_Intron|EIF4G3_uc001bed.2_Missense_Mutation_p.P426L|EIF4G3_uc001bef.2_Missense_Mutation_p.P425L|EIF4G3_uc001bee.2_Missense_Mutation_p.P432L|EIF4G3_uc001beg.2_Missense_Mutation_p.P425L|EIF4G3_uc010odk.1_Missense_Mutation_p.P426L|EIF4G3_uc001beh.2_Missense_Mutation_p.P437L	NM_003760	NP_003751	O43432	IF4G3_HUMAN	eukaryotic translation initiation factor 4	426					interspecies interaction between organisms|regulation of translational initiation|RNA metabolic process	eukaryotic translation initiation factor 4F complex	protein binding|RNA cap binding|translation initiation factor activity			skin(1)	1		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)		TGGAGTGTgaggaggagaagc	0.403000													4	168	---	---	---	---	0	0	0.014758	0	0
ZNF362	149076	broad.mit.edu	37	1	33747210	33747210	+	Missense_Mutation	SNP	T	C	C			TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr1:33747210T>C	uc001bxc.1	+	6	876	c.706T>C	c.(706-708)TTT>CTT	p.F236L		NM_152493	NP_689706	Q5T0B9	ZN362_HUMAN	zinc finger protein 362	236	C2H2-type 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				CCCACTGACCTTTTTCACCAA	0.562000													3	148	---	---	---	---	0	0	0.004672	0	0
PRG4	10216	broad.mit.edu	37	1	186276961	186276961	+	Missense_Mutation	SNP	A	C	C	rs145338869	byFrequency	TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr1:186276961A>C	uc001gru.3	+	7	2161	c.2110A>C	c.(2110-2112)ACT>CCT	p.T704P	PRG4_uc001grt.3_Missense_Mutation_p.T663P|PRG4_uc009wyl.2_Missense_Mutation_p.T611P|PRG4_uc009wym.2_Missense_Mutation_p.T570P|PRG4_uc010poo.1_Intron	NM_005807	NP_005798	Q92954	PRG4_HUMAN	proteoglycan 4 isoform A	704	59 X 8 AA repeats of K-X-P-X-P-T-T-X.|42; approximate.				cell proliferation|immune response	extracellular region	polysaccharide binding|protein binding|scavenger receptor activity			skin(1)	1						CCCTAAGGAGACTGCTCCAAC	0.597000													4	134	---	---	---	---	0	0	0.009096	0	0
EIF3F	8665	broad.mit.edu	37	11	8014547	8014547	+	Missense_Mutation	SNP	G	A	A			TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr11:8014547G>A	uc001mfw.2	+	4	662	c.629G>A	c.(628-630)CGC>CAC	p.R210H	EIF3F_uc010rbj.1_Missense_Mutation_p.R61H	NM_003754	NP_003745	O00303	EIF3F_HUMAN	eukaryotic translation initiation factor 3,	210						cytosol|eukaryotic translation initiation factor 3 complex	protein binding|translation initiation factor activity			lung(1)	1				Epithelial(150;1.44e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)		CAGAACGGCCGCATGAGCATC	0.562000													4	153	---	---	---	---	0	0	0.014758	0	0
EFEMP2	30008	broad.mit.edu	37	11	65635868	65635868	+	Missense_Mutation	SNP	G	A	A			TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr11:65635868G>A	uc001ofy.3	-	9	1066	c.872C>T	c.(871-873)GCG>GTG	p.A291V	EFEMP2_uc001ofz.2_RNA|EFEMP2_uc001oga.2_Missense_Mutation_p.A291V	NM_016938	NP_058634	O95967	FBLN4_HUMAN	EGF-containing fibulin-like extracellular matrix	291	EGF-like 6; calcium-binding (Potential).				blood coagulation	basement membrane|membrane	calcium ion binding|extracellular matrix structural constituent|protein binding|transmembrane receptor activity			ovary(1)	1				READ - Rectum adenocarcinoma(159;0.169)		GCACTGGTGCGCACCAGACTC	0.642000													3	93	---	---	---	---	0	0	0.009096	0	0
NADSYN1	55191	broad.mit.edu	37	11	71185490	71185490	+	Missense_Mutation	SNP	G	A	A			TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr11:71185490G>A	uc001oqn.2	+	9	842	c.716G>A	c.(715-717)CGC>CAC	p.R239H	NADSYN1_uc001oqm.2_RNA|NADSYN1_uc001oqo.2_5'UTR	NM_018161	NP_060631	Q6IA69	NADE_HUMAN	NAD synthetase 1	239	CN hydrolase.				NAD biosynthetic process|water-soluble vitamin metabolic process	cytosol	ATP binding|hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds|NAD+ synthase (glutamine-hydrolyzing) activity|protein binding			ovary(2)	2					L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)	GACGGGGACCGCCTGTACTAC	0.562000													8	122	---	---	---	---	0	0	0.003163	0	0
POLE	5426	broad.mit.edu	37	12	133218793	133218793	+	Missense_Mutation	SNP	C	G	G			TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr12:133218793C>G	uc001uks.1	-	38	5187	c.5143G>C	c.(5143-5145)GAG>CAG	p.E1715Q	POLE_uc001ukq.1_5'Flank|POLE_uc001ukr.1_Missense_Mutation_p.E519Q|POLE_uc010tbq.1_RNA	NM_006231	NP_006222	Q07864	DPOE1_HUMAN	DNA-directed DNA polymerase epsilon	1715					base-excision repair, gap-filling|DNA synthesis involved in DNA repair|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|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	chromatin binding|DNA binding|DNA-directed DNA polymerase activity|nucleotide binding|protein binding|zinc ion binding			ovary(3)|skin(3)|lung(1)|central_nervous_system(1)	8	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)		CTGTTGATCTCAACAGTGGCT	0.557000								DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					5	237	---	---	---	---	0	0	0.001984	0	0
FAM48A	55578	broad.mit.edu	37	13	37598529	37598529	+	Silent	SNP	T	C	C			TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr13:37598529T>C	uc001uwg.2	-	18	1628	c.1380A>G	c.(1378-1380)AAA>AAG	p.K460K	FAM48A_uc010abt.2_Silent_p.K461K|FAM48A_uc001uwh.2_Silent_p.K461K|FAM48A_uc001uwi.2_Silent_p.K460K|FAM48A_uc001uwj.2_Silent_p.K461K|FAM48A_uc001uwk.2_Silent_p.K460K|FAM48A_uc010tes.1_Silent_p.K424K|FAM48A_uc001uwl.1_Silent_p.K460K|FAM48A_uc001uwd.2_5'Flank|FAM48A_uc001uwe.2_5'UTR|FAM48A_uc001uwf.2_Silent_p.K38K	NM_001014286	NP_001014308	Q8NEM7	FA48A_HUMAN	family with sequence similarity 48, member A	460					autophagy|gastrulation	SAGA-type complex	protein binding				0		Lung NSC(96;2.09e-06)|Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.0959)		all cancers(112;6.06e-07)|Epithelial(112;1.87e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00794)|BRCA - Breast invasive adenocarcinoma(63;0.0128)|GBM - Glioblastoma multiforme(144;0.0477)		GGGGTCGATGTTTTACACCCT	0.353000													3	93	---	---	---	---	0	0	0.014758	0	0
G2E3	55632	broad.mit.edu	37	14	31061616	31061616	+	Missense_Mutation	SNP	C	G	G			TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr14:31061616C>G	uc001wqk.2	+	5	479	c.325C>G	c.(325-327)CAG>GAG	p.Q109E	G2E3_uc010tpe.1_Missense_Mutation_p.Q63E|G2E3_uc010tpf.1_Missense_Mutation_p.Q63E	NM_017769	NP_060239	Q7L622	G2E3_HUMAN	G2/M-phase specific E3 ubiquitin ligase	109	PHD-type 1.				apoptosis|multicellular organismal development|protein modification process	Golgi apparatus|nucleolus	acid-amino acid ligase activity|protein binding|zinc ion binding			ovary(2)|skin(1)	3						ATGTGGACTTCAGAGAGAATG	0.353000													3	76	---	---	---	---	0	0	0.014758	0	0
MIR329-1	574408	broad.mit.edu	37	14	101493161	101493161	+	RNA	SNP	A	T	T			TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr14:101493161A>T	hsa-mir-329-1|MI0001725	+			c.40A>T			MIR329-2_hsa-mir-329-2|MI0001726_5'Flank|MIR494_hsa-mir-494|MI0003134_5'Flank|uc010txm.1_5'Flank																	0						TGTTTCTTTAATGAGGACGAA	0.468000													5	161	---	---	---	---	0	0	0.014758	0	0
ADAM6	8755	broad.mit.edu	37	14	107087385	107087385	+	RNA	SNP	T	C	C	rs114856426	by1000genomes	TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr14:107087385T>C	uc010tyt.1	-	108		c.5042A>G								Parts of antibodies, mostly variable regions.												0						TGGAGCCTGGTGGACCCAGTG	0.522000													4	72	---	---	---	---	0	0	0.003080	0	0
Unknown	0	broad.mit.edu	37	15	102300091	102300091	+	5'Flank	SNP	A	G	G			TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr15:102300091A>G	uc002bzk.2	-						uc002bzn.2_5'Flank|uc010uso.1_5'Flank|uc002bzs.2_5'Flank|uc010usv.1_5'Flank|uc002cam.2_RNA|uc010usx.1_5'Flank|uc002cao.2_5'Flank|uc002cap.2_5'Flank|uc002caq.2_5'Flank|uc010usz.1_5'Flank|uc010uta.1_5'Flank|uc002cas.2_5'Flank|uc002cat.1_5'Flank|uc002cau.2_5'Flank|uc010utb.1_5'Flank|uc002cav.2_5'Flank|uc002caw.2_5'Flank|uc002cax.2_5'Flank|uc010utc.1_5'Flank|uc002cay.2_5'Flank|uc002cbb.2_5'Flank|uc002cbc.1_5'Flank|uc002cbd.2_5'Flank|uc002cbe.2_5'Flank|uc002cbg.2_5'Flank|uc002cbh.2_5'Flank|uc002cbi.2_5'Flank|uc002cbk.2_5'Flank|uc002cbl.2_5'Flank|uc010utd.1_5'Flank|uc002cbm.2_5'Flank|uc002cbn.2_5'Flank|uc010ute.1_5'Flank					DQ593627																		GAAGACACTCATGGAGGAGTC	0.582000													3	23	---	---	---	---	0	0	0.004672	0	0
MKL2	57496	broad.mit.edu	37	16	14304130	14304130	+	Missense_Mutation	SNP	C	T	T			TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr16:14304130C>T	uc010uza.1	+	4	340	c.185C>T	c.(184-186)ACG>ATG	p.T62M	MKL2_uc002dcg.2_Missense_Mutation_p.T62M|MKL2_uc002dch.2_Missense_Mutation_p.T51M|MKL2_uc010uzb.1_Missense_Mutation_p.T11M	NM_014048	NP_054767	Q9ULH7	MKL2_HUMAN	megakaryoblastic leukemia 2 protein	51	RPEL 1.				cell differentiation|muscle organ development|positive regulation of striated muscle tissue development|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		identical protein binding|nucleic acid binding|transcription coactivator activity			ovary(3)|kidney(1)|pancreas(1)	5						CAAAGGAGGACGAGAGAACAA	0.483000													5	116	---	---	---	---	0	0	0.001168	0	0
CIRH1A	84916	broad.mit.edu	37	16	69177170	69177170	+	Missense_Mutation	SNP	G	A	A			TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr16:69177170G>A	uc002ews.3	+	6	712	c.616G>A	c.(616-618)GAT>AAT	p.D206N	CIRH1A_uc002ewr.2_Missense_Mutation_p.D206N|CIRH1A_uc002ewt.3_Missense_Mutation_p.D123N|CIRH1A_uc010cfi.2_Missense_Mutation_p.D123N|CIRH1A_uc010cfj.1_Missense_Mutation_p.D25N	NM_032830	NP_116219	Q969X6	CIR1A_HUMAN	cirhin	206	WD 5.					nucleolus	protein binding				0				OV - Ovarian serous cystadenocarcinoma(108;0.125)		CTTCTTGTCCGATGGCACTAT	0.522000													4	252	---	---	---	---	0	0	0.009096	0	0
DNAH2	146754	broad.mit.edu	37	17	7662780	7662780	+	Missense_Mutation	SNP	G	A	A			TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr17:7662780G>A	uc002giu.1	+	15	2503	c.2489G>A	c.(2488-2490)CGC>CAC	p.R830H		NM_020877	NP_065928	Q9P225	DYH2_HUMAN	dynein heavy chain domain 3	830	Stem (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(6)|skin(6)|central_nervous_system(1)	13		all_cancers(10;4.66e-07)|Prostate(122;0.081)				CGGCTGGACCGCATGATGGAG	0.527000													4	171	---	---	---	---	0	0	0.009096	0	0
SNF8	11267	broad.mit.edu	37	17	47018424	47018424	+	Missense_Mutation	SNP	T	A	A			TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr17:47018424T>A	uc002ioj.2	-	3	164	c.106A>T	c.(106-108)ATG>TTG	p.M36L	SNF8_uc002iok.2_Missense_Mutation_p.M36L	NM_007241	NP_009172	Q96H20	SNF8_HUMAN	EAP30 subunit of ELL complex	36	Potential.				cellular membrane organization|endosome transport|protein transport|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytosol|late endosome membrane|transcription factor complex	transcription factor binding				0						TGCTTTGACATCTGTTGGATG	0.512000													4	222	---	---	---	---	0	0	0.001168	0	0
AMZ2P1	201283	broad.mit.edu	37	17	62968690	62968690	+	RNA	SNP	A	G	G	rs138671696	by1000genomes	TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr17:62968690A>G	uc002jez.3	-	4		c.641T>C			AMZ2P1_uc002jfa.3_RNA|AMZ2P1_uc002jfb.3_RNA|AMZ2P1_uc010del.2_RNA					Homo sapiens cDNA FLJ32065 fis, clone OCBBF1000086, weakly similar to Archeobacterial metalloproteinase-like protein 2 (EC 3.-.-.-).												0						AAAATTCCACAAGTCTCTTGG	0.373000													6	156	---	---	---	---	0	0	0.001168	0	0
SLC26A11	284129	broad.mit.edu	37	17	78201660	78201660	+	Missense_Mutation	SNP	C	G	G			TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr17:78201660C>G	uc002jyb.1	+	7	906	c.637C>G	c.(637-639)CTG>GTG	p.L213V	SLC26A11_uc002jyc.1_Missense_Mutation_p.L213V|SLC26A11_uc002jyd.1_Missense_Mutation_p.L213V|SLC26A11_uc010dhv.1_Missense_Mutation_p.L213V	NM_173626	NP_775897	Q86WA9	S2611_HUMAN	solute carrier family 26, member 11	213	Helical; (Potential).					endoplasmic reticulum|Golgi apparatus|integral to membrane|lysosomal membrane|plasma membrane	anion:anion antiporter activity|secondary active sulfate transmembrane transporter activity				0	all_neural(118;0.0538)		OV - Ovarian serous cystadenocarcinoma(97;0.0344)|BRCA - Breast invasive adenocarcinoma(99;0.0908)			GCTGCTGCTGCTGGTGCTGAA	0.682000													3	220	---	---	---	---	0	0	0.014758	0	0
ZNF44	51710	broad.mit.edu	37	19	12384688	12384688	+	Missense_Mutation	SNP	G	A	A			TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr19:12384688G>A	uc010xmj.1	-	5	731	c.526C>T	c.(526-528)CAC>TAC	p.H176Y	ZNF44_uc002mtl.2_Intron|ZNF44_uc010dyr.1_Intron|ZNF44_uc010xmi.1_RNA|ZNF44_uc002mtn.3_RNA|ZNF44_uc010dys.2_Missense_Mutation_p.H128Y	NM_001164276	NP_001157748	P15621	ZNF44_HUMAN	zinc finger protein 44 isoform 1	176					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|microtubule cytoskeleton|nucleus	DNA binding|protein binding|zinc ion binding			ovary(1)	1		Renal(1328;0.157)		GBM - Glioblastoma multiforme(1328;0.0164)|Lung(535;0.179)		CGGTGTTTGTGTCCAGTATCA	0.443000													4	161	---	---	---	---	0	0	0.001168	0	0
C2orf42	54980	broad.mit.edu	37	2	70408980	70408980	+	Silent	SNP	T	A	A			TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr2:70408980T>A	uc002sgh.2	-	3	466	c.138A>T	c.(136-138)ACA>ACT	p.T46T		NM_017880	NP_060350	Q9NWW7	CB042_HUMAN	hypothetical protein LOC54980	46											0						TGGTTCCACATGTCTTGTTCT	0.493000													4	145	---	---	---	---	0	0	0.001168	0	0
Unknown	0	broad.mit.edu	37	22	18844888	18844888	+	RNA	SNP	A	G	G			TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr22:18844888A>G	uc002zoe.2	+	4		c.2142A>G			uc002zof.2_5'Flank					Homo sapiens cDNA FLJ76361 complete cds.																		GCTCACGGAAATACAGCTTCA	0.587000													3	123	---	---	---	---	0	0	0.014758	0	0
FGD5	152273	broad.mit.edu	37	3	14861821	14861821	+	Missense_Mutation	SNP	G	A	A			TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr3:14861821G>A	uc003bzc.2	+	1	1353	c.1243G>A	c.(1243-1245)GTC>ATC	p.V415I	FGD5_uc011avk.1_Missense_Mutation_p.V415I	NM_152536	NP_689749	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5	415					actin cytoskeleton organization|filopodium assembly|regulation of Cdc42 GTPase activity|regulation of cell shape	cytoskeleton|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(3)|kidney(1)|pancreas(1)	5						TGATGTGGTGGTCGTGCTGGA	0.682000													3	54	---	---	---	---	0	0	0.009096	0	0
NIPBL	25836	broad.mit.edu	37	5	36985887	36985887	+	Missense_Mutation	SNP	A	G	G			TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr5:36985887A>G	uc003jkl.3	+	10	3104	c.2605A>G	c.(2605-2607)AAA>GAA	p.K869E	NIPBL_uc003jkk.3_Missense_Mutation_p.K869E|NIPBL_uc003jkm.1_Missense_Mutation_p.K748E	NM_133433	NP_597677	Q6KC79	NIPBL_HUMAN	delangin isoform A	869					brain development|cellular protein localization|cellular response to X-ray|cognition|developmental growth|ear morphogenesis|embryonic arm morphogenesis|embryonic digestive tract morphogenesis|external genitalia morphogenesis|eye morphogenesis|face morphogenesis|gall bladder development|maintenance of mitotic sister chromatid cohesion|metanephros development|negative regulation of transcription from RNA polymerase II promoter|outflow tract morphogenesis|positive regulation of histone deacetylation|regulation of developmental growth|regulation of embryonic development|regulation of hair cycle|response to DNA damage stimulus|sensory perception of sound|uterus morphogenesis	SMC loading complex	chromo shadow domain binding|histone deacetylase binding|protein C-terminus binding|protein N-terminus binding			ovary(4)|lung(2)|large_intestine(1)|breast(1)|kidney(1)	9	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			ACTAGAACGAAAACACAGGCA	0.398000													7	75	---	---	---	---	0	0	0.001984	0	0
PTGER4	5734	broad.mit.edu	37	5	40681354	40681354	+	Missense_Mutation	SNP	G	C	C			TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr5:40681354G>C	uc003jlz.2	+	2	851	c.259G>C	c.(259-261)GGG>CGG	p.G87R		NM_000958	NP_000949	P35408	PE2R4_HUMAN	prostaglandin E receptor 4, subtype EP4	87	Extracellular (Potential).				G-protein signaling, coupled to cAMP nucleotide second messenger|immune response	integral to membrane|plasma membrane	prostaglandin E receptor activity			lung(2)	2						CCAATGGCCCGGGGGCCAGCC	0.612000											OREG0016588	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	166	---	---	---	---	0	0	0.009096	0	0
BDP1	55814	broad.mit.edu	37	5	70840993	70840993	+	Missense_Mutation	SNP	C	T	T			TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr5:70840993C>T	uc003kbp.1	+	32	6954	c.6691C>T	c.(6691-6693)CCC>TCC	p.P2231S	BDP1_uc003kbo.2_Missense_Mutation_p.P2231S|BDP1_uc003kbq.1_RNA|BDP1_uc003kbr.1_RNA	NM_018429	NP_060899	A6H8Y1	BDP1_HUMAN	transcription factor-like nuclear regulator	2231					regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter	nucleoplasm	DNA binding			skin(2)	2		Lung NSC(167;0.000422)|Prostate(74;0.00815)|Ovarian(174;0.0176)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;5.28e-56)|Epithelial(20;2.31e-50)		TGTTGAAGAGCCCCAGATAAA	0.468000													22	78	---	---	---	---	0	0	0.005443	0	0
SPZ1	84654	broad.mit.edu	37	5	79616605	79616605	+	Missense_Mutation	SNP	C	G	G			TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr5:79616605C>G	uc003kgn.2	+	1	816	c.571C>G	c.(571-573)CAG>GAG	p.Q191E	uc011ctk.1_RNA	NM_032567	NP_115956	Q9BXG8	SPZ1_HUMAN	spermatogenic leucine zipper 1	191	Basic motif (By similarity).				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			ovary(1)	1		Lung NSC(167;0.0393)|all_lung(232;0.0428)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;3.43e-47)|Epithelial(54;2.25e-41)|all cancers(79;4.19e-36)		AAAGAAACAGCAGATGATAAT	0.353000													3	95	---	---	---	---	0	0	0.004672	0	0
SOX30	11063	broad.mit.edu	37	5	157078329	157078329	+	Missense_Mutation	SNP	G	A	A			TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr5:157078329G>A	uc003lxb.1	-	1	1100	c.758C>T	c.(757-759)CCG>CTG	p.P253L	SOX30_uc003lxc.1_Missense_Mutation_p.P253L|SOX30_uc011dds.1_Intron	NM_178424	NP_848511	O94993	SOX30_HUMAN	SRY (sex determining region Y)-box 30 isoform a	253					regulation of transcription from RNA polymerase II promoter|regulation of transcription, DNA-dependent|response to corticosteroid stimulus|transcription, DNA-dependent	nucleus|nucleus	sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity			ovary(1)|central_nervous_system(1)	2	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			TTGCTGGTGCGGCCCAAAGGC	0.647000													3	42	---	---	---	---	0	0	0.004672	0	0
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	T	T			TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr7:140453136A>T	uc003vwc.3	-	15	1860	c.1799T>A	c.(1798-1800)GTG>GAG	p.V600E		NM_004333	NP_004324	P15056	BRAF_HUMAN	B-Raf	600	Protein kinase.		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions).|V -> E (in sarcoma, colorectal adenocarcinoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis).		activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission	cytosol|nucleus|plasma membrane	ATP binding|metal ion binding	p.V600E(16892)|p.V600?(325)|p.V600K(176)|p.V600R(36)|p.V600M(25)|p.V600A(23)|p.V600D(21)|p.V600G(11)|p.V600_K601>E(8)|p.T599_V600insTT(3)|p.T599_R603>I(2)|p.T599_V600>IAL(2)|p.V600L(2)|p.T599_V600insT(2)|p.V600_W604del(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insV(1)|p.T599_V600insDFGLAT(1)	KIAA1549/BRAF(229)|AKAP9_ENST00000356239/BRAF(10)|AGTRAP/BRAF(2)|FCHSD1/BRAF(2)|SLC45A3/BRAF(2)	thyroid(8166)|large_intestine(5052)|skin(3798)|NS(368)|central_nervous_system(284)|ovary(236)|lung(78)|eye(53)|prostate(44)|endometrium(30)|biliary_tract(28)|soft_tissue(27)|haematopoietic_and_lymphoid_tissue(22)|breast(18)|upper_aerodigestive_tract(13)|stomach(13)|pancreas(10)|small_intestine(10)|testis(7)|bone(6)|cervix(5)|genital_tract(4)|oesophagus(3)|urinary_tract(3)|adrenal_gland(3)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|meninges(1)|kidney(1)|autonomic_ganglia(1)|pituitary(1)|salivary_gland(1)	18290	Melanoma(164;0.00956)				Sorafenib(DB00398)	TCGAGATTTCACTGTAGCTAG	0.368000	V600E(UACC257_SKIN)|V600D(K029AX_SKIN)|V600E(HS695T_SKIN)|V600E(COLO679_SKIN)|V600E(BT474_BREAST)|V600E(IGR39_SKIN)|V600E(A101D_SKIN)|V600E(COLO783_SKIN)|V600E(IGR37_SKIN)|V600E(A375_SKIN)|V600E(WM793_SKIN)|V600E(COLO818_SKIN)|V600E(HS294T_SKIN)|V600E(SKMEL28_SKIN)|V600E(DU4475_BREAST)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(IGR1_SKIN)|V600E(SKHEP1_LIVER)|V600E(WM983B_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(RVH421_SKIN)|V600D(WM2664_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(SKMEL24_SKIN)|V600D(WM115_SKIN)|V600E(MALME3M_SKIN)|V600E(A673_BONE)|V600E(C32_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(COLO800_SKIN)|V600E(COLO741_SKIN)|V600E(HS939T_SKIN)|V600E(COLO205_LARGE_INTESTINE)|V600E(K029AX_SKIN)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(SH4_SKIN)|V600E(WM88_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(COLO849_SKIN)|V600E(MELHO_SKIN)|V600E(BHT101_THYROID)|V600E(G361_SKIN)|V600E(UACC62_SKIN)|V600E(BCPAP_THYROID)|V600E(8505C_THYROID)|V600E(SW1417_LARGE_INTESTINE)|V600E(COLO829_SKIN)|V600E(RKO_LARGE_INTESTINE)|V600E(A2058_SKIN)|V600E(RPMI7951_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(SKMEL5_SKIN)|V600E(ES2_OVARY)|V600E(LOXIMVI_SKIN)	61	Mis|T|O	AKAP9|KIAA1549	melanoma|colorectal|papillary thyroid|borderline ov|Non small-cell lung cancer (NSCLC)|cholangiocarcinoma|pilocytic astrocytoma		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous_syndrome				45	82	---	---	---	---	0	0	0.014410	0	0
DECR1	1666	broad.mit.edu	37	8	91057101	91057101	+	Missense_Mutation	SNP	A	G	G			TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr8:91057101A>G	uc003yek.1	+	8	904	c.763A>G	c.(763-765)ACT>GCT	p.T255A	DECR1_uc011lgc.1_Missense_Mutation_p.T246A|DECR1_uc011lgd.1_RNA	NM_001359	NP_001350	Q16698	DECR_HUMAN	2,4-dienoyl CoA reductase 1 precursor	255					fatty acid beta-oxidation|protein homotetramerization	mitochondrial matrix|nucleus|plasma membrane	2,4-dienoyl-CoA reductase (NADPH) activity|NADPH binding|oxidoreductase activity, acting on NADH or NADPH				0			BRCA - Breast invasive adenocarcinoma(11;0.00953)			TCTGGACCCAACTGGAACATT	0.408000													3	160	---	---	---	---	0	0	0.014758	0	0
GPR172A	79581	broad.mit.edu	37	8	145583036	145583036	+	Missense_Mutation	SNP	A	G	G	rs141698844		TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr8:145583036A>G	uc003zcc.1	+	2	240	c.83A>G	c.(82-84)AAT>AGT	p.N28S	FBXL6_uc003zbz.2_5'Flank|FBXL6_uc003zca.2_5'Flank|FBXL6_uc003zcb.2_5'Flank|FBXL6_uc010mfx.2_5'UTR|GPR172A_uc003zcd.1_Missense_Mutation_p.N28S|GPR172A_uc003zce.1_Missense_Mutation_p.N28S|GPR172A_uc010mfy.1_Missense_Mutation_p.N28S|GPR172A_uc003zcf.1_Missense_Mutation_p.N28S|GPR172A_uc011llc.1_Intron	NM_024531	NP_078807	Q9HAB3	RFT3_HUMAN	G protein-coupled receptor 172A precursor	28	Helical; (Potential).					integral to plasma membrane	receptor activity|riboflavin transporter activity				0	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;4.43e-40)|Epithelial(56;1.48e-39)|all cancers(56;1.49e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0441)|Colorectal(110;0.055)			GCTGCGGTCAATGGGATCTGG	0.662000													3	72	---	---	---	---	0	0	0.009096	0	0
DOCK11	139818	broad.mit.edu	37	X	117819770	117819770	+	Nonstop_Mutation	SNP	A	G	G			TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chrX:117819770A>G	uc004eqp.2	+	53	6285	c.6222A>G	c.(6220-6222)TGA>TGG	p.*2074W	DOCK11_uc004eqq.2_Nonstop_Mutation_p.*1853W	NM_144658	NP_653259	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	2074					blood coagulation	cytosol	GTP binding			ovary(3)	3						CTGAAGTGTGAGGAAATGCAG	0.393000													3	132	---	---	---	---	0	0	0.014758	0	0
FAM122B	159090	broad.mit.edu	37	X	133919917	133919917	+	Silent	SNP	T	C	C			TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chrX:133919917T>C	uc004exr.2	-	7	651	c.501A>G	c.(499-501)AAA>AAG	p.K167K	FAM122B_uc004exq.2_Silent_p.K186K|FAM122B_uc004exs.2_Silent_p.K168K|FAM122B_uc004ext.2_Silent_p.K115K|FAM122B_uc004exu.2_RNA|FAM122B_uc011mvp.1_Silent_p.K134K|FAM122B_uc004exv.2_Silent_p.K186K	NM_145284	NP_660327	Q7Z309	F122B_HUMAN	hypothetical protein LOC159090	167											0	Acute lymphoblastic leukemia(192;0.000127)					gctacatACCTTTTCTTTTAA	0.204000													3	89	---	---	---	---	0	0	0.009096	0	0
NLGN4Y	22829	broad.mit.edu	37	Y	16734111	16734111	+	Missense_Mutation	SNP	C	G	G			TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chrY:16734111C>G	uc004ftg.2	+	2	364	c.112C>G	c.(112-114)CTC>GTC	p.L38V	NLGN4Y_uc004fte.2_Intron|NLGN4Y_uc011nas.1_Missense_Mutation_p.L38V|NLGN4Y_uc004ftf.2_5'UTR|NLGN4Y_uc004fth.2_Missense_Mutation_p.L38V|NLGN4Y_uc004fti.3_Missense_Mutation_p.L38V	NM_014893	NP_055708	Q8NFZ3	NLGNY_HUMAN	neuroligin 4, Y-linked isoform 1	38					brainstem development|cell adhesion|cerebellum development|male courtship behavior|positive regulation of organ growth|social behavior|synapse assembly|territorial aggressive behavior|vocalization behavior	cell surface|integral to plasma membrane|synapse	neurexin binding|receptor activity				0						CAAGTTCACCCTCATTGACAG	0.463000													5	66	---	---	---	---	0	0	0.001168	0	0
Unknown	0	broad.mit.edu	37	1	5050112	5050113	+	IGR	DEL	TC	-	-			TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr1:5050112_5050113delTC								AJAP1 (206262 upstream) : NPHP4 (872757 downstream)																							aggccttctgtctctctctctc	0.000													4	8	---	---	---	---					
RPTN	126638	broad.mit.edu	37	1	152127917	152127920	+	Frame_Shift_Del	DEL	TGTC	-	-			TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr1:152127917_152127920delTGTC	uc001ezs.1	-	3	1720_1723	c.1655_1658delGACA	c.(1654-1659)AGACAAfs	p.R552fs		NM_001122965	NP_001116437	Q6XPR3	RPTN_HUMAN	repetin	552_553	Gln-rich.					proteinaceous extracellular matrix	calcium ion binding				0						ACTCTGGCCTTGTCTGTCTGTCTG	0.505													7	1555	---	---	---	---					
PLEKHA6	22874	broad.mit.edu	37	1	204192635	204192635	+	Frame_Shift_Del	DEL	G	-	-			TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr1:204192635delG	uc001hau.2	-	22	3427	c.3110delC	c.(3109-3111)CCAfs	p.P1037fs		NM_014935	NP_055750	Q9Y2H5	PKHA6_HUMAN	phosphoinositol 3-phosphate-binding protein-3	1037										ovary(3)|pancreas(1)	4	all_cancers(21;0.0222)|Breast(84;0.179)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|BRCA - Breast invasive adenocarcinoma(75;0.0833)|Kidney(21;0.0934)|Epithelial(59;0.229)			GGCGCCCCGTGGGGATTCAGA	0.592													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	10	37969749	37969756	+	IGR	DEL	CGGGGCTG	-	-	rs72149588		TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr10:37969749_37969756delCGGGGCTG								ANKRD30A (448254 upstream) : ZNF248 (120691 downstream)																							CAGGGGAGGCCGGGGCTGCAAGGGGGAG	0.688													2	4	---	---	---	---					
ADCY6	112	broad.mit.edu	37	12	49183367	49183367	+	5'Flank	DEL	G	-	-	rs10711161		TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr12:49183367delG	uc001rsj.3	-						ADCY6_uc001rsi.3_5'Flank	NM_015270	NP_056085	O43306	ADCY6_HUMAN	adenylate cyclase 6 isoform a						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane	ATP binding|metal ion binding				0						ccctgccccagccccagcccc	0.383													4	2	---	---	---	---					
ATP5G2	517	broad.mit.edu	37	12	54072125	54072127	+	5'Flank	DEL	CAC	-	-			TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr12:54072125_54072127delCAC	uc009znc.2	-						ATP5G2_uc001sec.2_5'Flank|ATP5G2_uc001sed.2_5'Flank	NM_001002031	NP_001002031	Q06055	AT5G2_HUMAN	ATP synthase, H+ transporting, mitochondrial F0						ATP hydrolysis coupled proton transport|ATP synthesis coupled proton transport	integral to membrane|mitochondrial proton-transporting ATP synthase complex|proton-transporting ATP synthase complex, coupling factor F(o)	hydrogen ion transmembrane transporter activity|lipid binding			ovary(1)	1						tcatcatcgtcaccaccaccacc	0.099													3	6	---	---	---	---					
Unknown	0	broad.mit.edu	37	14	53463039	53463041	+	IGR	DEL	ACC	-	-			TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr14:53463039_53463041delACC								FERMT2 (45224 upstream) : DDHD1 (40418 downstream)																							aaccaccactaccaccaccacca	0.005													4	2	---	---	---	---					
Unknown	0	broad.mit.edu	37	15	21914638	21914639	+	IGR	INS	-	CT	CT	rs112777882		TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr15:21914638_21914639insCT								NF1P1 (780013 upstream) : LOC646214 (17875 downstream)																							tcctccttctcctcttccttct	0.282													3	6	---	---	---	---					
CHD2	1106	broad.mit.edu	37	15	93545433	93545434	+	Frame_Shift_Ins	INS	-	A	A			TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr15:93545433_93545434insA	uc002bsp.2	+	33	4739_4740	c.4164_4165insA	c.(4162-4167)ATGAAAfs	p.M1388fs	CHD2_uc002bso.1_Frame_Shift_Ins_p.M1388fs	NM_001271	NP_001262	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	1388_1389					regulation of transcription from RNA polymerase II promoter	nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding			ovary(1)|skin(1)	2	Lung NSC(78;0.00976)|all_lung(78;0.016)		BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)			AAAGTCCAATgaaaaaaaaaca	0.158													10	99	---	---	---	---					
LOC595101	595101	broad.mit.edu	37	16	30347982	30347983	+	5'Flank	INS	-	T	T	rs148333845		TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr16:30347982_30347983insT	uc002dxp.1	-							NR_002453				Homo sapiens cDNA FLJ39663 fis, clone SMINT2007187.												0						CTCTGtttctattttttttttt	0.233													4	6	---	---	---	---					
Unknown	0	broad.mit.edu	37	17	6464640	6464641	+	IGR	INS	-	CTC	CTC	rs143155894	by1000genomes	TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr17:6464640_6464641insCTC								PITPNM3 (4763 upstream) : KIAA0753 (17005 downstream)																							tcttcctccttctcttctttct	0.000													3	6	---	---	---	---					
SUZ12P	440423	broad.mit.edu	37	17	29096086	29096087	+	RNA	INS	-	T	T			TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr17:29096086_29096087insT	uc002hfn.1	+	6		c.1598_1599insT			SUZ12P_uc002hfo.2_Intron|SUZ12P_uc002hfq.2_Intron					Homo sapiens cDNA clone IMAGE:5299523, containing frame-shift errors.												0						AATATTGGTAATTTTTTTTTTT	0.347													4	9	---	---	---	---					
Unknown	0	broad.mit.edu	37	18	11492784	11492787	+	IGR	DEL	GTGT	-	-			TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr18:11492784_11492787delGTGT								FAM38B (790805 upstream) : GNAL (196349 downstream)																							aaactacaacgtgtgtgtgtgtgt	0.005													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	2	43333170	43333172	+	IGR	DEL	CCT	-	-			TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr2:43333170_43333172delCCT								HAAO (313419 upstream) : ZFP36L2 (116370 downstream)																							TGCCTGTGTCCCTCCTCCTCCTC	0.571											OREG0014577	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	21	11144773	11144774	+	IGR	DEL	TG	-	-	rs72428671		TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr21:11144773_11144774delTG								BAGE (45836 upstream) : None (None downstream)																							TGGAtgtgtctgtgtgtgtgtg	0.371													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	4	146488179	146488181	+	IGR	DEL	TGC	-	-			TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr4:146488179_146488181delTGC								SMAD1 (7856 upstream) : MMAA (52359 downstream)																							caccccgccatgctgctgctgct	0.000													3	6	---	---	---	---					
Unknown	0	broad.mit.edu	37	5	180215028	180215030	+	IGR	DEL	GCA	-	-			TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr5:180215028_180215030delGCA								OR2Y1 (47970 upstream) : MGAT1 (2513 downstream)																							AAGCAGGAATGCAGCAGCAGCAG	0.586													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	7	1236298	1236298	+	IGR	DEL	G	-	-			TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr7:1236298delG								ZFAND2A (36443 upstream) : UNCX (36356 downstream)																							GTGATGAAgaggggggggtgg	0.050													3	6	---	---	---	---					
Unknown	0	broad.mit.edu	37	7	26316301	26316302	+	IGR	INS	-	AAAT	AAAT	rs142084046	by1000genomes	TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr7:26316301_26316302insAAAT								CBX3 (63327 upstream) : SNX10 (15213 downstream)																							TGCCCCCTCAAaaataaataaa	0.267													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	7	47996414	47996416	+	IGR	DEL	ATG	-	-			TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr7:47996414_47996416delATG								PKD1L1 (8377 upstream) : HUS1 (6567 downstream)																							TGATAACCAAatgatgatgatga	0.202													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	8	38479805	38479806	+	IGR	INS	-	AC	AC	rs137977718	by1000genomes	TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr8:38479805_38479806insAC								RNF5P1 (21030 upstream) : TACC1 (105898 downstream)																							TGCCCCAGCAAacacacacaca	0.267													4	3	---	---	---	---					
KCNQ3	3786	broad.mit.edu	37	8	133150232	133150233	+	Frame_Shift_Ins	INS	-	T	T			TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr8:133150232_133150233insT	uc003ytj.2	-	12	1824_1825	c.1599_1600insA	c.(1597-1602)AAATTCfs	p.K533fs	KCNQ3_uc010mdt.2_Frame_Shift_Ins_p.K533fs	NM_004519	NP_004510	O43525	KCNQ3_HUMAN	potassium voltage-gated channel KQT-like protein	533_534					axon guidance|synaptic transmission	voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(2)|breast(1)|central_nervous_system(1)|skin(1)	5	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)			GTCTCCTTGAATTTTTTTTTAT	0.455													7	210	---	---	---	---					
ROR2	4920	broad.mit.edu	37	9	94486026	94486028	+	In_Frame_Del	DEL	TCC	-	-			TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chr9:94486026_94486028delTCC	uc004arj.1	-	9	2947_2949	c.2748_2750delGGA	c.(2746-2751)GAGGAA>GAA	p.916_917EE>E	ROR2_uc004ari.1_Intron	NM_004560	NP_004551	Q01974	ROR2_HUMAN	receptor tyrosine kinase-like orphan receptor 2	916_917	Cytoplasmic (Potential).				negative regulation of cell proliferation|positive regulation of cell migration|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding			lung(8)|central_nervous_system(5)|ovary(3)|large_intestine(2)|stomach(1)|breast(1)	20						GACAGAGCCTTCCTCCTCCTCCT	0.645													7	228	---	---	---	---					
Unknown	0	broad.mit.edu	37	X	140233410	140233411	+	IGR	INS	-	AAAAT	AAAAT			TCGA-E3-A3DY-01A-11D-A20C-08	TCGA-E3-A3DY-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	7d4b3f8a-7f25-4f3b-8858-3ef0171dd446	f0611285-bed3-4543-a8ce-0e78419d38b5	g.chrX:140233410_140233411insAAAAT								SPANXB2 (147540 upstream) : LDOC1 (36529 downstream)																							GTTTATGTTAAaaaataaaata	0.178													4	7	---	---	---	---					
