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
VPS13D	55187	broad.mit.edu	37	1	12387912	12387912	+	Splice_Site	SNP	G	A	A			TCGA-IM-A3U3-01A-11D-A22D-08	TCGA-IM-A3U3-10A-01D-A22D-08									Somatic	Phase_I	Capture				Illumina GAIIx	8d433dcf-1aa3-462a-8ab3-6de005ad8f69	cf90d01b-1750-4167-9b0a-ca680081e70f	g.chr1:12387912G>A	uc001atv.2	+	36	8338	c.8197_splice	c.e36+1	p.R2733_splice	VPS13D_uc001atw.2_Splice_Site_p.R2733_splice|VPS13D_uc001atx.2_Splice_Site_p.R1921_splice|VPS13D_uc001aty.1_Splice_Site_p.R471_splice	NM_015378	NP_056193	Q5THJ4	VP13D_HUMAN	vacuolar protein sorting 13D isoform 1						protein localization					ovary(4)|pancreas(1)	5	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		ACCTTTTCCCGTGAGTGTTGT	0.403000													3	38	---	---	---	---	0	0	1	0	0
CROCCL1	84809	broad.mit.edu	37	1	16952952	16952952	+	RNA	SNP	G	A	A	rs1762946	by1000genomes	TCGA-IM-A3U3-01A-11D-A22D-08	TCGA-IM-A3U3-10A-01D-A22D-08									Somatic	Phase_I	Capture				Illumina GAIIx	8d433dcf-1aa3-462a-8ab3-6de005ad8f69	cf90d01b-1750-4167-9b0a-ca680081e70f	g.chr1:16952952G>A	uc010ocf.1	-	1		c.43C>T			CROCCL1_uc009vov.1_RNA|CROCCL1_uc001aze.2_RNA|CROCCL1_uc001azf.2_RNA|CROCCL1_uc001azg.1_RNA					Homo sapiens mRNA for FLJ00313 protein.												0						TCTGCCCTCAGCTTGGTCACG	0.622000													5	56	---	---	---	---	0	0	1	0	0
ADC	113451	broad.mit.edu	37	1	33583639	33583639	+	Missense_Mutation	SNP	C	T	T			TCGA-IM-A3U3-01A-11D-A22D-08	TCGA-IM-A3U3-10A-01D-A22D-08									Somatic	Phase_I	Capture				Illumina GAIIx	8d433dcf-1aa3-462a-8ab3-6de005ad8f69	cf90d01b-1750-4167-9b0a-ca680081e70f	g.chr1:33583639C>T	uc001bwr.2	+	11	1753	c.1166C>T	c.(1165-1167)GCC>GTC	p.A389V	ADC_uc001bws.2_Missense_Mutation_p.A389V|ADC_uc009vue.2_Missense_Mutation_p.A389V|ADC_uc001bwt.1_Missense_Mutation_p.A294V|ADC_uc001bwu.2_Missense_Mutation_p.A294V|ADC_uc001bwv.2_Missense_Mutation_p.A294V|ADC_uc001bww.2_Missense_Mutation_p.A294V|ADC_uc001bwx.1_Missense_Mutation_p.A366V|ADC_uc009vug.2_Missense_Mutation_p.A409V	NM_052998	NP_443724	Q96A70	ADC_HUMAN	ODC antizyme inhibitor-2	389					polyamine biosynthetic process|spermatogenesis	cytosol	arginine decarboxylase activity			ovary(2)	2		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)			L-Arginine(DB00125)|Pyridoxal Phosphate(DB00114)	AACATGGGCGCCTACACTGTG	0.632000													13	56	---	---	---	---	0	0	1	0	0
ATPAF1	64756	broad.mit.edu	37	1	47110844	47110844	+	Missense_Mutation	SNP	T	C	C			TCGA-IM-A3U3-01A-11D-A22D-08	TCGA-IM-A3U3-10A-01D-A22D-08									Somatic	Phase_I	Capture				Illumina GAIIx	8d433dcf-1aa3-462a-8ab3-6de005ad8f69	cf90d01b-1750-4167-9b0a-ca680081e70f	g.chr1:47110844T>C	uc001cqh.2	-	7	778	c.673A>G	c.(673-675)ATA>GTA	p.I225V	ATPAF1_uc001cqg.2_Intron|ATPAF1_uc009vyk.2_Missense_Mutation_p.I74V|ATPAF1_uc010omg.1_Missense_Mutation_p.I137V|ATPAF1_uc001cqi.2_Intron	NM_022745	NP_073582	Q5TC12	ATPF1_HUMAN	ATP synthase mitochondrial F1 complex assembly	225					protein complex assembly	mitochondrion	protein binding				0	Acute lymphoblastic leukemia(166;0.155)					TGAATATTTATAAGTGCAGTG	0.443000													48	117	---	---	---	---	0	0	1	0	0
HIPK1	204851	broad.mit.edu	37	1	114499825	114499825	+	Missense_Mutation	SNP	C	T	T			TCGA-IM-A3U3-01A-11D-A22D-08	TCGA-IM-A3U3-10A-01D-A22D-08									Somatic	Phase_I	Capture				Illumina GAIIx	8d433dcf-1aa3-462a-8ab3-6de005ad8f69	cf90d01b-1750-4167-9b0a-ca680081e70f	g.chr1:114499825C>T	uc001eem.2	+	7	1833	c.1672C>T	c.(1672-1674)CCC>TCC	p.P558S	HIPK1_uc001eel.2_Missense_Mutation_p.P558S|HIPK1_uc001een.2_Missense_Mutation_p.P558S|HIPK1_uc001eeo.2_Missense_Mutation_p.P184S|HIPK1_uc001eep.2_Missense_Mutation_p.P164S	NM_198268	NP_938009	Q86Z02	HIPK1_HUMAN	homeodomain-interacting protein kinase 1 isoform	558					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(4)	4	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.09e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		GATCAAGAGTCCCTTCACTAC	0.388000													6	122	---	---	---	---	0	0	1	0	0
ANK3	288	broad.mit.edu	37	10	61835974	61835974	+	Silent	SNP	C	T	T			TCGA-IM-A3U3-01A-11D-A22D-08	TCGA-IM-A3U3-10A-01D-A22D-08									Somatic	Phase_I	Capture				Illumina GAIIx	8d433dcf-1aa3-462a-8ab3-6de005ad8f69	cf90d01b-1750-4167-9b0a-ca680081e70f	g.chr10:61835974C>T	uc001jky.2	-	37	4857	c.4665G>A	c.(4663-4665)GCG>GCA	p.A1555A	ANK3_uc001jkw.2_Intron|ANK3_uc009xpa.2_Intron|ANK3_uc001jkx.2_Intron|ANK3_uc010qih.1_Intron|ANK3_uc001jkz.3_Intron|ANK3_uc001jkv.2_Intron|ANK3_uc009xpb.1_Intron	NM_020987	NP_066267	Q12955	ANK3_HUMAN	ankyrin 3 isoform 1	1555	Ser-rich.				establishment of protein localization|signal transduction	basolateral plasma membrane|cytoplasm|cytoskeleton	protein binding			skin(9)|ovary(6)|pancreas(2)|central_nervous_system(2)	19						ATGTAGTTGACGCGCCTAATG	0.418000													6	212	---	---	---	---	0	0	1	0	0
Unknown	0	broad.mit.edu	37	11	89774252	89774252	+	Missense_Mutation	SNP	G	A	A	rs145791878	by1000genomes	TCGA-IM-A3U3-01A-11D-A22D-08	TCGA-IM-A3U3-10A-01D-A22D-08									Somatic	Phase_I	Capture				Illumina GAIIx	8d433dcf-1aa3-462a-8ab3-6de005ad8f69	cf90d01b-1750-4167-9b0a-ca680081e70f	g.chr11:89774252G>A	uc010rua.1	+	7	1016	c.893G>A	c.(892-894)AGT>AAT	p.S298N		NM_020358	NP_065091			ring finger protein 18																		GAAGCCAACAGTGATATCTTT	0.323000													3	29	---	---	---	---	0	0	1	0	0
STT3A	3703	broad.mit.edu	37	11	125476246	125476246	+	Silent	SNP	C	T	T			TCGA-IM-A3U3-01A-11D-A22D-08	TCGA-IM-A3U3-10A-01D-A22D-08									Somatic	Phase_I	Capture				Illumina GAIIx	8d433dcf-1aa3-462a-8ab3-6de005ad8f69	cf90d01b-1750-4167-9b0a-ca680081e70f	g.chr11:125476246C>T	uc001qcd.2	+	8	776	c.666C>T	c.(664-666)CAC>CAT	p.H222H	STT3A_uc009zbm.2_Silent_p.H222H|STT3A_uc001qce.2_Silent_p.H222H|STT3A_uc010sbg.1_Silent_p.H130H|STT3A_uc009zbn.2_Translation_Start_Site	NM_152713	NP_689926	P46977	STT3A_HUMAN	integral membrane protein 1	222	Helical; (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	integral to membrane|oligosaccharyltransferase complex	dolichyl-diphosphooligosaccharide-protein glycotransferase activity				0	all_hematologic(175;0.228)	Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0919)|all_lung(97;0.0994)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0996)		TTCCTCTCCACGTCCTCGTGC	0.478000													4	170	---	---	---	---	0	0	1	0	0
NAV3	89795	broad.mit.edu	37	12	78400935	78400935	+	Missense_Mutation	SNP	A	C	C			TCGA-IM-A3U3-01A-11D-A22D-08	TCGA-IM-A3U3-10A-01D-A22D-08									Somatic	Phase_I	Capture				Illumina GAIIx	8d433dcf-1aa3-462a-8ab3-6de005ad8f69	cf90d01b-1750-4167-9b0a-ca680081e70f	g.chr12:78400935A>C	uc001syp.2	+	8	1790	c.1617A>C	c.(1615-1617)CAA>CAC	p.Q539H	NAV3_uc001syo.2_Missense_Mutation_p.Q539H	NM_014903	NP_055718	Q8IVL0	NAV3_HUMAN	neuron navigator 3	539						nuclear outer membrane	ATP binding|nucleoside-triphosphatase activity			large_intestine(6)|ovary(5)|lung(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	17						CAGTAAAGCAAACCATTTCAC	0.468000										HNSCC(70;0.22)			6	48	---	---	---	---	0	0	1	0	0
Unknown	0	broad.mit.edu	37	16	15023280	15023280	+	Splice_Site	SNP	T	C	C			TCGA-IM-A3U3-01A-11D-A22D-08	TCGA-IM-A3U3-10A-01D-A22D-08									Somatic	Phase_I	Capture				Illumina GAIIx	8d433dcf-1aa3-462a-8ab3-6de005ad8f69	cf90d01b-1750-4167-9b0a-ca680081e70f	g.chr16:15023280T>C	uc010uzk.1	+	6	1123	c.847_splice	c.e6+2	p.G283_splice	NPIP_uc002dcx.3_Splice_Site					SubName: Full=cDNA FLJ57488, highly similar to Polycystin-1;																		CGCTGGCGGGTGAGGAGATCG	0.701000													4	12	---	---	---	---	0	0	1	0	0
Unknown	0	broad.mit.edu	37	2	905904	905904	+	5'Flank	SNP	T	A	A			TCGA-IM-A3U3-01A-11D-A22D-08	TCGA-IM-A3U3-10A-01D-A22D-08									Somatic	Phase_I	Capture				Illumina GAIIx	8d433dcf-1aa3-462a-8ab3-6de005ad8f69	cf90d01b-1750-4167-9b0a-ca680081e70f	g.chr2:905904T>A	uc010ewg.2	-						uc010ewh.1_Missense_Mutation_p.E14D					Homo sapiens cDNA FLJ46162 fis, clone TESTI4002520.																		GGTGTTTCAGTTCCTCCCGGG	0.607000													5	322	---	---	---	---	0	0	1	0	0
FAM161A	84140	broad.mit.edu	37	2	62081111	62081111	+	Missense_Mutation	SNP	G	C	C			TCGA-IM-A3U3-01A-11D-A22D-08	TCGA-IM-A3U3-10A-01D-A22D-08									Somatic	Phase_I	Capture				Illumina GAIIx	8d433dcf-1aa3-462a-8ab3-6de005ad8f69	cf90d01b-1750-4167-9b0a-ca680081e70f	g.chr2:62081111G>C	uc010ypo.1	-	1	168	c.66C>G	c.(64-66)ATC>ATG	p.I22M	FAM161A_uc002sbm.3_Missense_Mutation_p.I22M|FAM161A_uc002sbn.3_Translation_Start_Site|FAM161A_uc010fcm.1_RNA|FAM161A_uc010fcn.1_Translation_Start_Site	NM_032180	NP_115556	Q3B820	F161A_HUMAN	hypothetical protein LOC84140	22					response to stimulus|visual perception	centrosome				large_intestine(2)|ovary(1)	3						GCGCTCCAGTGATGGGATTTA	0.672000													15	20	---	---	---	---	0	0	1	0	0
HK2	3099	broad.mit.edu	37	2	75113626	75113626	+	Missense_Mutation	SNP	G	A	A			TCGA-IM-A3U3-01A-11D-A22D-08	TCGA-IM-A3U3-10A-01D-A22D-08									Somatic	Phase_I	Capture				Illumina GAIIx	8d433dcf-1aa3-462a-8ab3-6de005ad8f69	cf90d01b-1750-4167-9b0a-ca680081e70f	g.chr2:75113626G>A	uc002snd.2	+	15	3971	c.2045G>A	c.(2044-2046)AGC>AAC	p.S682N		NM_000189	NP_000180	P52789	HXK2_HUMAN	hexokinase 2	682	Substrate 2 binding.|Catalytic.				apoptotic mitochondrial changes|glucose transport|glycolysis|transmembrane transport	cytosol|mitochondrial outer membrane	ATP binding|glucokinase activity			ovary(1)|lung(1)	2						GGCACGGGCAGCAATGCCTGC	0.592000													3	92	---	---	---	---	0	0	1	0	0
ABCB11	8647	broad.mit.edu	37	2	169781177	169781177	+	Missense_Mutation	SNP	T	C	C			TCGA-IM-A3U3-01A-11D-A22D-08	TCGA-IM-A3U3-10A-01D-A22D-08									Somatic	Phase_I	Capture				Illumina GAIIx	8d433dcf-1aa3-462a-8ab3-6de005ad8f69	cf90d01b-1750-4167-9b0a-ca680081e70f	g.chr2:169781177T>C	uc002ueo.1	-	27	3881	c.3755A>G	c.(3754-3756)GAA>GGA	p.E1252G	ABCB11_uc010zda.1_Missense_Mutation_p.E670G|ABCB11_uc010zdb.1_Missense_Mutation_p.E728G	NM_003742	NP_003733	O95342	ABCBB_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP),	1252	Cytoplasmic (Potential).|ABC transporter 2.				bile acid biosynthetic process	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus|membrane fraction	ATP binding|bile acid-exporting ATPase activity|canalicular bile acid transmembrane transporter activity|sodium-exporting ATPase activity, phosphorylative mechanism			ovary(2)|large_intestine(2)|breast(1)	5					Adenosine triphosphate(DB00171)|Bosentan(DB00559)|Glibenclamide(DB01016)	CTTTTCACTTTCTGTGTCTAA	0.363000													6	72	---	---	---	---	0	0	1	0	0
TTN	7273	broad.mit.edu	37	2	179598614	179598614	+	Missense_Mutation	SNP	G	T	T			TCGA-IM-A3U3-01A-11D-A22D-08	TCGA-IM-A3U3-10A-01D-A22D-08									Somatic	Phase_I	Capture				Illumina GAIIx	8d433dcf-1aa3-462a-8ab3-6de005ad8f69	cf90d01b-1750-4167-9b0a-ca680081e70f	g.chr2:179598614G>T	uc010zfg.1	-	50	11994	c.11770C>A	c.(11770-11772)CCA>ACA	p.P3924T	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.P585T	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	4851							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ACAAAGGTTGGAGGTTCTAGT	0.368000													6	34	---	---	---	---	8.12818e-05	8.12818e-05	1	1	0
CHRND	1144	broad.mit.edu	37	2	233398945	233398945	+	Missense_Mutation	SNP	G	A	A			TCGA-IM-A3U3-01A-11D-A22D-08	TCGA-IM-A3U3-10A-01D-A22D-08									Somatic	Phase_I	Capture				Illumina GAIIx	8d433dcf-1aa3-462a-8ab3-6de005ad8f69	cf90d01b-1750-4167-9b0a-ca680081e70f	g.chr2:233398945G>A	uc002vsw.2	+	11	1268	c.1264G>A	c.(1264-1266)GCA>ACA	p.A422T	CHRND_uc010zmg.1_Missense_Mutation_p.A407T|CHRND_uc010fyc.2_Missense_Mutation_p.A295T|CHRND_uc010zmh.1_Missense_Mutation_p.A228T	NM_000751	NP_000742	Q07001	ACHD_HUMAN	nicotinic acetylcholine receptor delta	422	Cytoplasmic (Potential).				muscle contraction|musculoskeletal movement|neuromuscular process|skeletal muscle tissue growth|synaptic transmission	cell junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	nicotinic acetylcholine-activated cation-selective channel activity|receptor activity			ovary(1)|breast(1)|skin(1)	3		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;1.89e-16)|BRCA - Breast invasive adenocarcinoma(100;0.00078)|Lung(119;0.00579)|LUSC - Lung squamous cell carcinoma(224;0.00754)		CCGGCCCCCAGCAAGCTCTGA	0.592000													3	59	---	---	---	---	0	0	1	0	0
LOC728323	728323	broad.mit.edu	37	2	243061183	243061183	+	RNA	SNP	C	T	T			TCGA-IM-A3U3-01A-11D-A22D-08	TCGA-IM-A3U3-10A-01D-A22D-08									Somatic	Phase_I	Capture				Illumina GAIIx	8d433dcf-1aa3-462a-8ab3-6de005ad8f69	cf90d01b-1750-4167-9b0a-ca680081e70f	g.chr2:243061183C>T	uc010zpd.1	+	4		c.421C>T			LOC728323_uc010zpe.1_RNA|LOC728323_uc010zpf.1_RNA|LOC728323_uc010zpg.1_RNA	NR_024437				Homo sapiens cDNA FLJ60027 complete cds, moderately similar to F-box only protein 25.												0						ATTCAAGATACCCGAAGGTTC	0.358000													3	58	---	---	---	---	0	0	1	0	0
ARFGEF2	10564	broad.mit.edu	37	20	47611096	47611096	+	Missense_Mutation	SNP	C	T	T			TCGA-IM-A3U3-01A-11D-A22D-08	TCGA-IM-A3U3-10A-01D-A22D-08									Somatic	Phase_I	Capture				Illumina GAIIx	8d433dcf-1aa3-462a-8ab3-6de005ad8f69	cf90d01b-1750-4167-9b0a-ca680081e70f	g.chr20:47611096C>T	uc002xtx.3	+	22	3234	c.3082C>T	c.(3082-3084)CAC>TAC	p.H1028Y	ARFGEF2_uc010zyf.1_Missense_Mutation_p.H321Y	NM_006420	NP_006411	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine	1028					exocytosis|intracellular signal transduction|regulation of ARF protein signal transduction	cytosol|Golgi membrane	ARF guanyl-nucleotide exchange factor activity			breast(3)|upper_aerodigestive_tract(1)	4			BRCA - Breast invasive adenocarcinoma(12;0.00148)|Colorectal(8;0.198)			CCTGAAGGGCCACACATTGGC	0.572000													5	37	---	---	---	---	0	0	1	0	0
Unknown	0	broad.mit.edu	37	22	18844888	18844888	+	RNA	SNP	A	G	G			TCGA-IM-A3U3-01A-11D-A22D-08	TCGA-IM-A3U3-10A-01D-A22D-08									Somatic	Phase_I	Capture				Illumina GAIIx	8d433dcf-1aa3-462a-8ab3-6de005ad8f69	cf90d01b-1750-4167-9b0a-ca680081e70f	g.chr22:18844888A>G	uc002zoe.2	+	4		c.2142A>G			uc002zof.2_5'Flank					Homo sapiens cDNA FLJ76361 complete cds.																		GCTCACGGAAATACAGCTTCA	0.587000													5	63	---	---	---	---	0	0	1	0	0
DUSP7	1849	broad.mit.edu	37	3	52084880	52084880	+	Missense_Mutation	SNP	G	A	A			TCGA-IM-A3U3-01A-11D-A22D-08	TCGA-IM-A3U3-10A-01D-A22D-08									Somatic	Phase_I	Capture				Illumina GAIIx	8d433dcf-1aa3-462a-8ab3-6de005ad8f69	cf90d01b-1750-4167-9b0a-ca680081e70f	g.chr3:52084880G>A	uc003dct.2	-	3	1290	c.1211C>T	c.(1210-1212)ACG>ATG	p.T404M		NM_001947	NP_001938	Q16829	DUS7_HUMAN	dual specificity phosphatase 7	404					inactivation of MAPK activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	MAP kinase tyrosine/serine/threonine phosphatase activity|protein binding|protein tyrosine phosphatase activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;5.14e-05)|Kidney(197;0.000534)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		GTTGGTGGGCGTGGAAAAGTA	0.622000													3	53	---	---	---	---	0	0	1	0	0
CCDC66	285331	broad.mit.edu	37	3	56597934	56597934	+	Missense_Mutation	SNP	A	G	G			TCGA-IM-A3U3-01A-11D-A22D-08	TCGA-IM-A3U3-10A-01D-A22D-08									Somatic	Phase_I	Capture				Illumina GAIIx	8d433dcf-1aa3-462a-8ab3-6de005ad8f69	cf90d01b-1750-4167-9b0a-ca680081e70f	g.chr3:56597934A>G	uc003dhz.2	+	4	412	c.325A>G	c.(325-327)AAA>GAA	p.K109E	CCDC66_uc003dhy.2_5'UTR|CCDC66_uc003dhu.2_Missense_Mutation_p.K75E|CCDC66_uc003dhx.2_RNA|CCDC66_uc003dhv.2_RNA|CCDC66_uc003dhw.2_Missense_Mutation_p.K109E	NM_001141947	NP_001135419	A2RUB6	CCD66_HUMAN	coiled-coil domain containing 66 isoform 1	109										breast(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0478)|Kidney(284;0.0597)|OV - Ovarian serous cystadenocarcinoma(275;0.233)		TCATATCCAGAAAGAGATTTC	0.358000													4	22	---	---	---	---	0	0	1	0	0
CBLB	868	broad.mit.edu	37	3	105464772	105464772	+	Silent	SNP	G	T	T			TCGA-IM-A3U3-01A-11D-A22D-08	TCGA-IM-A3U3-10A-01D-A22D-08									Somatic	Phase_I	Capture				Illumina GAIIx	8d433dcf-1aa3-462a-8ab3-6de005ad8f69	cf90d01b-1750-4167-9b0a-ca680081e70f	g.chr3:105464772G>T	uc003dwc.2	-	6	1156	c.834C>A	c.(832-834)ACC>ACA	p.T278T	CBLB_uc011bhi.1_Silent_p.T300T|CBLB_uc003dwd.1_Silent_p.T278T|CBLB_uc003dwe.1_Silent_p.T278T|CBLB_uc011bhj.1_RNA	NM_170662	NP_733762	Q13191	CBLB_HUMAN	Cas-Br-M (murine) ecotropic retroviral	278	Cbl-PTB.|SH2-like.				cell surface receptor linked signaling pathway|NLS-bearing substrate import into nucleus	cytoplasm|nucleus	calcium ion binding|ligase activity|signal transducer activity|zinc ion binding			lung(4)|ovary(3)|breast(1)|skin(1)	9						TTCCGGGTTTGGTGCTATATT	0.373000			Mis S		AML								10	169	---	---	---	---	4.3838e-07	4.47707e-07	1	1	0
DZIP3	9666	broad.mit.edu	37	3	108405390	108405390	+	Silent	SNP	A	G	G			TCGA-IM-A3U3-01A-11D-A22D-08	TCGA-IM-A3U3-10A-01D-A22D-08									Somatic	Phase_I	Capture				Illumina GAIIx	8d433dcf-1aa3-462a-8ab3-6de005ad8f69	cf90d01b-1750-4167-9b0a-ca680081e70f	g.chr3:108405390A>G	uc003dxd.2	+	28	3530	c.3108A>G	c.(3106-3108)AGA>AGG	p.R1036R	DZIP3_uc003dxf.1_Silent_p.R1036R|DZIP3_uc011bhm.1_Silent_p.R487R	NM_014648	NP_055463	Q86Y13	DZIP3_HUMAN	DAZ interacting protein 3, zinc finger	1036					protein polyubiquitination	cytoplasm	polyubiquitin binding|RNA binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2						ATTGGGAGAGAATTACAGACA	0.498000													20	129	---	---	---	---	0	0	1	0	0
KIAA2018	205717	broad.mit.edu	37	3	113377559	113377559	+	Silent	SNP	T	C	C			TCGA-IM-A3U3-01A-11D-A22D-08	TCGA-IM-A3U3-10A-01D-A22D-08									Somatic	Phase_I	Capture				Illumina GAIIx	8d433dcf-1aa3-462a-8ab3-6de005ad8f69	cf90d01b-1750-4167-9b0a-ca680081e70f	g.chr3:113377559T>C	uc003eam.2	-	7	3381	c.2970A>G	c.(2968-2970)TCA>TCG	p.S990S	KIAA2018_uc003eal.2_Silent_p.S934S	NM_001009899	NP_001009899	Q68DE3	K2018_HUMAN	hypothetical protein LOC205717	990					regulation of transcription, DNA-dependent	membrane|nucleus	calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity			skin(2)|ovary(1)	3						GCATTGTATCTGATGAATCTT	0.393000													3	105	---	---	---	---	0	0	1	0	0
SLC41A3	54946	broad.mit.edu	37	3	125786908	125786908	+	Missense_Mutation	SNP	G	A	A			TCGA-IM-A3U3-01A-11D-A22D-08	TCGA-IM-A3U3-10A-01D-A22D-08									Somatic	Phase_I	Capture				Illumina GAIIx	8d433dcf-1aa3-462a-8ab3-6de005ad8f69	cf90d01b-1750-4167-9b0a-ca680081e70f	g.chr3:125786908G>A	uc003eij.2	-	2	381	c.155C>T	c.(154-156)CCA>CTA	p.P52L	SLC41A3_uc003eil.2_Missense_Mutation_p.P52L|SLC41A3_uc003eik.2_Missense_Mutation_p.P52L|SLC41A3_uc011bkh.1_Intron|SLC41A3_uc010hsd.1_Missense_Mutation_p.P52L	NM_001008485	NP_001008485	Q96GZ6	S41A3_HUMAN	solute carrier family 41, member 3 isoform 1	52						integral to membrane|plasma membrane	cation transmembrane transporter activity				0				GBM - Glioblastoma multiforme(114;0.167)		AGTCTCCAGTGGCTTGGGGGT	0.632000													13	126	---	---	---	---	0	0	1	0	0
GOLPH3	64083	broad.mit.edu	37	5	32126343	32126343	+	Missense_Mutation	SNP	G	A	A			TCGA-IM-A3U3-01A-11D-A22D-08	TCGA-IM-A3U3-10A-01D-A22D-08									Somatic	Phase_I	Capture				Illumina GAIIx	8d433dcf-1aa3-462a-8ab3-6de005ad8f69	cf90d01b-1750-4167-9b0a-ca680081e70f	g.chr5:32126343G>A	uc003jhp.1	-	4	1157	c.872C>T	c.(871-873)GCG>GTG	p.A291V		NM_022130	NP_071413	Q9H4A6	GOLP3_HUMAN	golgi phosphoprotein 3	291					cell proliferation|positive regulation of TOR signaling cascade|regulation of mitochondrion organization	cytosol|endosome|Golgi cisterna membrane|mitochondrial intermembrane space|plasma membrane|trans-Golgi network	protein binding			ovary(1)	1						CGCCACCACCGCCCACAGAAC	0.498000													10	179	---	---	---	---	0	0	1	0	0
PCDHA11	56138	broad.mit.edu	37	5	140249717	140249717	+	Silent	SNP	C	T	T			TCGA-IM-A3U3-01A-11D-A22D-08	TCGA-IM-A3U3-10A-01D-A22D-08									Somatic	Phase_I	Capture				Illumina GAIIx	8d433dcf-1aa3-462a-8ab3-6de005ad8f69	cf90d01b-1750-4167-9b0a-ca680081e70f	g.chr5:140249717C>T	uc003lia.2	+	1	1887	c.1029C>T	c.(1027-1029)AAC>AAT	p.N343N	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Intron|PCDHA10_uc003lhx.2_Intron|PCDHA11_uc011dae.1_Silent_p.N343N	NM_018902	NP_061725	Q9Y5I1	PCDAB_HUMAN	protocadherin alpha 11 isoform 1 precursor	343	Extracellular (Potential).|Cadherin 3.				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGGACACCAACGATAACTCTC	0.512000													3	97	---	---	---	---	0	0	1	0	0
CD74	972	broad.mit.edu	37	5	149782174	149782174	+	Missense_Mutation	SNP	C	T	T	rs139226964		TCGA-IM-A3U3-01A-11D-A22D-08	TCGA-IM-A3U3-10A-01D-A22D-08									Somatic	Phase_I	Capture				Illumina GAIIx	8d433dcf-1aa3-462a-8ab3-6de005ad8f69	cf90d01b-1750-4167-9b0a-ca680081e70f	g.chr5:149782174C>T	uc003lsc.2	-	8	843	c.832G>A	c.(832-834)GAG>AAG	p.E278K	CD74_uc003lsb.2_Missense_Mutation_p.E78K|CD74_uc003lse.2_Nonsense_Mutation_p.W152*|CD74_uc003lsd.2_Missense_Mutation_p.E214K|CD74_uc003lsf.1_Missense_Mutation_p.E278K	NM_001025159	NP_001020330	P04233	HG2A_HUMAN	CD74 antigen isoform a	278	Extracellular (Potential).				antigen processing and presentation of endogenous antigen|cell proliferation|immunoglobulin mediated immune response|intracellular protein transport|negative regulation of apoptosis|negative regulation of DNA damage response, signal transduction by p53 class mediator|negative regulation of peptide secretion|positive regulation of B cell proliferation|positive regulation of chemokine (C-X-C motif) ligand 2 production|positive regulation of cytokine-mediated signaling pathway|positive regulation of ERK1 and ERK2 cascade|positive regulation of fibroblast proliferation|positive regulation of macrophage cytokine production|positive regulation of neutrophil chemotaxis|positive regulation of peptidyl-tyrosine phosphorylation|prostaglandin biosynthetic process|protein complex assembly|regulation of macrophage activation	endoplasmic reticulum membrane|Golgi apparatus|integral to membrane|lysosome|receptor complex	beta-amyloid binding|cytokine receptor activity|identical protein binding|MHC class II protein binding			breast(1)	1		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GACGGGTCCTCCAGTTCCAGT	0.602000			T	ROS1	NSCLC								4	183	---	---	---	---	0	0	1	0	0
CFB	629	broad.mit.edu	37	6	31911265	31911265	+	5'Flank	SNP	C	T	T			TCGA-IM-A3U3-01A-11D-A22D-08	TCGA-IM-A3U3-10A-01D-A22D-08									Somatic	Phase_I	Capture				Illumina GAIIx	8d433dcf-1aa3-462a-8ab3-6de005ad8f69	cf90d01b-1750-4167-9b0a-ca680081e70f	g.chr6:31911265C>T	uc003nyj.3	+						C2_uc003nyc.2_Missense_Mutation_p.R297C|C2_uc011doo.1_Missense_Mutation_p.R264C|C2_uc011dop.1_Missense_Mutation_p.R296C|C2_uc003nyf.2_Missense_Mutation_p.R510C|C2_uc010jtk.2_Missense_Mutation_p.R378C|C2_uc011doq.1_Missense_Mutation_p.R481C|C2_uc003nyg.2_Missense_Mutation_p.R287C|CFB_uc011dor.1_Missense_Mutation_p.R357C|C2_uc003nyh.1_Missense_Mutation_p.R161C|CFB_uc011dos.1_5'Flank|CFB_uc003nyi.2_5'Flank	NM_001710	NP_001701	P00751	CFAB_HUMAN	complement factor B preproprotein						complement activation, alternative pathway|proteolysis	extracellular region|plasma membrane	complement binding|serine-type endopeptidase activity			skin(1)	1						TCATTGCTTCCGCGATGGCAA	0.597000													21	174	---	---	---	---	0	0	1	0	0
GTF2IRD1	9569	broad.mit.edu	37	7	73927266	73927266	+	Missense_Mutation	SNP	G	A	A			TCGA-IM-A3U3-01A-11D-A22D-08	TCGA-IM-A3U3-10A-01D-A22D-08									Somatic	Phase_I	Capture				Illumina GAIIx	8d433dcf-1aa3-462a-8ab3-6de005ad8f69	cf90d01b-1750-4167-9b0a-ca680081e70f	g.chr7:73927266G>A	uc003uaq.2	+	3	623	c.230G>A	c.(229-231)CGG>CAG	p.R77Q	GTF2IRD1_uc010lbq.2_Missense_Mutation_p.R77Q|GTF2IRD1_uc003uap.2_Missense_Mutation_p.R77Q|GTF2IRD1_uc003uar.1_Missense_Mutation_p.R77Q	NM_016328	NP_057412	Q9UHL9	GT2D1_HUMAN	GTF2I repeat domain containing 1 isoform 1	77						nucleus	DNA binding|protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			ovary(4)	4						CTGAATGCCCGGAAGGAGCTA	0.637000													3	98	---	---	---	---	0	0	1	0	0
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	T	T			TCGA-IM-A3U3-01A-11D-A22D-08	TCGA-IM-A3U3-10A-01D-A22D-08									Somatic	Phase_I	Capture				Illumina GAIIx	8d433dcf-1aa3-462a-8ab3-6de005ad8f69	cf90d01b-1750-4167-9b0a-ca680081e70f	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				37	56	---	---	---	---	0	0	1	0	0
TMEM71	137835	broad.mit.edu	37	8	133740227	133740227	+	Missense_Mutation	SNP	C	T	T			TCGA-IM-A3U3-01A-11D-A22D-08	TCGA-IM-A3U3-10A-01D-A22D-08									Somatic	Phase_I	Capture				Illumina GAIIx	8d433dcf-1aa3-462a-8ab3-6de005ad8f69	cf90d01b-1750-4167-9b0a-ca680081e70f	g.chr8:133740227C>T	uc003ytp.2	-	6	719	c.490G>A	c.(490-492)GAT>AAT	p.D164N	TMEM71_uc003ytm.1_5'UTR|TMEM71_uc003ytn.2_Missense_Mutation_p.D146N|TMEM71_uc003yto.2_Intron	NM_144649	NP_653250	Q6P5X7	TMM71_HUMAN	transmembrane protein 71 isoform 1	165						integral to membrane				ovary(2)	2	all_neural(3;2.72e-06)|Medulloblastoma(3;7.08e-05)|Ovarian(258;0.00438)|Esophageal squamous(12;0.00507)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;4.46e-05)			CAGTCTAAATCATCTGCTGAA	0.373000													9	60	---	---	---	---	0	0	1	0	0
GOLGA1	2800	broad.mit.edu	37	9	127651460	127651460	+	Missense_Mutation	SNP	G	A	A			TCGA-IM-A3U3-01A-11D-A22D-08	TCGA-IM-A3U3-10A-01D-A22D-08									Somatic	Phase_I	Capture				Illumina GAIIx	8d433dcf-1aa3-462a-8ab3-6de005ad8f69	cf90d01b-1750-4167-9b0a-ca680081e70f	g.chr9:127651460G>A	uc004bpc.2	-	18	2065	c.1723C>T	c.(1723-1725)CCA>TCA	p.P575S	GOLGA1_uc010mws.2_RNA	NM_002077	NP_002068	Q92805	GOGA1_HUMAN	golgin 97	575	Potential.					Golgi cisterna membrane				ovary(1)	1						GCCTGCAATGGGCCCCGCAGC	0.647000													5	87	---	---	---	---	0	0	1	0	0
Unknown	0	broad.mit.edu	37	MT	3659	3659	+	RNA	SNP	G	A	A			TCGA-IM-A3U3-01A-11D-A22D-08	TCGA-IM-A3U3-10A-01D-A22D-08									Somatic	Phase_I	Capture				Illumina GAIIx	8d433dcf-1aa3-462a-8ab3-6de005ad8f69	cf90d01b-1750-4167-9b0a-ca680081e70f	g.chrM:3659G>A	uc004cos.3	+	2		c.1952G>A			uc011mfh.1_5'Flank					Homo sapiens mRNA expressed only in placental villi, clone SMAP47.																		CTCAATCCTCTGATCAGGGTG	0.512000													27	18	---	---	---	---	0	0	1	0	0
Unknown	0	broad.mit.edu	37	MT	11711	11711	+	RNA	SNP	G	A	A			TCGA-IM-A3U3-01A-11D-A22D-08	TCGA-IM-A3U3-10A-01D-A22D-08									Somatic	Phase_I	Capture				Illumina GAIIx	8d433dcf-1aa3-462a-8ab3-6de005ad8f69	cf90d01b-1750-4167-9b0a-ca680081e70f	g.chrM:11711G>A	uc004cov.3	+	1		c.1134G>A			uc004cow.1_5'Flank|uc004cox.3_5'Flank					Homo sapiens potential LAG1 interactor mRNA, partial cds.																		TTCTCATAATCGCCCACGGAC	0.483000													10	37	---	---	---	---	0	0	1	0	0
NAP1L3	4675	broad.mit.edu	37	X	92928233	92928233	+	Missense_Mutation	SNP	C	T	T			TCGA-IM-A3U3-01A-11D-A22D-08	TCGA-IM-A3U3-10A-01D-A22D-08									Somatic	Phase_I	Capture				Illumina GAIIx	8d433dcf-1aa3-462a-8ab3-6de005ad8f69	cf90d01b-1750-4167-9b0a-ca680081e70f	g.chrX:92928233C>T	uc004efq.2	-	1	376	c.71G>A	c.(70-72)AGC>AAC	p.S24N	FAM133A_uc004efr.1_5'Flank	NM_004538	NP_004529	Q99457	NP1L3_HUMAN	nucleosome assembly protein 1-like 3	24	Ser-rich.				nucleosome assembly	chromatin assembly complex				ovary(1)|skin(1)	2						ACTAGTCGAGCTAGCCATCTC	0.328000													23	67	---	---	---	---	0	0	1	0	0
TBC1D8B	54885	broad.mit.edu	37	X	106108793	106108793	+	Missense_Mutation	SNP	G	A	A			TCGA-IM-A3U3-01A-11D-A22D-08	TCGA-IM-A3U3-10A-01D-A22D-08									Somatic	Phase_I	Capture				Illumina GAIIx	8d433dcf-1aa3-462a-8ab3-6de005ad8f69	cf90d01b-1750-4167-9b0a-ca680081e70f	g.chrX:106108793G>A	uc004emo.2	+	15	2522	c.2357G>A	c.(2356-2358)CGT>CAT	p.R786H	MORC4_uc004emp.3_Intron	NM_017752	NP_060222	Q0IIM8	TBC8B_HUMAN	TBC1 domain family, member 8B (with GRAM domain)	786						intracellular	calcium ion binding|Rab GTPase activator activity			ovary(2)|central_nervous_system(1)|skin(1)	4						TTAAAGTTGCGTGTTGTATCA	0.303000													6	65	---	---	---	---	0	0	1	0	0
ABCD1	215	broad.mit.edu	37	X	152991293	152991293	+	Missense_Mutation	SNP	G	A	A			TCGA-IM-A3U3-01A-11D-A22D-08	TCGA-IM-A3U3-10A-01D-A22D-08									Somatic	Phase_I	Capture				Illumina GAIIx	8d433dcf-1aa3-462a-8ab3-6de005ad8f69	cf90d01b-1750-4167-9b0a-ca680081e70f	g.chrX:152991293G>A	uc004fif.2	+	1	971	c.572G>A	c.(571-573)CGC>CAC	p.R191H	BCAP31_uc004fid.2_5'Flank|BCAP31_uc011myz.1_5'Flank|BCAP31_uc011mza.1_5'Flank|BCAP31_uc004fie.2_5'Flank	NM_000033	NP_000024	P33897	ABCD1_HUMAN	ATP-binding cassette, sub-family D (ALD), member	191	ABC transmembrane type-1.				fatty acid beta-oxidation using acyl-CoA oxidase|peroxisomal membrane transport|peroxisome organization	cytosol|integral to peroxisomal membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances|identical protein binding|peroxisomal fatty-acyl-CoA transporter activity				0	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					GGGCGGCTTCGCAACCCTGAC	0.647000													15	103	---	---	---	---	0	0	1	0	0
RENBP	5973	broad.mit.edu	37	X	153207421	153207421	+	Missense_Mutation	SNP	C	G	G			TCGA-IM-A3U3-01A-11D-A22D-08	TCGA-IM-A3U3-10A-01D-A22D-08									Somatic	Phase_I	Capture				Illumina GAIIx	8d433dcf-1aa3-462a-8ab3-6de005ad8f69	cf90d01b-1750-4167-9b0a-ca680081e70f	g.chrX:153207421C>G	uc004fjo.1	-	7	921	c.751G>C	c.(751-753)GGG>CGG	p.G251R	RENBP_uc011mzh.1_Intron	NM_002910	NP_002901	P51606	RENBP_HUMAN	renin binding protein	251					mannose metabolic process|regulation of blood pressure		endopeptidase inhibitor activity|mannose-6-phosphate isomerase activity|N-acylglucosamine 2-epimerase activity			ovary(1)|pancreas(1)	2	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)				N-Acetyl-D-glucosamine(DB00141)	TGCTGTCTCCCCAGGCAGCCA	0.627000													56	195	---	---	---	---	0	0	1	0	0
DMAP1	55929	broad.mit.edu	37	1	44684778	44684780	+	In_Frame_Del	DEL	GAA	-	-			TCGA-IM-A3U3-01A-11D-A22D-08	TCGA-IM-A3U3-10A-01D-A22D-08									Somatic	Phase_I	Capture				Illumina GAIIx	8d433dcf-1aa3-462a-8ab3-6de005ad8f69	cf90d01b-1750-4167-9b0a-ca680081e70f	g.chr1:44684778_44684780delGAA	uc001clq.1	+	7	851_853	c.771_773delGAA	c.(769-774)CGGAAG>CGG	p.K259del	DMAP1_uc001clr.1_In_Frame_Del_p.K259del|DMAP1_uc001cls.1_In_Frame_Del_p.K259del|DMAP1_uc010oku.1_In_Frame_Del_p.K249del	NM_001034024	NP_001029196	Q9NPF5	DMAP1_HUMAN	DNA methyltransferase 1 associated protein 1	259	Potential.				DNA methylation|histone H2A acetylation|histone H4 acetylation|negative regulation of transcription, DNA-dependent|regulation of growth|transcription, DNA-dependent	NuA4 histone acetyltransferase complex	DNA binding|protein binding				0	Acute lymphoblastic leukemia(166;0.155)					TTGAGGCCCGGAAGAAGGAGCGG	0.606													8	81	---	---	---	---					
Unknown	0	broad.mit.edu	37	12	13004257	13004258	+	IGR	INS	-	A	A			TCGA-IM-A3U3-01A-11D-A22D-08	TCGA-IM-A3U3-10A-01D-A22D-08									Somatic	Phase_I	Capture				Illumina GAIIx	8d433dcf-1aa3-462a-8ab3-6de005ad8f69	cf90d01b-1750-4167-9b0a-ca680081e70f	g.chr12:13004257_13004258insA								DDX47 (21348 upstream) : RPL13AP20 (24153 downstream)																							TGATTATTGTTAAAAAAAAAAA	0.396													7	8	---	---	---	---					
CEP290	80184	broad.mit.edu	37	12	88512305	88512305	+	Frame_Shift_Del	DEL	T	-	-	rs77980773		TCGA-IM-A3U3-01A-11D-A22D-08	TCGA-IM-A3U3-10A-01D-A22D-08									Somatic	Phase_I	Capture				Illumina GAIIx	8d433dcf-1aa3-462a-8ab3-6de005ad8f69	cf90d01b-1750-4167-9b0a-ca680081e70f	g.chr12:88512305delT	uc001tar.2	-	17	2010	c.1666delA	c.(1666-1668)ATTfs	p.I556fs	CEP290_uc001tat.2_Frame_Shift_Del_p.I318fs|CEP290_uc009zsl.1_RNA	NM_025114	NP_079390	O15078	CE290_HUMAN	centrosomal protein 290kDa	556	Potential.				cilium assembly|eye photoreceptor cell development|G2/M transition of mitotic cell cycle|hindbrain development|otic vesicle formation|positive regulation of transcription, DNA-dependent|pronephros development|protein transport	cell surface|centrosome|cytosol|nucleus|photoreceptor connecting cilium	protein binding			ovary(5)|breast(1)|pancreas(1)	7						ATTTGACGAATTTTTTTTTTC	0.308													4	6	---	---	---	---					
C15orf51	196968	broad.mit.edu	37	15	100340240	100340240	+	RNA	DEL	A	-	-			TCGA-IM-A3U3-01A-11D-A22D-08	TCGA-IM-A3U3-10A-01D-A22D-08									Somatic	Phase_I	Capture				Illumina GAIIx	8d433dcf-1aa3-462a-8ab3-6de005ad8f69	cf90d01b-1750-4167-9b0a-ca680081e70f	g.chr15:100340240delA	uc010urx.1	-	4		c.687delT			C15orf51_uc010ury.1_RNA|uc002bvp.2_5'Flank|C15orf51_uc010urz.1_RNA|C15orf51_uc010bow.2_RNA|uc002bvt.1_5'Flank	NR_003260				Homo sapiens cDNA FLJ43799 fis, clone TESTI4000288.												0						AGGAGTGTCTATTTCTTCCCA	0.632													2	4	---	---	---	---					
LYPD3	27076	broad.mit.edu	37	19	43969653	43969655	+	In_Frame_Del	DEL	AGC	-	-	rs141441894	byFrequency	TCGA-IM-A3U3-01A-11D-A22D-08	TCGA-IM-A3U3-10A-01D-A22D-08									Somatic	Phase_I	Capture				Illumina GAIIx	8d433dcf-1aa3-462a-8ab3-6de005ad8f69	cf90d01b-1750-4167-9b0a-ca680081e70f	g.chr19:43969653_43969655delAGC	uc002owl.1	-	1	177_179	c.69_71delGCT	c.(67-72)CTGCTT>CTT	p.23_24LL>L	LYPD3_uc002owm.2_In_Frame_Del_p.23_24LL>L	NM_014400	NP_055215	O95274	LYPD3_HUMAN	GPI-anchored metastasis-associated protein	23_24						anchored to plasma membrane				pancreas(1)	1		Prostate(69;0.0153)				ACCTCCGCGAAGCAGCAGCAGCA	0.675													7	276	---	---	---	---					
NKPD1	284353	broad.mit.edu	37	19	45655769	45655771	+	In_Frame_Del	DEL	CTG	-	-			TCGA-IM-A3U3-01A-11D-A22D-08	TCGA-IM-A3U3-10A-01D-A22D-08									Somatic	Phase_I	Capture				Illumina GAIIx	8d433dcf-1aa3-462a-8ab3-6de005ad8f69	cf90d01b-1750-4167-9b0a-ca680081e70f	g.chr19:45655769_45655771delCTG	uc010xxi.1	-	4	1924_1926	c.1924_1926delCAG	c.(1924-1926)CAGdel	p.Q642del		NM_198478	NP_940880			NTPase, KAP family P-loop domain containing 1												0		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00863)|GBM - Glioblastoma multiforme(486;0.231)		CAAAGTCCCCCTGCTGCTGCTGC	0.704													4	7	---	---	---	---					
TYMP	1890	broad.mit.edu	37	22	50968827	50968828	+	5'Flank	DEL	AG	-	-			TCGA-IM-A3U3-01A-11D-A22D-08	TCGA-IM-A3U3-10A-01D-A22D-08									Somatic	Phase_I	Capture				Illumina GAIIx	8d433dcf-1aa3-462a-8ab3-6de005ad8f69	cf90d01b-1750-4167-9b0a-ca680081e70f	g.chr22:50968827_50968828delAG	uc003bmb.3	-						TYMP_uc003bmc.3_5'Flank|TYMP_uc003bmd.3_5'Flank|TYMP_uc010hbd.2_5'Flank|TYMP_uc003bme.3_5'Flank|TYMP_uc003bmf.3_5'Flank|TYMP_uc011arz.1_5'Flank	NM_001113756	NP_001107228	P19971	TYPH_HUMAN	endothelial cell growth factor 1						angiogenesis|cell differentiation|chemotaxis|DNA replication|mitochondrial genome maintenance|pyrimidine base metabolic process|pyrimidine nucleoside catabolic process|pyrimidine nucleoside salvage|pyrimidine nucleotide metabolic process	cytosol	growth factor activity|platelet-derived growth factor receptor binding|pyrimidine-nucleoside phosphorylase activity|thymidine phosphorylase activity			ovary(1)	1		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.206)|LUAD - Lung adenocarcinoma(64;0.247)	Capecitabine(DB01101)|Docetaxel(DB01248)|Floxuridine(DB00322)|Fluorouracil(DB00544)|Sulfasalazine(DB00795)|Tamoxifen(DB00675)	CAGGACGCGCAGAGAGAGAGAG	0.708													2	4	---	---	---	---					
HLA-J	3137	broad.mit.edu	37	6	29977389	29977393	+	Frame_Shift_Del	DEL	CTTCT	-	-			TCGA-IM-A3U3-01A-11D-A22D-08	TCGA-IM-A3U3-10A-01D-A22D-08									Somatic	Phase_I	Capture				Illumina GAIIx	8d433dcf-1aa3-462a-8ab3-6de005ad8f69	cf90d01b-1750-4167-9b0a-ca680081e70f	g.chr6:29977389_29977393delCTTCT	uc003rtl.3	+	5	770_774	c.408_412delCTTCT	c.(406-414)GACTTCTCTfs	p.D136fs	HLA-G_uc011dmb.1_3'UTR|NCRNA00171_uc011dme.1_Intron|HLA-J_uc003nou.3_RNA|HLA-J_uc003nov.3_RNA					Homo sapiens major histocompatibility complex, class I, J (pseudogene), mRNA (cDNA clone IMAGE:4694038).												0						AGAACCCTGACTTCTCTTTCTGCAA	0.488													10	31	---	---	---	---					
TG	7038	broad.mit.edu	37	8	133935742	133935743	+	Frame_Shift_Del	DEL	CA	-	-			TCGA-IM-A3U3-01A-11D-A22D-08	TCGA-IM-A3U3-10A-01D-A22D-08									Somatic	Phase_I	Capture				Illumina GAIIx	8d433dcf-1aa3-462a-8ab3-6de005ad8f69	cf90d01b-1750-4167-9b0a-ca680081e70f	g.chr8:133935742_133935743delCA	uc003ytw.2	+	22	4729_4730	c.4688_4689delCA	c.(4687-4689)TCAfs	p.S1563fs	TG_uc010mdw.2_Frame_Shift_Del_p.S322fs|TG_uc011ljb.1_5'UTR|TG_uc003ytx.1_Intron	NM_003235	NP_003226	P01266	THYG_HUMAN	thyroglobulin precursor	1563	Thyroglobulin type-1 11.				hormone biosynthetic process|signal transduction|thyroid gland development|thyroid hormone generation	extracellular space	hormone activity			ovary(8)|breast(4)|pancreas(1)|central_nervous_system(1)|skin(1)	15	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		CTTGAGGACTCACAGTGTTTGA	0.594													10	34	---	---	---	---					
Unknown	0	broad.mit.edu	37	9	44084399	44084400	+	IGR	INS	-	TAATC	TAATC			TCGA-IM-A3U3-01A-11D-A22D-08	TCGA-IM-A3U3-10A-01D-A22D-08									Somatic	Phase_I	Capture				Illumina GAIIx	8d433dcf-1aa3-462a-8ab3-6de005ad8f69	cf90d01b-1750-4167-9b0a-ca680081e70f	g.chr9:44084399_44084400insTAATC								FAM75A6 (453669 upstream) : FAM27C (905836 downstream)																							GATAAAGACTATATATAAAAAT	0.277													5	4	---	---	---	---					
CUL4B	8450	broad.mit.edu	37	X	119694117	119694119	+	In_Frame_Del	DEL	GAG	-	-			TCGA-IM-A3U3-01A-11D-A22D-08	TCGA-IM-A3U3-10A-01D-A22D-08									Somatic	Phase_I	Capture				Illumina GAIIx	8d433dcf-1aa3-462a-8ab3-6de005ad8f69	cf90d01b-1750-4167-9b0a-ca680081e70f	g.chrX:119694117_119694119delGAG	uc004esw.2	-	3	866_868	c.429_431delCTC	c.(427-432)TCCTCA>TCA	p.143_144SS>S	CUL4B_uc004esv.2_In_Frame_Del_p.125_126SS>S	NM_003588	NP_003579	Q13620	CUL4B_HUMAN	cullin 4B isoform 1	143_144	Ser-rich.				cell cycle|DNA repair|ubiquitin-dependent protein catabolic process	Cul4B-RING ubiquitin ligase complex|nucleus	protein binding|ubiquitin protein ligase binding			lung(1)|central_nervous_system(1)|pancreas(1)	3						TGGTGAAGATgaggaggaggagg	0.424													7	84	---	---	---	---					
