Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Genome_Change	Annotation_Transcript	Transcript_Strand	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	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	DrugBank	i_ACHILLES_Top_Genes	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	i_CCLE_SEQ_overlapping_mutations	i_CCLE_SEQ_total_mutations_in_gene	MUTSIG_Significant_Genes	OREGANNO_ID	OREGANNO_Values	i_tumor_f	i_init_t_lod	i_t_lod_fstar	i_t_alt_count	i_t_ref_count	i_normal_best_gt	i_failure_reasons	i_judgement	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	dataset	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	type	classification	start	end	gene	chr	ref_allele	tum_allele1	tum_allele2	context_orig	context65	gene_name	newbase	categ	categ_ignoring_null_categ
WSCD2	9671	broad.mit.edu	36	12	107128162	107128162	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0178-01	TCGA-06-0178-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr12:107128162A>C	uc001tms.1	+	c.632A>C	c.(631-633)AAC>ACC	p.N211T	WSCD2_uc001tmt.1_Missense_Mutation_p.N211T	NM_014653	NP_055468	Q2TBF2	WSCD2_HUMAN	WSC domain containing 2	211	WSC 1.					integral to membrane		p.N211T(1)		ovary(1)|large_intestine(1)|breast(1)	3														0.357143	9.570117	9.821829	5	9	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	107128162	107128162	17981	12	A	C	C	2	2	WSCD2	C	4	4
TFAP4	7023	broad.mit.edu	36	16	4251937	4251937	+	Silent	SNP	C	G	G			TCGA-06-0178-01	TCGA-06-0178-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:4251937C>G	uc002cwb.1	-	c.369G>C	c.(367-369)TCG>TCC	p.S123S		NM_003223	NP_003214	Q01664	TFAP4_HUMAN	transcription factor AP-4 (activating enhancer	123					DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|negative regulation by host of viral transcription|negative regulation of cell cycle arrest|negative regulation of cell proliferation|negative regulation of cyclin-dependent protein kinase activity|negative regulation of DNA binding|negative regulation of gene-specific transcription|positive regulation by host of viral transcription|positive regulation of apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein complex assembly|regulation of S phase of mitotic cell cycle	transcriptional repressor complex	E-box binding|histone deacetylase binding|protein homodimerization activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity			ovary(1)	1												OREG0023575	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.307692	6.587625	7.021305	4	9	CC		KEEP	---	---	---	---	capture			Silent	SNP	4251937	4251937	16320	16	C	G	G	19	19	TFAP4	G	3	3
GON4L	54856	broad.mit.edu	36	1	153988942	153988942	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0178-01	TCGA-06-0178-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:153988942A>G	uc001flz.2	-	c.5906T>C	c.(5905-5907)CTC>CCC	p.L1969P	GON4L_uc001fly.1_Missense_Mutation_p.L1968P|GON4L_uc009wrh.1_Missense_Mutation_p.L1968P|GON4L_uc001fma.1_Missense_Mutation_p.L1969P|GON4L_uc001flx.1_5'Flank|GON4L_uc009wrg.1_Non-coding_Transcript	NM_001037533	NP_001032622	Q3T8J9	GON4L_HUMAN	gon-4-like isoform a	1969					regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			ovary(3)	3	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)													0.3125	6.81022	7.347972	5	11	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	153988942	153988942	6845	1	A	G	G	11	11	GON4L	G	4	4
PIK3CD	5293	broad.mit.edu	36	1	9703423	9703423	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0178-01	TCGA-06-0178-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:9703423T>G	uc001aqe.2	+	c.1630T>G	c.(1630-1632)TCT>GCT	p.S544A	PIK3CD_uc001aqb.2_Missense_Mutation_p.S520A	NM_005026	NP_005017	O00329	PK3CD_HUMAN	phosphoinositide-3-kinase, catalytic, delta	536					phosphatidylinositol-mediated signaling|protein phosphorylation	phosphatidylinositol 3-kinase complex|plasma membrane	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity|protein binding			lung(2)|central_nervous_system(1)	3	all_lung(157;0.222)	all_lung(118;2.44e-05)|Lung NSC(185;4.08e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)								859				0.307692	8.073382	8.51586	4	9	TT		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (279;0.0231)|Colorectal(212;7.52e-08)|COAD - Colon adenocarcinoma(227;1.78e-05)|Kidney(185;0.000322)|KIRC - Kidney renal clear cell carcinoma(229;0.00114)|BRCA - Breast invasive adenocarcinoma(304;0.0021)|STAD - Stomach adenocarcinoma(132;0.00395)|READ - Rectum adenocarcinoma(331;0.0419)	Missense_Mutation	SNP	9703423	9703423	12339	1	T	G	G	58	58	PIK3CD	G	4	4
TRIO	7204	broad.mit.edu	36	5	14450227	14450227	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0178-01	TCGA-06-0178-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:14450227C>G	uc003jff.1	+	c.4387C>G	c.(4387-4389)CGA>GGA	p.R1463G	TRIO_uc003jfg.1_Non-coding_Transcript|TRIO_uc003jfh.1_Missense_Mutation_p.R1112G	NM_007118	NP_009049	O75962	TRIO_HUMAN	triple functional domain (PTPRF interacting)	1463	DH 1.				apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|protein phosphorylation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|breast(2)|stomach(1)|kidney(1)	16	Lung NSC(4;0.000742)								p.R1463G(HUH6-Tumor)	1300				0.428571	7.358235	7.433466	6	8	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	14450227	14450227	17102	5	C	G	G	27	27	TRIO	G	3	3
HLA-A	3105	broad.mit.edu	36	6	30018573	30018573	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0178-01	TCGA-06-0178-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:30018573G>A	uc003non.1	+	c.134G>A	c.(133-135)CGC>CAC	p.R45H	HLA-H_uc010jrp.1_Intron|HCG4P6_uc003nog.1_Intron|HLA-A_uc003nok.1_5'UTR|HLA-A_uc003nom.1_5'UTR|HLA-A_uc003noo.1_Missense_Mutation_p.R45H|HLA-A_uc010jrr.1_Missense_Mutation_p.R45H|HLA-A_uc003nol.1_Missense_Mutation_p.R45H	NM_002116	NP_002107	P04439	1A03_HUMAN	major histocompatibility complex, class I, A	45	Extracellular (Potential).|Alpha-1.				antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|regulation of immune response|type I interferon-mediated signaling pathway	integral to plasma membrane|MHC class I protein complex	MHC class I receptor activity|protein binding	p.R41fs*31(1)		ovary(1)	1											Multiple Myeloma(9;0.094)			0.151515	9.256093	13.09179	5	28	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	30018573	30018573	7486	6	G	A	A	38	38	HLA-A	A	1	1
JRK	8629	broad.mit.edu	36	8	143742951	143742951	+	Silent	SNP	C	T	T			TCGA-06-0178-01	TCGA-06-0178-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:143742951C>T	uc003ywp.1	-	c.1527G>A	c.(1525-1527)GCG>GCA	p.A509A	JRK_uc003ywo.1_Silent_p.A509A|JRK_uc010mew.1_Missense_Mutation_p.R510H	NM_003724	NP_003715			jerky isoform a												0	all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;2.31e-05)												0.52381	32.721336	32.731503	11	10	CC		KEEP	---	---	---	---	capture			Silent	SNP	143742951	143742951	8268	8	C	T	T	27	27	JRK	T	1	1
TCEA1	6917	broad.mit.edu	36	8	55085600	55085600	+	Silent	SNP	T	C	C			TCGA-06-0178-01	TCGA-06-0178-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr8:55085600T>C	uc003xru.1	-	c.69A>G	c.(67-69)GGA>GGG	p.G23G	TCEA1_uc003xrv.1_Intron|TCEA1_uc003xrw.1_Non-coding_Transcript	NM_006756	NP_006747	P23193	TCEA1_HUMAN	transcription elongation factor A 1 isoform 1	23	TFIIS N-terminal.				positive regulation of viral transcription|regulation of transcription from RNA polymerase II promoter|transcription elongation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	nucleoplasm	DNA binding|general RNA polymerase II transcription factor activity|transcription elongation regulator activity|translation elongation factor activity|zinc ion binding				0		Lung NSC(129;0.109)|all_epithelial(80;0.11)|all_lung(136;0.181)							p.G23G(CMK115-Tumor)|p.G23G(SNU503-Tumor)|p.G23G(HCC70-Tumor)|p.G23G(HS688A.T-Tumor)|p.G23G(SNU8-Tumor)|p.G23G(MUTZ3-Tumor)|p.G23G(RS5-Tumor)|p.G23G(PECAPJ41CLONED2-Tumor)|p.G23G(SNU478-Tumor)|p.G23G(MDAMB134VI-Tumor)|p.G23G(SKM1-Tumor)	405				0.571429	10.986431	11.019809	8	6	TT		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(7;9.1e-07)|Epithelial(17;9.44e-05)|all cancers(17;0.000699)		Silent	SNP	55085600	55085600	16193	8	T	C	C	54	54	TCEA1	C	4	4
PRDM12	59335	broad.mit.edu	36	9	132546603	132546603	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0178-01	TCGA-06-0178-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr9:132546603A>C	uc004bzt.1	+	c.830A>C	c.(829-831)AAC>ACC	p.N277T		NM_021619	NP_067632	Q9H4Q4	PRD12_HUMAN	PR domain containing 12	277	C2H2-type 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_hematologic(13;0.0433)|Acute lymphoblastic leukemia(5;0.0534)												0.3	6.619929	6.978115	3	7	AA		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(145;0.000344)	Missense_Mutation	SNP	132546603	132546603	12895	9	A	C	C	2	2	PRDM12	C	4	4
AQP3	360	broad.mit.edu	36	9	33437465	33437465	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0178-01	TCGA-06-0178-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:33437465G>C	uc003zsx.1	-	c.64C>G	c.(64-66)CTC>GTC	p.L22V	SUGT1P1_uc010mjq.1_Intron|AQP3_uc003zsv.1_Missense_Mutation_p.L22V|AQP3_uc010mju.1_Missense_Mutation_p.L22V	NM_004925	NP_004916	Q92482	AQP3_HUMAN	aquaporin 3	22	Cytoplasmic (Potential).				excretion|odontogenesis|positive regulation of immune system process|regulation of keratinocyte differentiation|response to calcium ion|response to retinoic acid|response to vitamin D	basolateral plasma membrane|cell-cell junction|cytoplasm|integral to membrane	glycerol channel activity|water channel activity				0														0.375	7.121511	7.231773	3	5	GG		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.0899)	Missense_Mutation	SNP	33437465	33437465	838	9	G	C	C	34	34	AQP3	C	3	3
MICALCL	84953	broad.mit.edu	36	11	12272963	12272965	+	In_Frame_Del	DEL	CTA	-	-			TCGA-06-0178-01	TCGA-06-0178-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:12272963_12272965delCTA	uc001mkg.1	+	c.1409_1411delCTA	c.(1408-1413)CCTACA>CCA	p.T471del		NM_032867	NP_116256	Q6ZW33	MICLK_HUMAN	MICAL C-terminal like	471					cell differentiation|multicellular organismal development|spermatogenesis	cytoplasm	mitogen-activated protein kinase binding				0				Epithelial(150;0.00177)										0.62			8	5				---	---	---	---	capture_indel			In_Frame_Del	DEL	12272963	12272965	9962	11	CTA	-	-	24	24	MICALCL	-	5	5
MYO1D	4642	broad.mit.edu	36	17	28227970	28227970	+	Frame_Shift_Del	DEL	C	-	-			TCGA-06-0178-01	TCGA-06-0178-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:28227970_28227970delC	uc002hho.1	-	c.34_34delG	c.(34-36)GCAfs	p.A12fs	MYO1D_uc002hhp.1_Frame_Shift_Del_p.A12fs	NM_015194	NP_056009	O94832	MYO1D_HUMAN	myosin ID	12	Myosin head-like.					myosin complex	actin binding|ATP binding|calmodulin binding			large_intestine(1)|ovary(1)|central_nervous_system(1)	3			BRCA - Breast invasive adenocarcinoma(9;0.0362)											0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	28227970	28227970	10466	17	C	-	-	26	26	MYO1D	-	5	5
