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_alt_allele	validation_method	validation_status	validation_tumor_sample	pox	qox	pox_cutoff	isArtifactMode	oxoGCut
WFS1	7466	broad.mit.edu	37	4	6302918	6302918	+	Missense_Mutation	SNP	G	G	C			TCGA-EL-A3CO-01A-11D-A19J-08	TCGA-EL-A3CO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba1f48c1-8d38-4a91-ba08-a8ecb63cac88	bc492b5b-036e-4452-ac96-4fa312ce29ef	g.chr4:6302918G>C	ENST00000226760.1	+	8	1566	c.1396G>C	c.(1396-1398)Ggc>Cgc	p.G466R	WFS1_ENST00000503569.1_Missense_Mutation_p.G466R	NM_001145853.1|NM_006005.3	NP_001139325.1|NP_005996.2	O76024	WFS1_HUMAN	Wolfram syndrome 1 (wolframin)	466					endoplasmic reticulum calcium ion homeostasis|endoplasmic reticulum unfolded protein response|ER overload response|ER-associated protein catabolic process|glucose homeostasis|kidney development|negative regulation of neuron apoptosis|negative regulation of sequence-specific DNA binding transcription factor activity|polyubiquitinated misfolded protein transport|positive regulation of calcium ion transport|positive regulation of growth|positive regulation of protein ubiquitination|positive regulation of proteolysis|protein stabilization|renal water homeostasis|sensory perception of sound|visual perception	dendrite|integral to endoplasmic reticulum membrane	activating transcription factor binding|ATPase binding|transporter activity|ubiquitin protein ligase binding			central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(6)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	21				Colorectal(103;0.0512)		GGTCACCGCCGGCCTGCTATC	0.642000													6	75					0	0	0.217242	0	0
AFM	173	broad.mit.edu	37	4	74357625	74357625	+	Missense_Mutation	SNP	T	T	G			TCGA-EL-A3CO-01A-11D-A19J-08	TCGA-EL-A3CO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba1f48c1-8d38-4a91-ba08-a8ecb63cac88	bc492b5b-036e-4452-ac96-4fa312ce29ef	g.chr4:74357625T>G	ENST00000226355.3	+	8	973	c.880T>G	c.(880-882)Tct>Gct	p.S294A		NM_001133.2	NP_001124.1	P43652	AFAM_HUMAN	afamin	294	Albumin 2.				vitamin transport		vitamin E binding			breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(9)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	32	Breast(15;0.00102)		Epithelial(6;5.69e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000324)|all cancers(17;0.000555)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			AAAACAAGATTCTATCTCCAG	0.358000													5	104					0	0	0.217242	0	0
SNHG14	0	broad.mit.edu	37	15	25448253	25448253	+	RNA	SNP	G	G	A			TCGA-EL-A3CO-01A-11D-A19J-08	TCGA-EL-A3CO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba1f48c1-8d38-4a91-ba08-a8ecb63cac88	bc492b5b-036e-4452-ac96-4fa312ce29ef	g.chr15:25448253G>A	ENST00000424208.1	+	0	2099				SNHG14_ENST00000424333.1_RNA	NR_003305.1																						TCATCCCGGCGTCCAGCCCCT	0.617000													7	51					0	0	0.248553	0	0
TMTC1	83857	broad.mit.edu	37	12	29689068	29689068	+	Missense_Mutation	SNP	T	T	C	rs71450781	by1000genomes	TCGA-EL-A3CO-01A-11D-A19J-08	TCGA-EL-A3CO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba1f48c1-8d38-4a91-ba08-a8ecb63cac88	bc492b5b-036e-4452-ac96-4fa312ce29ef	g.chr12:29689068T>C	ENST00000381224.2	-	13	2194	c.1721A>G	c.(1720-1722)tAc>tGc	p.Y574C	TMTC1_ENST00000539277.1_Intron|TMTC1_ENST00000256062.5_Intron|TMTC1_ENST00000551659.1_Intron|TMTC1_ENST00000552618.1_Intron|TMTC1_ENST00000319685.8_Intron			Q8IUR5	TMTC1_HUMAN	transmembrane and tetratricopeptide repeat containing 1	0						integral to membrane	binding			breast(1)|endometrium(4)|kidney(3)|large_intestine(17)|lung(45)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	75	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)					AAATCATTAGTACAAAAATCT	0.308000													3	18					0	0	0.115264	0	0
SYNE2	23224	broad.mit.edu	37	14	64680925	64680925	+	Missense_Mutation	SNP	A	A	G			TCGA-EL-A3CO-01A-11D-A19J-08	TCGA-EL-A3CO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba1f48c1-8d38-4a91-ba08-a8ecb63cac88	bc492b5b-036e-4452-ac96-4fa312ce29ef	g.chr14:64680925A>G	ENST00000357395.3	+	107	19369	c.8225A>G	c.(8224-8226)gAa>gGa	p.E2742G	SYNE2_ENST00000555002.1_Missense_Mutation_p.E2991G|SYNE2_ENST00000555022.1_Missense_Mutation_p.E235G|ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000458046.2_5'UTR|SYNE2_ENST00000554805.1_Missense_Mutation_p.E140G|SYNE2_ENST00000554584.1_Missense_Mutation_p.E6299G|SYNE2_ENST00000358025.3_Missense_Mutation_p.E6357G|SYNE2_ENST00000344113.4_Missense_Mutation_p.E6357G|SYNE2_ENST00000394768.2_Missense_Mutation_p.E2742G			Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	6357					centrosome localization|cytoskeletal anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration	cytoskeleton|filopodium membrane|focal adhesion|integral to membrane|lamellipodium membrane|mitochondrial part|nuclear outer membrane|nucleoplasm|sarcoplasmic reticulum membrane|SUN-KASH complex|Z disc	actin binding|protein binding			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		TTGGAAGATGAAAAGGAGGCC	0.458000													7	103					0	0	0.248553	0	0
RP11-24M17.5	0	broad.mit.edu	37	15	76067987	76067987	+	RNA	SNP	A	A	G	rs34243492	by1000genomes	TCGA-EL-A3CO-01A-11D-A19J-08	TCGA-EL-A3CO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba1f48c1-8d38-4a91-ba08-a8ecb63cac88	bc492b5b-036e-4452-ac96-4fa312ce29ef	g.chr15:76067987A>G	ENST00000395215.3	+	0	94																											GAAGAAACTCAACAGAGTAAA	0.537000													3	31					0	0	0.115264	0	0
ZNF235	9310	broad.mit.edu	37	19	44807571	44807571	+	Translation_Start_Site	SNP	C	C	A			TCGA-EL-A3CO-01A-11D-A19J-08	TCGA-EL-A3CO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba1f48c1-8d38-4a91-ba08-a8ecb63cac88	bc492b5b-036e-4452-ac96-4fa312ce29ef	g.chr19:44807571C>A	ENST00000291182.4	-	0	89				ZNF235_ENST00000589799.1_De_novo_Start_InFrame|ZNF235_ENST00000589248.1_De_novo_Start_InFrame	NM_004234.4	NP_004225.3	Q14590	ZN235_HUMAN	zinc finger protein 235						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			NS(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	29		Prostate(69;0.0352)|all_neural(266;0.116)				TCCCCTCCTCCTTCTGGGAAA	0.438000													8	92					0.00307968	0.00324177	0.278610	1	0
FLOT1	10211	broad.mit.edu	37	6	30707994	30707994	+	Missense_Mutation	SNP	C	C	T			TCGA-EL-A3CO-01A-11D-A19J-08	TCGA-EL-A3CO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba1f48c1-8d38-4a91-ba08-a8ecb63cac88	bc492b5b-036e-4452-ac96-4fa312ce29ef	g.chr6:30707994C>T	ENST00000376389.3	-	8	884	c.664G>A	c.(664-666)Gcc>Acc	p.A222T	FLOT1_ENST00000470643.1_5'UTR|FLOT1_ENST00000456573.2_Missense_Mutation_p.A174T	NM_005803.2	NP_005794.1	O75955	FLOT1_HUMAN	flotillin 1	222						centriolar satellite|endosome|integral to membrane|melanosome|membrane fraction				breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|prostate(1)	13						ATGTCATAGGCGGCCTTCTTC	0.562000													4	51					0	0	0.150653	0	0
EIF1AX	1964	broad.mit.edu	37	X	20156731	20156731	+	Missense_Mutation	SNP	C	C	T			TCGA-EL-A3CO-01A-11D-A19J-08	TCGA-EL-A3CO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba1f48c1-8d38-4a91-ba08-a8ecb63cac88	bc492b5b-036e-4452-ac96-4fa312ce29ef	g.chrX:20156731C>T	ENST00000379607.5	-	2	229	c.26G>A	c.(25-27)gGt>gAt	p.G9D	EIF1AX_ENST00000379593.1_Intron	NM_001412.3	NP_001403.1	P47813	IF1AX_HUMAN	eukaryotic translation initiation factor 1A, X-linked	9						cytosol	translation initiation factor activity			endometrium(2)|lung(1)|ovary(1)|prostate(1)	5						TCTGTTTTTACCTCCTTTACC	0.313000													15	56					0	0	0.500413	0	0
TMTC1	83857	broad.mit.edu	37	12	29689066	29689066	+	Nonstop_Mutation	SNP	A	A	G	rs71450781	by1000genomes	TCGA-EL-A3CO-01A-11D-A19J-08	TCGA-EL-A3CO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba1f48c1-8d38-4a91-ba08-a8ecb63cac88	bc492b5b-036e-4452-ac96-4fa312ce29ef	g.chr12:29689066A>G	ENST00000381224.2	-	13	2196	c.1723T>C	c.(1723-1725)Taa>Caa	p.*575Q	TMTC1_ENST00000539277.1_Intron|TMTC1_ENST00000256062.5_Intron|TMTC1_ENST00000551659.1_Intron|TMTC1_ENST00000552618.1_Intron|TMTC1_ENST00000319685.8_Intron			Q8IUR5	TMTC1_HUMAN	transmembrane and tetratricopeptide repeat containing 1	0						integral to membrane	binding			breast(1)|endometrium(4)|kidney(3)|large_intestine(17)|lung(45)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	75	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)					ttAAATCATTAGTACAAAAAT	0.308000													3	18					0	0	0.115264	0	0
CDH8	1006	broad.mit.edu	37	16	61687935	61687935	+	Silent	SNP	G	G	A			TCGA-EL-A3CO-01A-11D-A19J-08	TCGA-EL-A3CO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba1f48c1-8d38-4a91-ba08-a8ecb63cac88	bc492b5b-036e-4452-ac96-4fa312ce29ef	g.chr16:61687935G>A	ENST00000577390.1	-	12	2931	c.1977C>T	c.(1975-1977)gaC>gaT	p.D659D	CDH8_ENST00000299345.6_Silent_p.D659D|CDH8_ENST00000577730.1_Silent_p.D659D	NM_001796.4	NP_001787.2	P55286	CADH8_HUMAN	cadherin 8, type 2	659					adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			biliary_tract(1)|breast(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(22)|liver(2)|lung(49)|ovary(6)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(4)	112		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)		TTTCTCGAACGTCTTCATCAT	0.393000													8	122					0	0	0.335167	0	0
KCNMA1	3778	broad.mit.edu	37	10	79011015	79011015	+	Splice_Site	SNP	C	C	T			TCGA-EL-A3CO-01A-11D-A19J-08	TCGA-EL-A3CO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba1f48c1-8d38-4a91-ba08-a8ecb63cac88	bc492b5b-036e-4452-ac96-4fa312ce29ef	g.chr10:79011015C>T	ENST00000286627.5	-	3	1493		c.e3-1		KCNMA1_ENST00000372443.1_Splice_Site|KCNMA1_ENST00000404857.1_Splice_Site|KCNMA1_ENST00000354353.5_Splice_Site|KCNMA1_ENST00000406533.3_Splice_Site|KCNMA1_ENST00000372440.1_Splice_Site|KCNMA1_ENST00000404771.3_Splice_Site|KCNMA1_ENST00000286628.8_Splice_Site	NM_002247.3	NP_002238.2	Q12791	KCMA1_HUMAN	potassium large conductance calcium-activated channel, subfamily M, alpha member 1						cellular potassium ion homeostasis|negative regulation of cell volume|platelet activation|positive regulation of apoptosis|regulation of membrane potential|response to calcium ion|response to carbon monoxide|response to hypoxia|response to osmotic stress|smooth muscle contraction involved in micturition	apical plasma membrane|caveola|integral to membrane|voltage-gated potassium channel complex	actin binding|calcium-activated potassium channel activity|large conductance calcium-activated potassium channel activity|metal ion binding|voltage-gated potassium channel activity	p.?(2)		breast(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(17)|lung(23)|ovary(2)|pancreas(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	68	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Chlorzoxazone(DB00356)|Cromoglicate(DB01003)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Enflurane(DB00228)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Trichlormethiazide(DB01021)	CTAAGACAACCTGTAAAAGAA	0.398000											OREG0020289	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	35					0	0	0.150653	0	0
AC016995.3	0	broad.mit.edu	37	2	38710017	38710019	+	RNA	DEL	AAT	AAT	-	rs2005502	by1000genomes	TCGA-EL-A3CO-01A-11D-A19J-08	TCGA-EL-A3CO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba1f48c1-8d38-4a91-ba08-a8ecb63cac88	bc492b5b-036e-4452-ac96-4fa312ce29ef	g.chr2:38710017_38710019delAAT	ENST00000417039.1	-	0	696																											TTCTTtaaaaaataaataaataa	0.246													2	4	---	---	---	---					
C12orf71	728858	broad.mit.edu	37	12	27234923	27234923	+	Frame_Shift_Del	DEL	C	C	-			TCGA-EL-A3CO-01A-11D-A19J-08	TCGA-EL-A3CO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba1f48c1-8d38-4a91-ba08-a8ecb63cac88	bc492b5b-036e-4452-ac96-4fa312ce29ef	g.chr12:27234923delC	ENST00000429849.2	-	1	524	c.494delG	c.(493-495)gcfs	p.G165fs		NM_001080406.1	NP_001073875.1	A8MTZ7	CL071_HUMAN	chromosome 12 open reading frame 71	165										endometrium(2)|large_intestine(1)|lung(4)|skin(1)	8						CGGAGGGGAGCCGCTGGATAG	0.423													2	4	---	---	---	---					
TRAV9-2	0	broad.mit.edu	37	14	22409532	22409540	+	RNA	DEL	TCTCTCTCT	TCTCTCTCT	-	rs57759840		TCGA-EL-A3CO-01A-11D-A19J-08	TCGA-EL-A3CO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba1f48c1-8d38-4a91-ba08-a8ecb63cac88	bc492b5b-036e-4452-ac96-4fa312ce29ef	g.chr14:22409532_22409540delTCTCTCTCT	ENST00000390441.2	+	0	102																											tctctctctctctctctctTTTTTTTTTT	0.411													4	2	---	---	---	---					
BACH1	571	broad.mit.edu	37	21	30699014	30699014	+	Frame_Shift_Del	DEL	A	A	-			TCGA-EL-A3CO-01A-11D-A19J-08	TCGA-EL-A3CO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba1f48c1-8d38-4a91-ba08-a8ecb63cac88	bc492b5b-036e-4452-ac96-4fa312ce29ef	g.chr21:30699014delA	ENST00000399921.1	+	3	1112	c.869delA	c.(868-870)gafs	p.E290fs	BACH1_ENST00000286800.3_Frame_Shift_Del_p.E290fs	NM_206866.1	NP_996749.1	O14867	BACH1_HUMAN	BTB and CNC homology 1, basic leucine zipper transcription factor 1	290						nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			breast(1)|endometrium(5)|kidney(2)|large_intestine(8)|liver(1)|lung(7)|ovary(1)|urinary_tract(2)	27						GAACCTGAAGAAACGAAGAAA	0.428													13	121	---	---	---	---					
AC008103.5	0	broad.mit.edu	37	22	18842473	18842473	+	RNA	DEL	G	G	-	rs66618606		TCGA-EL-A3CO-01A-11D-A19J-08	TCGA-EL-A3CO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba1f48c1-8d38-4a91-ba08-a8ecb63cac88	bc492b5b-036e-4452-ac96-4fa312ce29ef	g.chr22:18842473delG	ENST00000412938.1	+	0	2208																											AGCTGCTGGTGGGGAGGTCTT	0.647													7	8	---	---	---	---					
