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
HFM1	164045	broad.mit.edu	37	1	91859787	91859787	+	Silent	SNP	G	G	A			TCGA-VN-A88I-01A-11D-A34U-08	TCGA-VN-A88I-10A-01D-A34X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9ddf3f3e-d1b5-40c9-8781-91fc7ad54cb3	bd4e531f-404d-4daa-8842-9718b657a281	g.chr1:91859787G>A	ENST00000370425.3	-	4	455	c.357C>T	c.(355-357)ggC>ggT	p.G119G	HFM1_ENST00000294696.5_5'UTR|HFM1_ENST00000370424.3_Intron	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	119							ATP binding|ATP-dependent helicase activity|nucleic acid binding			breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(33)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	75		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)		ATGTCAGCTTGCCAGCAATAT	0.343													8	70	---	---	---	---
GON4L	54856	broad.mit.edu	37	1	155732049	155732049	+	Missense_Mutation	SNP	C	C	T			TCGA-VN-A88I-01A-11D-A34U-08	TCGA-VN-A88I-10A-01D-A34X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9ddf3f3e-d1b5-40c9-8781-91fc7ad54cb3	bd4e531f-404d-4daa-8842-9718b657a281	g.chr1:155732049C>T	ENST00000437809.1	-	23	4965	c.4843G>A	c.(4843-4845)Gac>Aac	p.D1615N	GON4L_ENST00000271883.5_Missense_Mutation_p.D1615N|GON4L_ENST00000368331.1_Missense_Mutation_p.D1615N	NM_001282856.1	NP_001269785.1	Q3T8J9	GON4L_HUMAN	gon-4-like (C. elegans)	1615					regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			NS(2)|breast(4)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	45	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)					TCGAGAATGTCCTCATCATAC	0.552													3	25	---	---	---	---
TM4SF4	7104	broad.mit.edu	37	3	149192703	149192703	+	Silent	SNP	C	C	G			TCGA-VN-A88I-01A-11D-A34U-08	TCGA-VN-A88I-10A-01D-A34X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9ddf3f3e-d1b5-40c9-8781-91fc7ad54cb3	bd4e531f-404d-4daa-8842-9718b657a281	g.chr3:149192703C>G	ENST00000305354.4	+	1	943	c.39C>G	c.(37-39)acC>acG	p.T13T		NM_004617.3	NP_004608.1	P48230	T4S4_HUMAN	transmembrane 4 L six family member 4	13						integral to membrane				large_intestine(3)|lung(4)|ovary(1)|prostate(1)	9			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)			TGGGGGGGACCCTCATTCCCC	0.527													3	36	---	---	---	---
PDS5A	23244	broad.mit.edu	37	4	39978175	39978175	+	Missense_Mutation	SNP	T	T	C			TCGA-VN-A88I-01A-11D-A34U-08	TCGA-VN-A88I-10A-01D-A34X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9ddf3f3e-d1b5-40c9-8781-91fc7ad54cb3	bd4e531f-404d-4daa-8842-9718b657a281	g.chr4:39978175T>C	ENST00000303538.8	-	2	562	c.23A>G	c.(22-24)aAg>aGg	p.K8R	PDS5A_ENST00000503396.1_Missense_Mutation_p.K8R	NM_001100399.1	NP_001093869.1	Q29RF7	PDS5A_HUMAN	PDS5, regulator of cohesion maintenance, homolog A (S. cerevisiae)	8					cell division|mitosis|negative regulation of DNA replication	chromatin|nucleus	identical protein binding			breast(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(9)|lung(14)|prostate(3)|skin(1)|urinary_tract(1)	39						AGTGGCAGGCTTGGGCTGCGC	0.587											OREG0016159	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	6	68	---	---	---	---
HDAC3	8841	broad.mit.edu	37	5	141005259	141005259	+	Missense_Mutation	SNP	G	G	A			TCGA-VN-A88I-01A-11D-A34U-08	TCGA-VN-A88I-10A-01D-A34X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9ddf3f3e-d1b5-40c9-8781-91fc7ad54cb3	bd4e531f-404d-4daa-8842-9718b657a281	g.chr5:141005259G>A	ENST00000305264.3	-	13	1131	c.1052C>T	c.(1051-1053)tCa>tTa	p.S351L	AC008781.7_ENST00000422040.2_RNA|HDAC3_ENST00000469207.1_Intron	NM_003883.3	NP_003874.2	O15379	HDAC3_HUMAN	histone deacetylase 3	351					anti-apoptosis|cellular lipid metabolic process|negative regulation of cell cycle|negative regulation of JNK cascade|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|spindle assembly|transcription, DNA-dependent	cytoplasm|histone deacetylase complex|spindle microtubule|transcriptional repressor complex	histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|transcription corepressor activity|transcription factor binding			endometrium(1)|large_intestine(2)|lung(3)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	13			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Vorinostat(DB02546)	GACCTGGCGTGAGTTCTGATT	0.498													7	43	---	---	---	---
GNL1	2794	broad.mit.edu	37	6	30515194	30515194	+	Missense_Mutation	SNP	G	G	A			TCGA-VN-A88I-01A-11D-A34U-08	TCGA-VN-A88I-10A-01D-A34X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9ddf3f3e-d1b5-40c9-8781-91fc7ad54cb3	bd4e531f-404d-4daa-8842-9718b657a281	g.chr6:30515194G>A	ENST00000376621.3	-	9	2183	c.1213C>T	c.(1213-1215)Ccc>Tcc	p.P405S		NM_005275.3	NP_005266.2	P36915	GNL1_HUMAN	guanine nucleotide binding protein-like 1	405	G.				response to DNA damage stimulus|signal transduction|T cell mediated immunity	extracellular space|intracellular	GTP binding|structural molecule activity			cervix(2)|endometrium(4)|large_intestine(1)|lung(10)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	25						TTCACAGAGGGGGTAAGAAAG	0.562													21	197	---	---	---	---
C9orf9	11092	broad.mit.edu	37	9	135765348	135765348	+	Missense_Mutation	SNP	C	C	T	rs2231412		TCGA-VN-A88I-01A-11D-A34U-08	TCGA-VN-A88I-10A-01D-A34X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9ddf3f3e-d1b5-40c9-8781-91fc7ad54cb3	bd4e531f-404d-4daa-8842-9718b657a281	g.chr9:135765348C>T	ENST00000350499.6	+	5	654	c.500C>T	c.(499-501)aCg>aTg	p.T167M	C9orf9_ENST00000356311.5_3'UTR|C9orf9_ENST00000372136.3_3'UTR	NM_018956.3	NP_061829.3	Q96E40	CI009_HUMAN	chromosome 9 open reading frame 9	0								p.?(1)		cervix(1)|large_intestine(1)|lung(1)|prostate(1)	4				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|GBM - Glioblastoma multiforme(294;4.84e-07)|Epithelial(140;1.28e-06)		TCACAGGGGACGACTTAGCTT	0.448													21	303	---	---	---	---
GLI1	2735	broad.mit.edu	37	12	57864213	57864213	+	Missense_Mutation	SNP	C	C	T			TCGA-VN-A88I-01A-11D-A34U-08	TCGA-VN-A88I-10A-01D-A34X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9ddf3f3e-d1b5-40c9-8781-91fc7ad54cb3	bd4e531f-404d-4daa-8842-9718b657a281	g.chr12:57864213C>T	ENST00000228682.2	+	12	1781	c.1690C>T	c.(1690-1692)Cct>Tct	p.P564S	GLI1_ENST00000546141.1_Missense_Mutation_p.P523S|GLI1_ENST00000543426.1_Missense_Mutation_p.P436S	NM_005269.2	NP_005260.1	P08151	GLI1_HUMAN	GLI family zinc finger 1	564					epidermal cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|osteoblast differentiation|positive regulation of DNA replication|positive regulation of smoothened signaling pathway|positive regulation of transcription from RNA polymerase II promoter	cytosol|nucleus	transcription regulatory region DNA binding|zinc ion binding			NS(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(8)|lung(22)|ovary(6)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69			GBM - Glioblastoma multiforme(3;3.99e-32)			CCTGGCCTCTCCTTTCCCCCC	0.647													5	42	---	---	---	---
ZC3H13	23091	broad.mit.edu	37	13	46554093	46554093	+	Missense_Mutation	SNP	A	A	C			TCGA-VN-A88I-01A-11D-A34U-08	TCGA-VN-A88I-10A-01D-A34X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9ddf3f3e-d1b5-40c9-8781-91fc7ad54cb3	bd4e531f-404d-4daa-8842-9718b657a281	g.chr13:46554093A>C	ENST00000242848.4	-	11	2115	c.1767T>G	c.(1765-1767)aaT>aaG	p.N589K	ZC3H13_ENST00000282007.3_Missense_Mutation_p.N589K			Q5T200	ZC3HD_HUMAN	zinc finger CCCH-type containing 13	589	Arg/Ser-rich.						nucleic acid binding|zinc ion binding			cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|lung(25)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	79		Lung NSC(96;7.26e-05)|Breast(56;0.000118)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;4.18e-05)		GATAGTTGCTATTACTACTGT	0.383													4	58	---	---	---	---
MGA	23269	broad.mit.edu	37	15	42003250	42003250	+	Nonsense_Mutation	SNP	C	C	G			TCGA-VN-A88I-01A-11D-A34U-08	TCGA-VN-A88I-10A-01D-A34X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9ddf3f3e-d1b5-40c9-8781-91fc7ad54cb3	bd4e531f-404d-4daa-8842-9718b657a281	g.chr15:42003250C>G	ENST00000219905.7	+	8	2968	c.2787C>G	c.(2785-2787)taC>taG	p.Y929*	MGA_ENST00000570161.1_Nonsense_Mutation_p.Y929*|MGA_ENST00000566586.1_Nonsense_Mutation_p.Y929*|MGA_ENST00000389936.4_Nonsense_Mutation_p.Y929*|MGA_ENST00000545763.1_Nonsense_Mutation_p.Y929*	NM_001164273.1	NP_001157745.1	Q8IWI9	MGAP_HUMAN	MGA, MAX dimerization protein	929						MLL1 complex	DNA binding|sequence-specific DNA binding transcription factor activity			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)		AGCAGAAATACTCTCATGTGA	0.378													12	100	---	---	---	---
TMEM5	10329	broad.mit.edu	37	12	64199185	64199186	+	Splice_Site	INS	-	-	T			TCGA-VN-A88I-01A-11D-A34U-08	TCGA-VN-A88I-10A-01D-A34X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9ddf3f3e-d1b5-40c9-8781-91fc7ad54cb3	bd4e531f-404d-4daa-8842-9718b657a281	g.chr12:64199185_64199186insT	ENST00000537373.1	+	5	1082		c.e5+1		TMEM5_ENST00000261234.6_Splice_Site	NM_001278237.1	NP_001265166.1	Q9Y2B1	TMEM5_HUMAN	transmembrane protein 5							integral to plasma membrane				breast(1)|large_intestine(3)|liver(2)|lung(7)|prostate(1)|skin(1)	15		Myeloproliferative disorder(1001;0.0255)	BRCA - Breast invasive adenocarcinoma(9;0.0985)	GBM - Glioblastoma multiforme(28;9e-08)|BRCA - Breast invasive adenocarcinoma(357;0.000175)		CAAGAGAACAGTAAGTTCTATG	0.347													7	82	---	---	---	---
ZNF585B	92285	broad.mit.edu	37	19	37677872	37677873	+	Frame_Shift_Ins	INS	-	-	T			TCGA-VN-A88I-01A-11D-A34U-08	TCGA-VN-A88I-10A-01D-A34X-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9ddf3f3e-d1b5-40c9-8781-91fc7ad54cb3	bd4e531f-404d-4daa-8842-9718b657a281	g.chr19:37677872_37677873insT	ENST00000532828.2	-	5	817_818	c.566_567insA	c.(565-567)aatfs	p.N189fs	ZNF585B_ENST00000527838.1_Intron|ZNF585B_ENST00000312908.5_Intron|ZNF585B_ENST00000531805.1_Frame_Shift_Ins_p.N134fs|CTC-454I21.3_ENST00000585860.2_Intron	NM_152279.3	NP_689492.3	Q52M93	Z585B_HUMAN	zinc finger protein 585B	189					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|zinc ion binding			NS(1)|breast(3)|endometrium(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)	29			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TTCCACATTCATTGCACTTATA	0.376													15	165	---	---	---	---
