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
DOCK4	9732	broad.mit.edu	37	7	111405275	111405275	+	Missense_Mutation	SNP	T	T	C			TCGA-HT-7879-01A-11D-2395-08	TCGA-HT-7879-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d315e0c-c20e-4f62-ae8b-42bdd9dbe053	826113c1-03bb-49be-82f0-e1dd43ec6cbc	g.chr7:111405275T>C	uc003vfy.3	-	39	4296	c.4027A>G	c.(4027-4029)Atg>Gtg	p.M1343V	DOCK4_uc011kml.2_Missense_Mutation_p.M179V|DOCK4_uc011kmm.2_Missense_Mutation_p.M205V|DOCK4_uc003vfw.3_Missense_Mutation_p.M748V|DOCK4_uc003vfx.3_Missense_Mutation_p.M1298V	NM_014705	NP_055520	Q8N1I0	DOCK4_HUMAN	Homo sapiens dedicator of cytokinesis 4 (DOCK4), mRNA.	1298	DHR-2.				cell chemotaxis	cytosol|endomembrane system|membrane|stereocilium	GTP binding|PDZ domain binding|Rac GTPase activator activity|Rac GTPase binding|SH3 domain binding|guanyl-nucleotide exchange factor activity|receptor tyrosine kinase binding			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(13)|lung(31)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(4)	72		Acute lymphoblastic leukemia(1;0.0441)				GAGGCTTCCATCATCTAGAAA	0.313000													2	7					0	0	1	0	0
PMEL	6490	broad.mit.edu	37	12	56350746	56350746	+	Silent	SNP	C	C	T	rs149851365	byFrequency	TCGA-HT-7879-01A-11D-2395-08	TCGA-HT-7879-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d315e0c-c20e-4f62-ae8b-42bdd9dbe053	826113c1-03bb-49be-82f0-e1dd43ec6cbc	g.chr12:56350746C>T	uc001sir.3	-	5	2004	c.1341G>A	c.(1339-1341)acG>acA	p.T447T	PMEL_uc001siq.3_Silent_p.T447T|PMEL_uc010spx.2_Silent_p.T361T|PMEL_uc001sip.3_Silent_p.T447T	NM_006928	NP_008859	P40967	PMEL_HUMAN	Homo sapiens premelanosome protein (PMEL), transcript variant 3, mRNA.	447					melanin biosynthetic process|melanosome organization	Golgi apparatus|endoplasmic reticulum membrane|extracellular region|integral to membrane|melanosome|multivesicular body membrane|plasma membrane	protein binding			NS(1)|breast(2)|endometrium(2)|large_intestine(4)|lung(4)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						TAATACTTTCCGTAGACATGA	0.502000													34	51					0	0	1	0	0
GAD2	2572	broad.mit.edu	37	10	26589805	26589805	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-7879-01A-11D-2395-08	TCGA-HT-7879-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d315e0c-c20e-4f62-ae8b-42bdd9dbe053	826113c1-03bb-49be-82f0-e1dd43ec6cbc	g.chr10:26589805G>A	uc001isp.2	+	15	2176	c.1673G>A	c.(1672-1674)cGc>cAc	p.R558H	GAD2_uc001isq.2_Missense_Mutation_p.R558H	NM_001134366	NP_001127838	Q05329	DCE2_HUMAN	Homo sapiens glutamate decarboxylase 2 (pancreatic islets and brain, 65kDa) (GAD2), transcript variant 2, mRNA.	558					glutamate decarboxylation to succinate|neurotransmitter biosynthetic process|neurotransmitter secretion	Golgi membrane|cell junction|clathrin sculpted gamma-aminobutyric acid transport vesicle membrane|cytosol|presynaptic membrane	glutamate decarboxylase activity|protein binding|pyridoxal phosphate binding			central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(26)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	48					L-Glutamic Acid(DB00142)	AATTTCTTCCGCATGGTCATC	0.463000													89	102					0	0	1	0	0
PKHD1	5314	broad.mit.edu	37	6	51897948	51897948	+	Missense_Mutation	SNP	T	T	C			TCGA-HT-7879-01A-11D-2395-08	TCGA-HT-7879-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d315e0c-c20e-4f62-ae8b-42bdd9dbe053	826113c1-03bb-49be-82f0-e1dd43ec6cbc	g.chr6:51897948T>C	uc003pah.1	-	28	3520	c.3244A>G	c.(3244-3246)Att>Gtt	p.I1082V	PKHD1_uc003pai.3_Missense_Mutation_p.I1082V	NM_138694	NP_619639	P08F94	PKHD1_HUMAN	Homo sapiens polycystic kidney and hepatic disease 1 (autosomal recessive) (PKHD1), transcript variant 1, mRNA.	1082	IPT/TIG 5.				cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity	p.R1081C(1)		NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					ACATTCACAATGCGTCCATCT	0.368000													27	45					0	0	1	0	0
EWSR1	2130	broad.mit.edu	37	22	29694857	29694857	+	Nonsense_Mutation	SNP	C	C	T			TCGA-HT-7879-01A-11D-2395-08	TCGA-HT-7879-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d315e0c-c20e-4f62-ae8b-42bdd9dbe053	826113c1-03bb-49be-82f0-e1dd43ec6cbc	g.chr22:29694857C>T	uc003aet.3	+	13	1880	c.1552C>T	c.(1552-1554)Cga>Tga	p.R518*	EWSR1_uc003aev.3_Nonsense_Mutation_p.R523*|EWSR1_uc003aex.3_Nonsense_Mutation_p.R517*|EWSR1_uc003aew.3_Nonsense_Mutation_p.R462*|EWSR1_uc003aey.3_Nonsense_Mutation_p.R313*|EWSR1_uc003aez.3_Nonsense_Mutation_p.R179*	NM_005243	NP_005234	Q01844	EWS_HUMAN	Homo sapiens Ewing sarcoma breakpoint region 1 (EWSR1), transcript variant 2, mRNA.	518					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	RNA binding|calmodulin binding|nucleotide binding|zinc ion binding		EWSR1/ATF1(347)|EWSR1/POU5F1(10)|EWSR1/PBX1(3)|EWSR1/DDIT3(45)|EWSR1/FEV(11)|EWSR1/CREB1(44)|EWSR1/SMARCA5(2)|EWSR1/ETV4(6)|EWSR1/ERG(178)|EWSR1/ZNF384(4)|EWSR1/ETV1(7)|EWSR1/FLI1(2569)|EWSR1/NR4A3(146)|EWSR1/SP3(3)|EWSR1/PATZ1(2)|EWSR1/WT1(234)|EWSR1/NFATC2(9)	breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|liver(1)|lung(6)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						CGTCCAGCACCGAGCTGGAGA	0.602000			T	"""FLI1, ERG, ZNF278, NR4A3, FEV, ATF1, ETV1, ETV4, WT1, ZNF384, CREB1, POU5F1,  PBX1"""	"""Ewing sarcoma,  desmoplastic small round cell tumor , ALL, clear cell sarcoma, sarcoma, myoepithelioma"""								51	88					0	0	1	0	0
STAM2	10254	broad.mit.edu	37	2	153003685	153003685	+	Silent	SNP	T	T	C			TCGA-HT-7879-01A-11D-2395-08	TCGA-HT-7879-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d315e0c-c20e-4f62-ae8b-42bdd9dbe053	826113c1-03bb-49be-82f0-e1dd43ec6cbc	g.chr2:153003685T>C	uc002tyc.4	-	4	788	c.438A>G	c.(436-438)gcA>gcG	p.A146A	STAM2_uc010foa.1_Silent_p.A146A|STAM2_uc002tyd.3_Silent_p.A146A	NM_005843	NP_005834	O75886	STAM2_HUMAN	Homo sapiens signal transducing adaptor molecule (SH3 domain and ITAM motif) 2 (STAM2), mRNA.	146					cellular membrane organization|endosome transport|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of epidermal growth factor receptor signaling pathway	cytosol|early endosome membrane	protein binding			endometrium(3)|large_intestine(4)|lung(8)|ovary(1)	16				BRCA - Breast invasive adenocarcinoma(221;0.22)		CCTGAGAACCTGCTGGAGGAA	0.373000													49	63					0	0	1	0	0
IDH1	3417	broad.mit.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-HT-7879-01A-11D-2395-08	TCGA-HT-7879-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d315e0c-c20e-4f62-ae8b-42bdd9dbe053	826113c1-03bb-49be-82f0-e1dd43ec6cbc	g.chr2:209113112C>T	uc002vcs.3	-	3	641	c.395G>A	c.(394-396)cGt>cAt	p.R132H	IDH1_uc002vct.3_Missense_Mutation_p.R132H|IDH1_uc002vcu.3_Missense_Mutation_p.R132H	NM_005896	NP_005887	O75874	IDHC_HUMAN	Homo sapiens isocitrate dehydrogenase 1 (NADP+), soluble (IDH1), mRNA.	132			R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate).|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation).|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).		2-oxoglutarate metabolic process|NADPH regeneration|cellular lipid metabolic process|glyoxylate cycle|isocitrate metabolic process|tricarboxylic acid cycle	cytosol|peroxisomal matrix	NAD binding|isocitrate dehydrogenase (NADP+) activity|magnesium ion binding|protein homodimerization activity	p.R132H(6425)|p.R132C(590)|p.R132?(189)|p.R132G(173)|p.R132S(140)|p.R132L(130)|p.R132V(2)|p.G131_R132>VL(2)|p.R132P(1)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		ATAAGCATGACGACCTATGAT	0.393000			Mis		gliobastoma								17	66					0	0	1	0	0
TP53	7157	broad.mit.edu	37	17	7578271	7578271	+	Missense_Mutation	SNP	T	T	A			TCGA-HT-7879-01A-11D-2395-08	TCGA-HT-7879-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d315e0c-c20e-4f62-ae8b-42bdd9dbe053	826113c1-03bb-49be-82f0-e1dd43ec6cbc	g.chr17:7578271T>A	uc002gim.2	-	5	772	c.578A>T	c.(577-579)cAt>cTt	p.H193L	TP53_uc002gig.1_Missense_Mutation_p.H193L|TP53_uc002gih.3_Missense_Mutation_p.H193L|TP53_uc010cne.1_5'Flank|TP53_uc010cng.1_Missense_Mutation_p.H61L|TP53_uc010cnf.1_Missense_Mutation_p.H61L|TP53_uc002gii.1_Missense_Mutation_p.H61L|TP53_uc010cni.1_Missense_Mutation_p.H193L|TP53_uc010cnh.1_Missense_Mutation_p.H193L|TP53_uc002gij.2_Missense_Mutation_p.H193L|TP53_uc010cnj.1_Intron|TP53_uc002gin.2_Missense_Mutation_p.H100L|TP53_uc002gio.2_Missense_Mutation_p.H61L|TP53_uc010vug.2_Missense_Mutation_p.H154L	NM_001126112	NP_001119587	P04637	P53_HUMAN	Homo sapiens tumor protein p53 (TP53), transcript variant 2, mRNA.	193	Interaction with AXIN1 (By similarity).|Interaction with HIPK1 (By similarity).|Required for interaction with FBXO42.		H -> D (in sporadic cancers; somatic mutation).|H -> L (in sporadic cancers; somatic mutation).|H -> N (in sporadic cancers; somatic mutation).|H -> P (in sporadic cancers; somatic mutation).|H -> Q (in sporadic cancers; somatic mutation).|H -> R (in LFS; germline mutation and in sporadic cancers; somatic mutation).|H -> Y (in sporadic cancers; somatic mutation).|QH -> HN (in a sporadic cancer; somatic mutation).|QH -> HY (in a sporadic cancer; somatic mutation).		DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|Ras protein signal transduction|activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to UV|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|determination of adult lifespan|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|regulation of mitochondrial membrane permeability|replicative senescence|response to X-ray|response to antibiotic|response to gamma radiation	PML body|cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|protein complex|replication fork	ATP binding|DNA strand annealing activity|RNA polymerase II transcription factor binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|histone acetyltransferase binding|p53 binding|protease binding|protein N-terminus binding|protein binding|protein heterodimerization activity|protein kinase binding|protein phosphatase 2A binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.H193R(152)|p.H193L(77)|p.Q192*(71)|p.H193P(32)|p.H193Y(27)|p.H193D(9)|p.0?(8)|p.A189_V197delAPPQHLIRV(8)|p.H193fs*16(6)|p.?(6)|p.Q192R(5)|p.P191_E198>Q(4)|p.H193N(4)|p.H61R(4)|p.H100R(4)|p.H100L(4)|p.H61L(4)|p.Q192H(3)|p.H193_I195delHLI(2)|p.P191fs*53(2)|p.H193H(2)|p.Q192Q(2)|p.Q192K(2)|p.H61P(2)|p.H100P(2)|p.H193_I195>AP(2)|p.A189fs*53(1)|p.K164_P219del(1)|p.P191fs*6(1)|p.A189_Q192>E(1)|p.P59_E66>Q(1)|p.P191fs*15(1)|p.P191_Q192delPQ(1)|p.Q192>XXXXXXXXX(1)|p.P98_E105>Q(1)|p.Q192del(1)|p.Q192fs*56(1)|p.Q192fs*16(1)|p.Q192fs*30(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		TCGGATAAGATGCTGAGGAGG	0.562000		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			22	44					0	0	1	0	0
OGT	8473	broad.mit.edu	37	X	70767813	70767813	+	Missense_Mutation	SNP	T	T	G			TCGA-HT-7879-01A-11D-2395-08	TCGA-HT-7879-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d315e0c-c20e-4f62-ae8b-42bdd9dbe053	826113c1-03bb-49be-82f0-e1dd43ec6cbc	g.chrX:70767813T>G	uc004eaa.2	+	4	826	c.588T>G	c.(586-588)aaT>aaG	p.N196K	BCYRN1_uc011mpt.1_Intron|OGT_uc004eab.2_Missense_Mutation_p.N186K|OGT_uc004eac.3_Missense_Mutation_p.N57K|OGT_uc004ead.3_5'UTR	NM_181672	NP_858058	O15294	OGT1_HUMAN	Homo sapiens O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase) (OGT), transcript variant 1, mRNA.	196					cellular response to retinoic acid|positive regulation of granulocyte differentiation|positive regulation of histone H3-K4 methylation|positive regulation of proteolysis|protein O-linked glycosylation|signal transduction	MLL5-L complex|cytosol	enzyme activator activity|protein N-acetylglucosaminyltransferase activity|protein binding	p.N196K(1)|p.N186K(1)		breast(6)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(5)|liver(3)|lung(9)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Renal(35;0.156)					CTTGGAGTAATCTTGGCTGTG	0.378000													73	9					0	0	1	0	0
MZT2A	653784	broad.mit.edu	37	2	132241765	132241765	+	Missense_Mutation	SNP	C	C	G			TCGA-HT-7879-01A-11D-2395-08	TCGA-HT-7879-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d315e0c-c20e-4f62-ae8b-42bdd9dbe053	826113c1-03bb-49be-82f0-e1dd43ec6cbc	g.chr2:132241765C>G	uc002tsw.4	-	2	461	c.346G>C	c.(346-348)Ggg>Cgg	p.G116R	MZT2A_uc002tsv.4_Non-coding_Transcript	NM_001085365	NP_001078834	Q6P582	MZT2A_HUMAN	Homo sapiens mitotic spindle organizing protein 2A (MZT2A), mRNA.	116						centrosome|gamma-tubulin ring complex|spindle		p.G116R(2)		breast(1)|lung(1)	2						AATACTCCCCCGAGGGCAGCG	0.632000													9	104					0	0	1	0	0
TBC1D9	23158	broad.mit.edu	37	4	141677165	141677165	+	Missense_Mutation	SNP	T	T	C			TCGA-HT-7879-01A-11D-2395-08	TCGA-HT-7879-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d315e0c-c20e-4f62-ae8b-42bdd9dbe053	826113c1-03bb-49be-82f0-e1dd43ec6cbc	g.chr4:141677165T>C	uc010ioj.3	-	0	307	c.35A>G	c.(34-36)aAc>aGc	p.N12S		NM_015130	NP_055945	Q6ZT07	TBCD9_HUMAN	Homo sapiens TBC1 domain family, member 9 (with GRAM domain) (TBC1D9), mRNA.	12						intracellular	Rab GTPase activator activity|calcium ion binding			endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	31	all_hematologic(180;0.162)	Medulloblastoma(177;0.00498)				CCACAGCGCGTTGGCCAGCAA	0.701000													7	19					0	0	1	0	0
MGC70870	403340	broad.mit.edu	37	GL000205.1	118201	118201	+	RNA	SNP	C	C	G			TCGA-HT-7879-01A-11D-2395-08	TCGA-HT-7879-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d315e0c-c20e-4f62-ae8b-42bdd9dbe053	826113c1-03bb-49be-82f0-e1dd43ec6cbc	g.chrGL000205.1:118201C>G	uc002kgk.4	+	0		c.1579C>G								Homo sapiens C-terminal binding protein 2 pseudogene (MGC70870), non-coding RNA.																		TCCCGGGAAGCTTAAGAAACT	0.507000													5	26					0	0	1	0	0
MLLT1	4298	broad.mit.edu	37	19	6270683	6270683	+	Missense_Mutation	SNP	C	C	A			TCGA-HT-7879-01A-11D-2395-08	TCGA-HT-7879-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d315e0c-c20e-4f62-ae8b-42bdd9dbe053	826113c1-03bb-49be-82f0-e1dd43ec6cbc	g.chr19:6270683C>A	uc002mek.3	-	1	264	c.100G>T	c.(100-102)Gtg>Ttg	p.V34L		NM_005934	NP_005925	Q03111	ENL_HUMAN	Homo sapiens myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 1 (MLLT1), mRNA.	34	YEATS.				regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleolus	DNA binding|protein binding			endometrium(3)|kidney(3)|large_intestine(2)|lung(5)|prostate(2)|skin(2)	17						CGGACAAACACCATCCAGTCG	0.622000			T	MLL	AL						OREG0025198	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	5	46					0.00198382	0.00198382	1	1	0
CDC20B	166979	broad.mit.edu	37	5	54429276	54429276	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-7879-01A-11D-2395-08	TCGA-HT-7879-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d315e0c-c20e-4f62-ae8b-42bdd9dbe053	826113c1-03bb-49be-82f0-e1dd43ec6cbc	g.chr5:54429276C>T	uc003jpo.2	-	5	838	c.661G>A	c.(661-663)Gtg>Atg	p.V221M	CDC20B_uc003jpn.2_Missense_Mutation_p.V221M|CDC20B_uc010ivu.2_Missense_Mutation_p.V221M|CDC20B_uc010ivv.2_Missense_Mutation_p.V221M	NM_001170402	NP_001163873	Q86Y33	CD20B_HUMAN	Homo sapiens cell division cycle 20 homolog B (S. cerevisiae) (CDC20B), transcript variant 3, mRNA.	221										kidney(1)|large_intestine(5)|lung(7)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	19		Lung NSC(810;0.000744)|Breast(144;0.159)|Prostate(74;0.194)	LUSC - Lung squamous cell carcinoma(15;0.225)			TGAATCTTCACCTCTGGTTGG	0.368000													36	53					0	0	1	0	0
PTBP3	9991	broad.mit.edu	37	9	114989706	114989706	+	Missense_Mutation	SNP	T	T	C			TCGA-HT-7879-01A-11D-2395-08	TCGA-HT-7879-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d315e0c-c20e-4f62-ae8b-42bdd9dbe053	826113c1-03bb-49be-82f0-e1dd43ec6cbc	g.chr9:114989706T>C	uc004bfv.3	-	11	1634	c.1451A>G	c.(1450-1452)cAt>cGt	p.H484R	MIR3134_uc022bma.1_Intron|PTBP3_uc004bfx.3_Missense_Mutation_p.H481R|PTBP3_uc004bfw.3_Missense_Mutation_p.H478R|PTBP3_uc011lwu.2_Missense_Mutation_p.H450R|PTBP3_uc004bfz.3_Missense_Mutation_p.H450R|PTBP3_uc004bfy.3_Missense_Mutation_p.H383R	NM_001244898	NP_001231827	O95758	ROD1_HUMAN	Homo sapiens polypyrimidine tract binding protein 3 (PTBP3), transcript variant 6, mRNA.	478	RRM 4.				anatomical structure morphogenesis|mRNA processing	nucleus	RNA binding|nucleotide binding										GTTGGAAAGATGCAGAGTGGC	0.368000													49	62					0	0	1	0	0
MYL9	10398	broad.mit.edu	37	20	35177631	35177631	+	Silent	SNP	C	C	T			TCGA-HT-7879-01A-11D-2395-08	TCGA-HT-7879-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d315e0c-c20e-4f62-ae8b-42bdd9dbe053	826113c1-03bb-49be-82f0-e1dd43ec6cbc	g.chr20:35177631C>T	uc002xfl.1	+	3	592	c.498C>T	c.(496-498)ggC>ggT	p.G166G	BC039668_uc002xfk.3_Intron|MYL9_uc002xfm.1_Silent_p.G112G	NM_006097	NP_006088	P24844	MYL9_HUMAN	Homo sapiens myosin, light chain 9, regulatory (MYL9), transcript variant 1, mRNA.	166	EF-hand 3.				axon guidance|muscle contraction|regulation of muscle contraction	cytosol|muscle myosin complex	calcium ion binding|structural constituent of muscle	p.G166C(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(2)	8	Breast(12;0.0192)	Myeloproliferative disorder(115;0.00878)				TCAAACATGGCGCCAAGGATA	0.602000													4	30					0	0	1	0	0
BAGE1	0	broad.mit.edu	37	GL000237.1	2603	2603	+	RNA	SNP	C	C	G			TCGA-HT-7879-01A-11D-2395-08	TCGA-HT-7879-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d315e0c-c20e-4f62-ae8b-42bdd9dbe053	826113c1-03bb-49be-82f0-e1dd43ec6cbc	g.chrGL000237.1:2603C>G	uc011mgu.1	-	0		c.84G>C								Homo sapiens B melanoma antigen variant f (BAGE1) mRNA, complete cds, alternatively spliced.																		gttacaggctccagcctccag	0.612000													2	11					0	0	1	0	0
CACNA1H	8912	broad.mit.edu	37	16	1265549	1265549	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-7879-01A-11D-2395-08	TCGA-HT-7879-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d315e0c-c20e-4f62-ae8b-42bdd9dbe053	826113c1-03bb-49be-82f0-e1dd43ec6cbc	g.chr16:1265549G>A	uc002cks.3	+	29	5448	c.5200G>A	c.(5200-5202)Ggc>Agc	p.G1734S	CACNA1H_uc002ckt.3_Missense_Mutation_p.G1728S|CACNA1H_uc002cku.3_Missense_Mutation_p.G440S|CACNA1H_uc010brj.3_Missense_Mutation_p.G445S|CACNA1H_uc002ckv.3_Missense_Mutation_p.G434S	NM_021098	NP_066921	O95180	CAC1H_HUMAN	Homo sapiens calcium channel, voltage-dependent, T type, alpha 1H subunit (CACNA1H), transcript variant 1, mRNA.	1734					aldosterone biosynthetic process|axon guidance|cellular response to hormone stimulus|cellular response to potassium ion|cortisol biosynthetic process|muscle contraction|myoblast fusion|positive regulation of acrosome reaction|regulation of heart contraction	voltage-gated calcium channel complex	low voltage-gated calcium channel activity	p.G1734C(2)|p.G1728C(1)		breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Flunarizine(DB04841)|Mibefradil(DB01388)	GATGGCTACGGGCATGCGCGC	0.721000													12	15					0	0	1	0	0
ROBO3	64221	broad.mit.edu	37	11	124750448	124750453	+	In_Frame_Del	DEL	CGGAGT	CGGAGT	-	rs55725290		TCGA-HT-7879-01A-11D-2395-08	TCGA-HT-7879-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d315e0c-c20e-4f62-ae8b-42bdd9dbe053	826113c1-03bb-49be-82f0-e1dd43ec6cbc	g.chr11:124750448_124750453delCGGAGT	uc001qbc.3	+	26	4262_4267	c.4093_4098delCGGAGT	c.(4093-4098)cggagtdel	p.RS1367del	ROBO3_uc001qbd.2_In_Frame_Del_p.RS292del|ROBO3_uc010sar.2_In_Frame_Del_p.RS416del|ROBO3_uc001qbe.3_In_Frame_Del_p.RS292del|ROBO3_uc001qbf.1_In_Frame_Del_p.RS251del	NM_022370	NP_071765	Q96MS0	ROBO3_HUMAN	Homo sapiens roundabout, axon guidance receptor, homolog 3 (Drosophila) (ROBO3), mRNA.	1367					axon midline choice point recognition	integral to membrane	receptor activity			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	35	all_hematologic(175;0.215)	Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|Breast(109;0.0481)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0296)		TGgccggagccggagtcggagtcaga	0.660													5	3	---	---	---	---					
TP53	7157	broad.mit.edu	37	17	7577150	7577151	+	Frame_Shift_Del	DEL	TT	TT	-	rs72661119		TCGA-HT-7879-01A-11D-2395-08	TCGA-HT-7879-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d315e0c-c20e-4f62-ae8b-42bdd9dbe053	826113c1-03bb-49be-82f0-e1dd43ec6cbc	g.chr17:7577150_7577151delTT	uc002gim.2	-	7	981_982	c.787_788delAA	c.(787-789)aatfs	p.N263fs	TP53_uc002gig.1_Intron|TP53_uc002gih.3_Frame_Shift_Del_p.N263fs|TP53_uc010cne.1_5'Flank|TP53_uc010cng.1_Frame_Shift_Del_p.N131fs|TP53_uc010cnf.1_Frame_Shift_Del_p.N131fs|TP53_uc002gii.1_Frame_Shift_Del_p.N131fs|TP53_uc010cni.1_Frame_Shift_Del_p.N263fs|TP53_uc010cnh.1_Frame_Shift_Del_p.N263fs|TP53_uc002gij.2_Frame_Shift_Del_p.N263fs|DL476366_uc021tpf.1_5'Flank|DL476309_uc021tpg.1_5'Flank|DL476358_uc021tph.1_5'Flank	NM_001126112	NP_001119587	P04637	P53_HUMAN	Homo sapiens tumor protein p53 (TP53), transcript variant 2, mRNA.	263	Interaction with AXIN1 (By similarity).|Interaction with E4F1.|Interaction with HIPK1 (By similarity).		GN -> PD (in a sporadic cancer; somatic mutation).|N -> D (in sporadic cancers; somatic mutation).|N -> H (in sporadic cancers; somatic mutation).|N -> I (in sporadic cancers; somatic mutation).|N -> K (in a sporadic cancer; somatic mutation).|N -> S (in a sporadic cancer; somatic mutation).		DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|Ras protein signal transduction|activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to UV|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|determination of adult lifespan|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|regulation of mitochondrial membrane permeability|replicative senescence|response to X-ray|response to antibiotic|response to gamma radiation	PML body|cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|protein complex|replication fork	ATP binding|DNA strand annealing activity|RNA polymerase II transcription factor binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|histone acetyltransferase binding|p53 binding|protease binding|protein N-terminus binding|protein binding|protein heterodimerization activity|protein kinase binding|protein phosphatase 2A binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.G262V(15)|p.0?(8)|p.N263fs*82(6)|p.G262fs*83(5)|p.G262_F270delGNLLGRNSF(4)|p.G262D(4)|p.N263D(4)|p.N263I(4)|p.N263H(4)|p.G262_S269delGNLLGRNS(4)|p.?(3)|p.G262fs*2(2)|p.G262del(2)|p.G262S(2)|p.S261_L264>R(2)|p.N263fs*5(2)|p.N263fs*84(2)|p.G262H(1)|p.G262G(1)|p.E258fs*71(1)|p.S261_G262insX(1)|p.N263K(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		TCCCAGTAGATTACCACTACTC	0.520		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			17	23	---	---	---	---					
ATRX	546	broad.mit.edu	37	X	76938001	76938001	+	Frame_Shift_Del	DEL	G	G	-			TCGA-HT-7879-01A-11D-2395-08	TCGA-HT-7879-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d315e0c-c20e-4f62-ae8b-42bdd9dbe053	826113c1-03bb-49be-82f0-e1dd43ec6cbc	g.chrX:76938001delG	uc004ecp.4	-	8	2979	c.2747delC	c.(2746-2748)gctfs	p.A916fs	ATRX_uc004ecq.4_Frame_Shift_Del_p.A878fs|ATRX_uc004eco.4_Frame_Shift_Del_p.A701fs|ATRX_uc004ecr.2_Frame_Shift_Del_p.A848fs|ATRX_uc010nlx.1_Frame_Shift_Del_p.A887fs|ATRX_uc010nly.1_Frame_Shift_Del_p.A861fs	NM_000489	NP_000480	P46100	ATRX_HUMAN	Homo sapiens alpha thalassemia/mental retardation syndrome X-linked (ATRX), transcript variant 1, mRNA.	916					DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent	nuclear heterochromatin	ATP binding|DNA binding|DNA helicase activity|chromo shadow domain binding|zinc ion binding	p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145					Phosphatidylserine(DB00144)	ATCAGTGGAAGCACTTGCTTG	0.418			"""Mis, F, N"""		"""Pancreatic neuroendocrine tumors, paediatric GBM"""		ATR-X (alpha thalassemia/mental retardation) syndrome						122	35	---	---	---	---					
