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
GAD2	2572	broad.mit.edu	37	10	26589805	26589805	+	Missense_Mutation	SNP	G	A	A			TCGA-HT-7879-01A-11D-2395-08	TCGA-HT-7879-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	2d315e0c-c20e-4f62-ae8b-42bdd9dbe053	826113c1-03bb-49be-82f0-e1dd43ec6cbc	g.chr10:26589805G>A	uc001isp.2	+	16	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	glutamate decarboxylase 2	558		Substrate.			glutamate decarboxylation to succinate|neurotransmitter biosynthetic process|neurotransmitter secretion	cell junction|clathrin sculpted gamma-aminobutyric acid transport vesicle membrane|cytosol|Golgi membrane|presynaptic membrane	glutamate decarboxylase activity|protein binding|pyridoxal phosphate binding			central_nervous_system(1)|skin(1)	2					L-Glutamic Acid(DB00142)	AATTTCTTCCGCATGGTCATC	0.463000													89	102					0	0	1	0	0
SILV	6490	broad.mit.edu	37	12	56350746	56350746	+	Silent	SNP	C	T	T	rs149851365	byFrequency	TCGA-HT-7879-01A-11D-2395-08	TCGA-HT-7879-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	2d315e0c-c20e-4f62-ae8b-42bdd9dbe053	826113c1-03bb-49be-82f0-e1dd43ec6cbc	g.chr12:56350746C>T	uc001sip.2	-	6	1372	c.1341G>A	c.(1339-1341)ACG>ACA	p.T447T	SILV_uc001siq.2_Silent_p.T447T|SILV_uc010spx.1_Silent_p.T361T|SILV_uc001sir.2_Silent_p.T447T	NM_006928	NP_008859	P40967	PMEL_HUMAN	silver homolog	447					melanin biosynthetic process|melanosome organization	endoplasmic reticulum membrane|extracellular region|Golgi apparatus|integral to membrane|melanosome|multivesicular body membrane|plasma membrane	protein binding				0						TAATACTTTCCGTAGACATGA	0.408000													34	51					0	0	1	0	0
CACNA1H	8912	broad.mit.edu	37	16	1265549	1265549	+	Missense_Mutation	SNP	G	A	A			TCGA-HT-7879-01A-11D-2395-08	TCGA-HT-7879-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	2d315e0c-c20e-4f62-ae8b-42bdd9dbe053	826113c1-03bb-49be-82f0-e1dd43ec6cbc	g.chr16:1265549G>A	uc002cks.2	+	30	5448	c.5200G>A	c.(5200-5202)GGC>AGC	p.G1734S	CACNA1H_uc002ckt.2_Missense_Mutation_p.G1728S|CACNA1H_uc002cku.2_Missense_Mutation_p.G440S|CACNA1H_uc010brj.2_Missense_Mutation_p.G445S|CACNA1H_uc002ckv.2_Missense_Mutation_p.G434S	NM_021098	NP_066921	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type,	1734	Helical; Name=S4 of repeat IV; (Potential).|IV.				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			breast(2)	2		Hepatocellular(780;0.00369)			Flunarizine(DB04841)|Mibefradil(DB01388)	GATGGCTACGGGCATGCGCGC	0.721000													12	15					0	0	1	0	0
TP53	7157	broad.mit.edu	37	17	7578271	7578271	+	Missense_Mutation	SNP	T	A	A			TCGA-HT-7879-01A-11D-2395-08	TCGA-HT-7879-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	2d315e0c-c20e-4f62-ae8b-42bdd9dbe053	826113c1-03bb-49be-82f0-e1dd43ec6cbc	g.chr17:7578271T>A	uc002gim.2	-	6	772	c.578A>T	c.(577-579)CAT>CTT	p.H193L	TP53_uc002gig.1_Missense_Mutation_p.H193L|TP53_uc002gih.2_Missense_Mutation_p.H193L|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.H61L|TP53_uc010cng.1_Missense_Mutation_p.H61L|TP53_uc002gii.1_Missense_Mutation_p.H61L|TP53_uc010cnh.1_Missense_Mutation_p.H193L|TP53_uc010cni.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.1_Missense_Mutation_p.H154L	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	193	Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		H -> D (in sporadic cancers; somatic mutation).|H -> Q (in sporadic cancers; somatic mutation).|H -> Y (in sporadic cancers; somatic mutation).|QH -> HN (in a sporadic cancer; somatic mutation).|H -> N (in sporadic cancers; somatic mutation).|QH -> HY (in a sporadic cancer; somatic mutation).|H -> L (in sporadic cancers; somatic mutation).|H -> P (in sporadic cancers; somatic mutation).|H -> R (in LFS; germline mutation and in sporadic cancers; somatic mutation).		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 drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|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|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|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|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.H193R(67)|p.H193L(31)|p.H193Y(26)|p.H193P(12)|p.0?(7)|p.H193D(7)|p.H193N(4)|p.A189_V197delAPPQHLIRV(4)|p.H193fs*16(3)|p.H193H(2)|p.P191fs*53(2)|p.K164_P219del(1)|p.P191fs*15(1)|p.P191fs*6(1)|p.H100L(1)|p.H61L(1)|p.H193_I195delHLI(1)|p.H193_I195>AP(1)|p.A189fs*53(1)		large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	22245		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	Hereditary_Adrenocortical_Cancer|Endometrial_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|Li-Fraumeni_syndrome|Osteosarcoma_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
MLLT1	4298	broad.mit.edu	37	19	6270683	6270683	+	Missense_Mutation	SNP	C	A	A			TCGA-HT-7879-01A-11D-2395-08	TCGA-HT-7879-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	2d315e0c-c20e-4f62-ae8b-42bdd9dbe053	826113c1-03bb-49be-82f0-e1dd43ec6cbc	g.chr19:6270683C>A	uc002mek.2	-	2	264	c.100G>T	c.(100-102)GTG>TTG	p.V34L		NM_005934	NP_005925	Q03111	ENL_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	34	YEATS.				regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleolus	DNA binding|protein binding			skin(1)	1						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
FAM128A	653784	broad.mit.edu	37	2	132241765	132241765	+	Missense_Mutation	SNP	C	G	G			TCGA-HT-7879-01A-11D-2395-08	TCGA-HT-7879-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	2d315e0c-c20e-4f62-ae8b-42bdd9dbe053	826113c1-03bb-49be-82f0-e1dd43ec6cbc	g.chr2:132241765C>G	uc002tsw.3	-	3	461	c.346G>C	c.(346-348)GGG>CGG	p.G116R	FAM128A_uc002tsv.3_RNA	NM_001085365	NP_001078834	Q6P582	MZT2A_HUMAN	hypothetical protein LOC653784	116						centrosome|gamma-tubulin ring complex|spindle					0				BRCA - Breast invasive adenocarcinoma(221;0.13)		AATACTCCCCCGAGGGCAGCG	0.632000													9	104					0	0	1	0	0
STAM2	10254	broad.mit.edu	37	2	153003685	153003685	+	Silent	SNP	T	C	C			TCGA-HT-7879-01A-11D-2395-08	TCGA-HT-7879-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	2d315e0c-c20e-4f62-ae8b-42bdd9dbe053	826113c1-03bb-49be-82f0-e1dd43ec6cbc	g.chr2:153003685T>C	uc002tyc.3	-	5	788	c.438A>G	c.(436-438)GCA>GCG	p.A146A	STAM2_uc010foa.1_Silent_p.A146A|STAM2_uc002tyd.2_Silent_p.A146A	NM_005843	NP_005834	O75886	STAM2_HUMAN	signal transducing adaptor molecule 2	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			ovary(1)	1				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	T	T	rs121913500		TCGA-HT-7879-01A-11D-2395-08	TCGA-HT-7879-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	2d315e0c-c20e-4f62-ae8b-42bdd9dbe053	826113c1-03bb-49be-82f0-e1dd43ec6cbc	g.chr2:209113112C>T	uc002vcs.2	-	4	641	c.395G>A	c.(394-396)CGT>CAT	p.R132H	IDH1_uc002vct.2_Missense_Mutation_p.R132H|IDH1_uc002vcu.2_Missense_Mutation_p.R132H	NM_005896	NP_005887	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132		Substrate.	R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation).|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).|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 -> 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).		2-oxoglutarate metabolic process|cellular lipid metabolic process|glyoxylate cycle|isocitrate metabolic process|NADPH regeneration|tricarboxylic acid cycle	cytosol|peroxisomal matrix	isocitrate dehydrogenase (NADP+) activity|magnesium ion binding|NAD binding|protein homodimerization activity	p.R132H(2023)|p.R132C(344)|p.R132?(210)|p.R132G(117)|p.R132S(79)|p.R132L(58)|p.R132V(1)|p.G131_R132>VL(1)		central_nervous_system(2156)|haematopoietic_and_lymphoid_tissue(606)|bone(74)|thyroid(22)|large_intestine(4)|skin(2)|prostate(2)|autonomic_ganglia(1)|soft_tissue(1)	2868				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
MYL9	10398	broad.mit.edu	37	20	35177631	35177631	+	Silent	SNP	C	T	T			TCGA-HT-7879-01A-11D-2395-08	TCGA-HT-7879-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	2d315e0c-c20e-4f62-ae8b-42bdd9dbe053	826113c1-03bb-49be-82f0-e1dd43ec6cbc	g.chr20:35177631C>T	uc002xfl.1	+	4	592	c.498C>T	c.(496-498)GGC>GGT	p.G166G	uc002xfk.3_Intron|MYL9_uc002xfm.1_Silent_p.G112G	NM_006097	NP_006088	P24844	MYL9_HUMAN	myosin regulatory light chain 9 isoform a	166	EF-hand 3.				axon guidance|muscle contraction|regulation of muscle contraction	cytosol|muscle myosin complex	calcium ion binding|structural constituent of muscle				0	Breast(12;0.0192)	Myeloproliferative disorder(115;0.00878)				TCAAACATGGCGCCAAGGATA	0.602000													4	30					0	0	1	0	0
EWSR1	2130	broad.mit.edu	37	22	29694857	29694857	+	Nonsense_Mutation	SNP	C	T	T			TCGA-HT-7879-01A-11D-2395-08	TCGA-HT-7879-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	2d315e0c-c20e-4f62-ae8b-42bdd9dbe053	826113c1-03bb-49be-82f0-e1dd43ec6cbc	g.chr22:29694857C>T	uc003aet.2	+	14	1880	c.1552C>T	c.(1552-1554)CGA>TGA	p.R518*	EWSR1_uc003aev.2_Nonsense_Mutation_p.R523*|EWSR1_uc003aew.2_Nonsense_Mutation_p.R462*|EWSR1_uc003aex.2_Nonsense_Mutation_p.R517*|EWSR1_uc003aey.2_Nonsense_Mutation_p.R313*|EWSR1_uc003aez.2_Nonsense_Mutation_p.R179*	NM_005243	NP_005234	Q01844	EWS_HUMAN	Ewing sarcoma breakpoint region 1 isoform 2	518	RanBP2-type.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	calmodulin binding|nucleotide binding|RNA binding|zinc ion binding		EWSR1/FLI1(2266)|EWSR1/ATF1(323)|EWSR1/WT1(231)|EWSR1/ERG(162)|EWSR1/NR4A3(140)|EWSR1/DDIT3(43)|EWSR1/CREB1(42)|EWSR1/FEV(10)|EWSR1/POU5F1(10)|EWSR1/ETV1(7)|EWSR1/ETV4(6)|EWSR1/ZNF384(4)|EWSR1/PBX1(3)|EWSR1/SP3(3)|EWSR1/PATZ1(2)	bone(2526)|soft_tissue(702)|skin(8)|autonomic_ganglia(4)|haematopoietic_and_lymphoid_tissue(4)|salivary_gland(2)|central_nervous_system(2)|NS(2)|pancreas(2)|lung(1)|ovary(1)	3254						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
TBC1D9	23158	broad.mit.edu	37	4	141677165	141677165	+	Missense_Mutation	SNP	T	C	C			TCGA-HT-7879-01A-11D-2395-08	TCGA-HT-7879-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	2d315e0c-c20e-4f62-ae8b-42bdd9dbe053	826113c1-03bb-49be-82f0-e1dd43ec6cbc	g.chr4:141677165T>C	uc010ioj.2	-	1	307	c.35A>G	c.(34-36)AAC>AGC	p.N12S		NM_015130	NP_055945	Q6ZT07	TBCD9_HUMAN	TBC1 domain family, member 9 (with GRAM domain)	12						intracellular	calcium ion binding|Rab GTPase activator activity			ovary(1)	1	all_hematologic(180;0.162)	Medulloblastoma(177;0.00498)				CCACAGCGCGTTGGCCAGCAA	0.701000													7	19					0	0	1	0	0
CDC20B	166979	broad.mit.edu	37	5	54429276	54429276	+	Missense_Mutation	SNP	C	T	T			TCGA-HT-7879-01A-11D-2395-08	TCGA-HT-7879-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	2d315e0c-c20e-4f62-ae8b-42bdd9dbe053	826113c1-03bb-49be-82f0-e1dd43ec6cbc	g.chr5:54429276C>T	uc003jpo.1	-	6	836	c.661G>A	c.(661-663)GTG>ATG	p.V221M	CDC20B_uc003jpn.1_Missense_Mutation_p.V221M|CDC20B_uc010ivu.1_Missense_Mutation_p.V221M|CDC20B_uc010ivv.1_Missense_Mutation_p.V221M	NM_152623	NP_689836	Q86Y33	CD20B_HUMAN	CDC20 cell division cycle 20 homolog B isoform	221											0		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
PKHD1	5314	broad.mit.edu	37	6	51897948	51897948	+	Missense_Mutation	SNP	T	C	C			TCGA-HT-7879-01A-11D-2395-08	TCGA-HT-7879-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	2d315e0c-c20e-4f62-ae8b-42bdd9dbe053	826113c1-03bb-49be-82f0-e1dd43ec6cbc	g.chr6:51897948T>C	uc003pah.1	-	29	3520	c.3244A>G	c.(3244-3246)ATT>GTT	p.I1082V	PKHD1_uc003pai.2_Missense_Mutation_p.I1082V	NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1	1082	IPT/TIG 5.|Extracellular (Potential).				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			lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1)	44	Lung NSC(77;0.0605)					ACATTCACAATGCGTCCATCT	0.368000													27	45					0	0	1	0	0
SPDYE7P	441251	broad.mit.edu	37	7	72339497	72339497	+	RNA	SNP	T	C	C	rs390732	by1000genomes	TCGA-HT-7879-01A-11D-2395-08	TCGA-HT-7879-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	2d315e0c-c20e-4f62-ae8b-42bdd9dbe053	826113c1-03bb-49be-82f0-e1dd43ec6cbc	g.chr7:72339497T>C	uc010lal.1	-	1		c.159A>G				NR_003666				Homo sapiens speedy homolog E7 (Xenopus laevis), pseudogene (SPDYE7P), non-coding RNA.												0						TCCTCAGATTTGTCCCACCAC	0.582000													6	43					0	0	1	0	0
DOCK4	9732	broad.mit.edu	37	7	111405275	111405275	+	Missense_Mutation	SNP	T	C	C			TCGA-HT-7879-01A-11D-2395-08	TCGA-HT-7879-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	2d315e0c-c20e-4f62-ae8b-42bdd9dbe053	826113c1-03bb-49be-82f0-e1dd43ec6cbc	g.chr7:111405275T>C	uc003vfx.2	-	38	4161	c.3892A>G	c.(3892-3894)ATG>GTG	p.M1298V	DOCK4_uc011kml.1_Missense_Mutation_p.M179V|DOCK4_uc011kmm.1_Missense_Mutation_p.M205V|DOCK4_uc003vfw.2_Missense_Mutation_p.M748V|DOCK4_uc003vfy.2_Missense_Mutation_p.M1343V	NM_014705	NP_055520	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	1298	DHR-2.				cell chemotaxis	cytosol|endomembrane system|membrane|stereocilium	GTP binding|guanyl-nucleotide exchange factor activity|PDZ domain binding|Rac GTPase activator activity|Rac GTPase binding|receptor tyrosine kinase binding|SH3 domain binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)	4		Acute lymphoblastic leukemia(1;0.0441)				GAGGCTTCCATCATCTAGAAA	0.313000													2	7					0	0	1	0	0
ROD1	9991	broad.mit.edu	37	9	114989706	114989706	+	Missense_Mutation	SNP	T	C	C			TCGA-HT-7879-01A-11D-2395-08	TCGA-HT-7879-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	2d315e0c-c20e-4f62-ae8b-42bdd9dbe053	826113c1-03bb-49be-82f0-e1dd43ec6cbc	g.chr9:114989706T>C	uc004bfw.2	-	13	1620	c.1433A>G	c.(1432-1434)CAT>CGT	p.H478R	ROD1_uc004bfv.2_Missense_Mutation_p.H484R|ROD1_uc004bfx.2_Missense_Mutation_p.H481R|ROD1_uc011lwu.1_Missense_Mutation_p.H450R|ROD1_uc004bfy.2_Missense_Mutation_p.H383R|ROD1_uc004bfz.2_Missense_Mutation_p.H450R	NM_005156	NP_005147	O95758	ROD1_HUMAN	ROD1 regulator of differentiation 1 isoform 1	478	RRM 4.				anatomical structure morphogenesis|mRNA processing	nucleus	nucleotide binding|RNA binding			skin(1)	1						GTTGGAAAGATGCAGAGTGGC	0.368000													49	62					0	0	1	0	0
OGT	8473	broad.mit.edu	37	X	70767813	70767813	+	Missense_Mutation	SNP	T	G	G			TCGA-HT-7879-01A-11D-2395-08	TCGA-HT-7879-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	2d315e0c-c20e-4f62-ae8b-42bdd9dbe053	826113c1-03bb-49be-82f0-e1dd43ec6cbc	g.chrX:70767813T>G	uc004eaa.1	+	5	805	c.588T>G	c.(586-588)AAT>AAG	p.N196K	BCYRN1_uc011mpt.1_Intron|OGT_uc004eab.1_Missense_Mutation_p.N186K|OGT_uc004eac.2_Missense_Mutation_p.N57K|OGT_uc004ead.2_5'UTR	NM_181672	NP_858058	O15294	OGT1_HUMAN	O-linked GlcNAc transferase isoform 1	196	TPR 5.				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	cytosol|MLL5-L complex	enzyme activator activity|protein binding|protein N-acetylglucosaminyltransferase activity			ovary(3)|kidney(1)|pancreas(1)	5	Renal(35;0.156)					CTTGGAGTAATCTTGGCTGTG	0.378000													73	9					0	0	1	0	0
ROBO3	64221	broad.mit.edu	37	11	124750448	124750453	+	In_Frame_Del	DEL	CGGAGT	-	-	rs71859853		TCGA-HT-7879-01A-11D-2395-08	TCGA-HT-7879-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	2d315e0c-c20e-4f62-ae8b-42bdd9dbe053	826113c1-03bb-49be-82f0-e1dd43ec6cbc	g.chr11:124750448_124750453delCGGAGT	uc001qbc.2	+	27	4285_4290	c.4093_4098delCGGAGT	c.(4093-4098)CGGAGTdel	p.RS1367del	ROBO3_uc001qbd.2_In_Frame_Del_p.RS292del|ROBO3_uc010sar.1_In_Frame_Del_p.RS416del|ROBO3_uc001qbe.2_In_Frame_Del_p.RS292del|ROBO3_uc001qbf.1_In_Frame_Del_p.RS251del	NM_022370	NP_071765	Q96MS0	ROBO3_HUMAN	roundabout, axon guidance receptor, homolog 3	1367_1368	Cytoplasmic (Potential).				axon midline choice point recognition	integral to membrane	receptor activity			breast(1)|central_nervous_system(1)	2	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	0.519													5	3	---	---	---	---					
TP53	7157	broad.mit.edu	37	17	7577150	7577151	+	Frame_Shift_Del	DEL	TT	-	-	rs72661119		TCGA-HT-7879-01A-11D-2395-08	TCGA-HT-7879-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	2d315e0c-c20e-4f62-ae8b-42bdd9dbe053	826113c1-03bb-49be-82f0-e1dd43ec6cbc	g.chr17:7577150_7577151delTT	uc002gim.2	-	8	981_982	c.787_788delAA	c.(787-789)AATfs	p.N263fs	TP53_uc002gig.1_Intron|TP53_uc002gih.2_Frame_Shift_Del_p.N263fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Frame_Shift_Del_p.N131fs|TP53_uc010cng.1_Frame_Shift_Del_p.N131fs|TP53_uc002gii.1_Frame_Shift_Del_p.N131fs|TP53_uc010cnh.1_Frame_Shift_Del_p.N263fs|TP53_uc010cni.1_Frame_Shift_Del_p.N263fs|TP53_uc002gij.2_Frame_Shift_Del_p.N263fs	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	263	|Interaction with E4F1.|Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		GN -> PD (in a sporadic cancer; somatic mutation).|N -> S (in a sporadic cancer; somatic mutation).|N -> K (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).		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 drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|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|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|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|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.0?(7)|p.N263fs*82(3)|p.?(3)|p.G262_F270delGNLLGRNSF(2)|p.N263D(2)|p.N263I(2)|p.G262_S269delGNLLGRNS(2)|p.N263H(2)|p.E258fs*71(1)|p.S261_L264>R(1)|p.N263fs*84(1)|p.N263K(1)|p.G262fs*2(1)		large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	22245		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	Hereditary_Adrenocortical_Cancer|Endometrial_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|Li-Fraumeni_syndrome|Osteosarcoma_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	-	-			TCGA-HT-7879-01A-11D-2395-08	TCGA-HT-7879-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	2d315e0c-c20e-4f62-ae8b-42bdd9dbe053	826113c1-03bb-49be-82f0-e1dd43ec6cbc	g.chrX:76938001delG	uc004ecp.3	-	9	2979	c.2747delC	c.(2746-2748)GCTfs	p.A916fs	ATRX_uc004ecq.3_Frame_Shift_Del_p.A878fs|ATRX_uc004eco.3_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	transcriptional regulator ATRX isoform 1	916					DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent	nuclear heterochromatin	ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1)	30					Phosphatidylserine(DB00144)	ATCAGTGGAAGCACTTGCTTG	0.418			Mis|F|N		Pancreatic neuroendocrine tumors		ATR-X (alpha thalassemia/mental retardation) syndrome						122	35	---	---	---	---					
