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
MALT1	10892	broad.mit.edu	37	18	56363642	56363642	+	Missense_Mutation	SNP	G	G	A			TCGA-P5-A735-01A-11D-A32B-08	TCGA-P5-A735-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28480ed8-d453-475f-a928-b02e55a6cb6e	a23c762e-4fd9-4110-9ee0-405694453b4f	g.chr18:56363642G>A	ENST00000348428.3	+	3	679	c.421G>A	c.(421-423)Gga>Aga	p.G141R	RP11-126O1.4_ENST00000588835.1_RNA|MALT1_ENST00000345724.3_Missense_Mutation_p.G141R	NM_006785.2|NM_173844.1	NP_006776.1|NP_776216.1	Q9UDY8	MALT1_HUMAN	mucosa associated lymphoid tissue lymphoma translocation gene 1	141	Ig-like C2-type 1.				activation of NF-kappaB-inducing kinase activity|anti-apoptosis|nuclear export|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-2 production|positive regulation of NF-kappaB transcription factor activity|positive regulation of phosphorylation|positive regulation of protein ubiquitination|positive regulation of T cell cytokine production|protein oligomerization|proteolysis|T cell receptor signaling pathway	CBM complex|cytosol|nucleus|perinuclear region of cytoplasm	cysteine-type endopeptidase activity|protein self-association|signal transducer activity|ubiquitin-protein ligase activity			central_nervous_system(1)|large_intestine(7)|lung(1)|ovary(2)|skin(1)	12						AGTCTTGGCTGGACAGTTTGT	0.313000			T	BIRC3	MALT								3	41					0	0	1	0	0
TP53	7157	broad.mit.edu	37	17	7579699	7579699	+	Splice_Site	SNP	C	C	T			TCGA-P5-A735-01A-11D-A32B-08	TCGA-P5-A735-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28480ed8-d453-475f-a928-b02e55a6cb6e	a23c762e-4fd9-4110-9ee0-405694453b4f	g.chr17:7579699C>T	ENST00000420246.2	-	3	229		c.e3+1		TP53_ENST00000445888.2_Splice_Site|TP53_ENST00000413465.2_Splice_Site|TP53_ENST00000455263.2_Splice_Site|TP53_ENST00000269305.4_Splice_Site|TP53_ENST00000359597.4_Splice_Site	NM_001126114.2|NM_001276696.1	NP_001119586.1|NP_001263625.1	P04637	P53_HUMAN	tumor protein p53						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|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|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 repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.?(11)|p.0?(8)|p.S33fs*10(1)|p.P13fs*18(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)		CTTGTCCTTACCAGAACGTTG	0.597000		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)			21	24					0	0	1	0	0
ELF4	2000	broad.mit.edu	37	X	129205311	129205311	+	Splice_Site	SNP	C	C	T			TCGA-P5-A735-01A-11D-A32B-08	TCGA-P5-A735-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28480ed8-d453-475f-a928-b02e55a6cb6e	a23c762e-4fd9-4110-9ee0-405694453b4f	g.chrX:129205311C>T	ENST00000308167.5	-	6	995	c.616_splice	c.e6+1	p.G206_splice	ELF4_ENST00000335997.7_Splice_Site_p.G206_splice	NM_001421.3	NP_001412.1	Q99607	ELF4_HUMAN	E74-like factor 4 (ets domain transcription factor)	206	RUNX1-binding.				natural killer cell proliferation|NK T cell proliferation|positive regulation of transcription from RNA polymerase II promoter	PML body	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	22						CTGTCCATACCTTTGCCATCC	0.612000			T	ERG	AML								10	23					0	0	1	0	0
CCDC110	256309	broad.mit.edu	37	4	186379853	186379853	+	Missense_Mutation	SNP	G	G	A			TCGA-P5-A735-01A-11D-A32B-08	TCGA-P5-A735-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28480ed8-d453-475f-a928-b02e55a6cb6e	a23c762e-4fd9-4110-9ee0-405694453b4f	g.chr4:186379853G>A	ENST00000307588.3	-	6	1963	c.1888C>T	c.(1888-1890)Ctt>Ttt	p.L630F	CCDC110_ENST00000393540.3_Missense_Mutation_p.L593F|CCDC110_ENST00000510617.1_Missense_Mutation_p.L630F	NM_152775.3	NP_689988.1	Q8TBZ0	CC110_HUMAN	coiled-coil domain containing 110	630						nucleus				NS(1)|breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(9)	30		all_lung(41;1.3e-11)|Lung NSC(41;2.25e-11)|Melanoma(20;7.86e-05)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|Colorectal(36;0.0381)|all_hematologic(60;0.0749)		OV - Ovarian serous cystadenocarcinoma(60;1.13e-10)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.00014)|STAD - Stomach adenocarcinoma(60;0.000777)|LUSC - Lung squamous cell carcinoma(40;0.00921)|COAD - Colon adenocarcinoma(29;0.0105)|READ - Rectum adenocarcinoma(43;0.164)		ATTTGAAGAAGTGTCTCTTGT	0.328000													24	67					0	0	1	0	0
SLC17A2	10246	broad.mit.edu	37	6	25921307	25921307	+	Silent	SNP	T	T	A			TCGA-P5-A735-01A-11D-A32B-08	TCGA-P5-A735-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28480ed8-d453-475f-a928-b02e55a6cb6e	a23c762e-4fd9-4110-9ee0-405694453b4f	g.chr6:25921307T>A	ENST00000377850.3	-	5	1013	c.489A>T	c.(487-489)acA>acT	p.T163T	SLC17A2_ENST00000360488.3_Silent_p.T163T|SLC17A2_ENST00000265425.3_Silent_p.T163T			O00624	NPT3_HUMAN	solute carrier family 17, member 2	163					phosphate metabolic process	integral to plasma membrane|membrane fraction	sodium:phosphate symporter activity			endometrium(3)|kidney(1)|large_intestine(9)|lung(12)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	31						TAAACTGACCTGTCCATGCCA	0.433000													13	22					0	0	1	0	0
IL36G	56300	broad.mit.edu	37	2	113742562	113742562	+	Missense_Mutation	SNP	T	T	A			TCGA-P5-A735-01A-11D-A32B-08	TCGA-P5-A735-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28480ed8-d453-475f-a928-b02e55a6cb6e	a23c762e-4fd9-4110-9ee0-405694453b4f	g.chr2:113742562T>A	ENST00000259205.4	+	5	515	c.446T>A	c.(445-447)aTc>aAc	p.I149N	IL36G_ENST00000376489.2_Missense_Mutation_p.I114N	NM_019618.2	NP_062564.1	Q9NZH8	IL36G_HUMAN	interleukin 36, gamma	149					cell-cell signaling	extracellular space	cytokine activity|interleukin-1 receptor antagonist activity			breast(1)|central_nervous_system(1)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)|skin(1)	14						GACCAGCCCATCATTCTGACT	0.488000													4	47					0	0	1	0	0
ARID1A	8289	broad.mit.edu	37	1	27101374	27101374	+	Silent	SNP	G	G	A			TCGA-P5-A735-01A-11D-A32B-08	TCGA-P5-A735-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28480ed8-d453-475f-a928-b02e55a6cb6e	a23c762e-4fd9-4110-9ee0-405694453b4f	g.chr1:27101374G>A	ENST00000324856.7	+	18	5027	c.4656G>A	c.(4654-4656)caG>caA	p.Q1552Q	ARID1A_ENST00000540690.1_Intron|ARID1A_ENST00000374152.2_Silent_p.Q1169Q|ARID1A_ENST00000457599.2_Intron	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1552					androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent	nBAF complex|npBAF complex|SWI/SNF complex	DNA binding|protein binding		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		GCACACGCCAGCCCCCATATG	0.597000			"""Mis, N, F, S, D"""		"""clear cell ovarian carcinoma, RCC"""								10	13					0	0	1	0	0
RP11-156P1.3	0	broad.mit.edu	37	17	45128792	45128792	+	RNA	SNP	G	G	T	rs143713325	by1000genomes	TCGA-P5-A735-01A-11D-A32B-08	TCGA-P5-A735-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28480ed8-d453-475f-a928-b02e55a6cb6e	a23c762e-4fd9-4110-9ee0-405694453b4f	g.chr17:45128792G>T	ENST00000575173.1	-	0	418																											AATTCAGGTTGTCAGAATGCA	0.373000													3	54					0.115264	0.115264	1	1	0
TACC2	10579	broad.mit.edu	37	10	123843843	123843843	+	Missense_Mutation	SNP	G	G	C			TCGA-P5-A735-01A-11D-A32B-08	TCGA-P5-A735-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28480ed8-d453-475f-a928-b02e55a6cb6e	a23c762e-4fd9-4110-9ee0-405694453b4f	g.chr10:123843843G>C	ENST00000369005.1	+	4	2168	c.1828G>C	c.(1828-1830)Gta>Cta	p.V610L	TACC2_ENST00000334433.3_Missense_Mutation_p.V610L|TACC2_ENST00000358010.1_Intron|TACC2_ENST00000515603.1_Missense_Mutation_p.V610L|TACC2_ENST00000515273.1_Missense_Mutation_p.V610L|TACC2_ENST00000513429.1_Intron|TACC2_ENST00000453444.2_Missense_Mutation_p.V610L	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	610						microtubule organizing center|nucleus	nuclear hormone receptor binding			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				TGATCCAGAAGTAGGCAAAGA	0.572000													13	19					0	0	1	0	0
CTD-2207O23.3	0	broad.mit.edu	37	19	7531821	7531821	+	Missense_Mutation	SNP	G	G	A	rs79986215	byFrequency	TCGA-P5-A735-01A-11D-A32B-08	TCGA-P5-A735-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28480ed8-d453-475f-a928-b02e55a6cb6e	a23c762e-4fd9-4110-9ee0-405694453b4f	g.chr19:7531821G>A	ENST00000593531.1	+	17	2231	c.2231G>A	c.(2230-2232)cGg>cAg	p.R744Q	ARHGEF18_ENST00000359920.6_Silent_p.T786T|ARHGEF18_ENST00000319670.9_Silent_p.T628T																							CGCCAGGCACGGAATCCGATC	0.627000													37	52					0	0	1	0	0
OTOF	9381	broad.mit.edu	37	2	26684997	26684997	+	Missense_Mutation	SNP	C	C	T			TCGA-P5-A735-01A-11D-A32B-08	TCGA-P5-A735-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28480ed8-d453-475f-a928-b02e55a6cb6e	a23c762e-4fd9-4110-9ee0-405694453b4f	g.chr2:26684997C>T	ENST00000272371.2	-	42	5371	c.5245G>A	c.(5245-5247)Gac>Aac	p.D1749N	OTOF_ENST00000339598.3_Missense_Mutation_p.D982N|OTOF_ENST00000338581.6_Missense_Mutation_p.D982N|OTOF_ENST00000403946.3_Missense_Mutation_p.D1749N|OTOF_ENST00000402415.3_Missense_Mutation_p.D1059N	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin	1749					cellular membrane fusion|sensory perception of sound|synaptic vesicle exocytosis	basolateral plasma membrane|cell junction|cytosol|endoplasmic reticulum membrane|integral to membrane|membrane fraction|synaptic vesicle membrane	calcium ion binding			NS(1)|autonomic_ganglia(1)|breast(9)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(35)|ovary(8)|pancreas(1)|prostate(5)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	106	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AAGAAGTCGTCGTCCTCCAAG	0.607000													6	127					0	0	1	0	0
SLC11A1	6556	broad.mit.edu	37	2	219251432	219251432	+	Silent	SNP	G	G	A			TCGA-P5-A735-01A-11D-A32B-08	TCGA-P5-A735-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28480ed8-d453-475f-a928-b02e55a6cb6e	a23c762e-4fd9-4110-9ee0-405694453b4f	g.chr2:219251432G>A	ENST00000233202.6	+	5	808	c.468G>A	c.(466-468)acG>acA	p.T156T	SLC11A1_ENST00000539932.1_Silent_p.T38T	NM_000578.3	NP_000569.3	P49279	NRAM1_HUMAN	solute carrier family 11 (proton-coupled divalent metal ion transporter), member 1	156					activation of protein kinase activity|antigen processing and presentation of peptide antigen|cadmium ion transmembrane transport|cellular cadmium ion homeostasis|cellular iron ion homeostasis|defense response to Gram-negative bacterium|defense response to protozoan|divalent metal ion export|inflammatory response|interleukin-2 production|interleukin-3 production|iron ion transport|L-arginine import|macrophage activation|MHC class II biosynthetic process|mRNA stabilization|multicellular organismal iron ion homeostasis|negative regulation of cytokine production|nitrite transport|phagocytosis|positive regulation of dendritic cell antigen processing and presentation|positive regulation of interferon-gamma production|positive regulation of phagocytosis|positive regulation of T-helper 1 type immune response|positive regulation of transcription from RNA polymerase II promoter|respiratory burst|response to interferon-gamma|response to lipopolysaccharide|T cell cytokine production|T cell proliferation involved in immune response|vacuolar acidification|wound healing	integral to plasma membrane|late endosome membrane|lysosome|phagocytic vesicle membrane|tertiary granule membrane	manganese ion transmembrane transporter activity|metal ion:hydrogen antiporter activity|protein homodimerization activity			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	19		Renal(207;0.0474)		Epithelial(149;1.16e-06)|all cancers(144;0.000195)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TCATCGGCACGGCCATTGCAT	0.582000													11	14					0	0	1	0	0
FAT1	2195	broad.mit.edu	37	4	187532792	187532792	+	Missense_Mutation	SNP	C	C	T			TCGA-P5-A735-01A-11D-A32B-08	TCGA-P5-A735-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28480ed8-d453-475f-a928-b02e55a6cb6e	a23c762e-4fd9-4110-9ee0-405694453b4f	g.chr4:187532792C>T	ENST00000441802.2	-	14	9810	c.9601G>A	c.(9601-9603)Gct>Act	p.A3201T		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	3201	Cadherin 29.				actin filament organization|anatomical structure morphogenesis|cell migration|cell-cell signaling|establishment or maintenance of cell polarity|homophilic cell adhesion	cell-cell junction|integral to plasma membrane|nucleus|perinuclear region of cytoplasm	calcium ion binding|protein binding			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						TGATCCACAGCTTTCAAAGAG	0.453000										HNSCC(5;0.00058)			4	12					0	0	1	0	0
PLEKHA4	0	broad.mit.edu	37	19	49348627	49348627	+	Splice_Site	SNP	C	C	G			TCGA-P5-A735-01A-11D-A32B-08	TCGA-P5-A735-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28480ed8-d453-475f-a928-b02e55a6cb6e	a23c762e-4fd9-4110-9ee0-405694453b4f	g.chr19:49348627C>G	ENST00000263265.6	-	16	2298	c.1743_splice	c.e16+1	p.K581_splice	PLEKHA4_ENST00000355496.5_Splice_Site_p.K556_splice	NM_020904.2	NP_065955.2	Q9H4M7	PKHA4_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 4	581						cytoplasm|membrane	1-phosphatidylinositol binding			NS(1)|breast(5)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(3)|skin(2)|urinary_tract(2)	30		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;0.000108)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.00027)|all cancers(93;0.00084)|GBM - Glioblastoma multiforme(486;0.0244)|Epithelial(262;0.0364)		TACAGCTTACCTTGGTTCCTA	0.572000													19	34					0	0	1	0	0
IDH1	3417	broad.mit.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-P5-A735-01A-11D-A32B-08	TCGA-P5-A735-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28480ed8-d453-475f-a928-b02e55a6cb6e	a23c762e-4fd9-4110-9ee0-405694453b4f	g.chr2:209113112C>T	ENST00000415913.1	-	4	776	c.395G>A	c.(394-396)cGt>cAt	p.R132H	IDH1_ENST00000446179.1_Missense_Mutation_p.R132H|IDH1_ENST00000345146.2_Missense_Mutation_p.R132H			O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	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|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(2774)|p.R132L(59)|p.R132V(1)|p.G131_R132>VL(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								25	26					0	0	1	0	0
CNTN4	152330	broad.mit.edu	37	3	3084667	3084667	+	Missense_Mutation	SNP	T	T	A			TCGA-P5-A735-01A-11D-A32B-08	TCGA-P5-A735-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28480ed8-d453-475f-a928-b02e55a6cb6e	a23c762e-4fd9-4110-9ee0-405694453b4f	g.chr3:3084667T>A	ENST00000397461.1	+	21	2902	c.2518T>A	c.(2518-2520)Tat>Aat	p.Y840N	CNTN4_ENST00000397459.2_Missense_Mutation_p.Y512N|CNTN4_ENST00000448906.2_Missense_Mutation_p.Y512N|CNTN4_ENST00000418658.1_Missense_Mutation_p.Y840N|CNTN4_ENST00000427331.1_Missense_Mutation_p.Y840N|CNTN4-AS1_ENST00000442749.2_RNA|CNTN4_ENST00000358480.3_Missense_Mutation_p.Y621N	NM_001206955.1	NP_001193884.1	Q8IWV2	CNTN4_HUMAN	contactin 4	840	Fibronectin type-III 3.				axon guidance|axonal fasciculation|brain development|negative regulation of neuron differentiation|neuron cell-cell adhesion|regulation of synaptic plasticity	anchored to membrane|axon|extracellular region|plasma membrane	protein binding			NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(19)|ovary(2)|pancreas(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		Ovarian(110;0.156)		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)		TTAGGTTAAATATTGGAGACA	0.353000													13	23					0	0	1	0	0
SPTA1	6708	broad.mit.edu	37	1	158641928	158641928	+	Missense_Mutation	SNP	C	C	T			TCGA-P5-A735-01A-11D-A32B-08	TCGA-P5-A735-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28480ed8-d453-475f-a928-b02e55a6cb6e	a23c762e-4fd9-4110-9ee0-405694453b4f	g.chr1:158641928C>T	ENST00000368148.3	-	11	1589	c.1409G>A	c.(1408-1410)cGt>cAt	p.R470H	SPTA1_ENST00000368147.3_Missense_Mutation_p.R470H	NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1 (elliptocytosis 2)	470					actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					CTCATACTGACGATGACGCTC	0.453000													31	23					0	0	1	0	0
TP53	7157	broad.mit.edu	37	17	7577096	7577096	+	Missense_Mutation	SNP	T	T	A			TCGA-P5-A735-01A-11D-A32B-08	TCGA-P5-A735-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28480ed8-d453-475f-a928-b02e55a6cb6e	a23c762e-4fd9-4110-9ee0-405694453b4f	g.chr17:7577096T>A	ENST00000420246.2	-	8	974	c.842A>T	c.(841-843)gAc>gTc	p.D281V	TP53_ENST00000445888.2_Missense_Mutation_p.D281V|TP53_ENST00000413465.2_Intron|TP53_ENST00000455263.2_Missense_Mutation_p.D281V|TP53_ENST00000269305.4_Missense_Mutation_p.D281V|TP53_ENST00000359597.4_Missense_Mutation_p.D281V	NM_001126114.2|NM_001276696.1	NP_001119586.1|NP_001263625.1	P04637	P53_HUMAN	tumor protein p53	281	Interaction with AXIN1 (By similarity).|Interaction with E4F1.|Interaction with HIPK1 (By similarity).		D -> A (in sporadic cancers; somatic mutation).|D -> E (in sporadic cancers; somatic mutation).|D -> G (in a brain tumor with no family history; germline mutation and in sporadic cancers; somatic mutation).|D -> H (in sporadic cancers; somatic mutation).|D -> N (in LFS; germline mutation and in sporadic cancers; somatic mutation).|D -> R (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|D -> V (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).|D -> Y (in sporadic cancers; somatic mutation).|DR -> EW (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|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|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 repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.D281G(10)|p.0?(8)|p.D281V(5)|p.?(2)|p.D281fs*63(2)|p.R280_D281delRD(2)|p.D281A(2)|p.D281>AGPY(2)|p.A276_R283delACPGRDRR(1)|p.D281R(1)|p.C275fs*20(1)|p.L265_K305del41(1)|p.D281_R282delDR(1)|p.F270_D281del12(1)|p.G279fs*59(1)|p.R280fs*62(1)|p.S269fs*21(1)|p.V272_K292del21(1)|p.C275_R283delCACPGRDRR(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)		TGTGCGCCGGTCTCTCCCAGG	0.552000		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)			10	26					0	0	1	0	0
PLEKHO2	80301	broad.mit.edu	37	15	65157873	65157873	+	Missense_Mutation	SNP	C	C	T			TCGA-P5-A735-01A-11D-A32B-08	TCGA-P5-A735-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28480ed8-d453-475f-a928-b02e55a6cb6e	a23c762e-4fd9-4110-9ee0-405694453b4f	g.chr15:65157873C>T	ENST00000323544.4	+	6	1387	c.1259C>T	c.(1258-1260)tCg>tTg	p.S420L	AC069368.3_ENST00000437723.1_Intron	NM_001195059.1|NM_025201.4	NP_001181988.1|NP_079477.2	Q8TD55	PKHO2_HUMAN	pleckstrin homology domain containing, family O member 2	420										NS(1)|breast(1)|cervix(3)|endometrium(1)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	25						AAGGTGGCCTCGGAACAGACG	0.632000													3	14					0	0	1	0	0
ADAMTS19	171019	broad.mit.edu	37	5	128862012	128862012	+	Missense_Mutation	SNP	A	A	G			TCGA-P5-A735-01A-11D-A32B-08	TCGA-P5-A735-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28480ed8-d453-475f-a928-b02e55a6cb6e	a23c762e-4fd9-4110-9ee0-405694453b4f	g.chr5:128862012A>G	ENST00000274487.4	+	4	1076	c.931A>G	c.(931-933)Agt>Ggt	p.S311G	CTC-575N7.1_ENST00000503616.1_RNA	NM_133638.3	NP_598377.3	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 19	311					proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			NS(1)|breast(4)|endometrium(10)|kidney(9)|large_intestine(14)|lung(34)|ovary(6)|pancreas(1)|prostate(6)|skin(6)	91		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.222)		AATAGCAGAAAGTGGAAGAGG	0.363000													21	22					0	0	1	0	0
L1CAM	3897	broad.mit.edu	37	X	153133835	153133835	+	Missense_Mutation	SNP	G	G	A			TCGA-P5-A735-01A-11D-A32B-08	TCGA-P5-A735-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28480ed8-d453-475f-a928-b02e55a6cb6e	a23c762e-4fd9-4110-9ee0-405694453b4f	g.chrX:153133835G>A	ENST00000370060.1	-	14	1814	c.1625C>T	c.(1624-1626)tCc>tTc	p.S542F	L1CAM_ENST00000361699.4_Missense_Mutation_p.S542F|L1CAM_ENST00000543994.1_Missense_Mutation_p.S544F|L1CAM_ENST00000538883.1_Missense_Mutation_p.S544F|L1CAM_ENST00000361981.3_Missense_Mutation_p.S537F|L1CAM_ENST00000370055.1_Missense_Mutation_p.S537F|L1CAM_ENST00000370057.3_Missense_Mutation_p.S542F	NM_001278116.1	NP_001265045.1	P32004	L1CAM_HUMAN	L1 cell adhesion molecule	542	Ig-like C2-type 6.		S -> P (in HSAS).		axon guidance|blood coagulation|cell death|leukocyte migration	integral to membrane				NS(1)|breast(4)|central_nervous_system(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|liver(1)|lung(31)|ovary(13)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	81	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					GGGGTCAAAGGAGGCCTGGCA	0.602000													72	108					0	0	1	0	0
CEBPZ	10153	broad.mit.edu	37	2	37447581	37447581	+	Missense_Mutation	SNP	T	T	C			TCGA-P5-A735-01A-11D-A32B-08	TCGA-P5-A735-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28480ed8-d453-475f-a928-b02e55a6cb6e	a23c762e-4fd9-4110-9ee0-405694453b4f	g.chr2:37447581T>C	ENST00000234170.5	-	5	2246	c.2101A>G	c.(2101-2103)Aga>Gga	p.R701G		NM_005760.2	NP_005751.2	Q03701	CEBPZ_HUMAN	CCAAT/enhancer binding protein (C/EBP), zeta	701					regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	DNA binding			breast(3)|endometrium(2)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28		all_hematologic(82;0.21)				AGAGGGTTTCTACTGAATGGA	0.308000													8	13					0	0	1	0	0
LBP	3929	broad.mit.edu	37	20	36993276	36993276	+	Missense_Mutation	SNP	C	C	T			TCGA-P5-A735-01A-11D-A32B-08	TCGA-P5-A735-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28480ed8-d453-475f-a928-b02e55a6cb6e	a23c762e-4fd9-4110-9ee0-405694453b4f	g.chr20:36993276C>T	ENST00000217407.2	+	8	952	c.791C>T	c.(790-792)gCt>gTt	p.A264V		NM_004139.3	NP_004130.2	P18428	LBP_HUMAN	lipopolysaccharide binding protein	264					acute-phase response|cellular defense response|cellular response to lipoteichoic acid|defense response to Gram-negative bacterium|defense response to Gram-positive bacterium|detection of molecule of bacterial origin|innate immune response|lipid transport|lipopolysaccharide transport|lipopolysaccharide-mediated signaling pathway|macrophage activation involved in immune response|negative regulation of tumor necrosis factor production|opsonization|positive regulation of interleukin-6 production|positive regulation of interleukin-8 production|positive regulation of macrophage activation|positive regulation of respiratory burst involved in inflammatory response|positive regulation of toll-like receptor 4 signaling pathway|positive regulation of tumor necrosis factor production|Toll signaling pathway	extracellular space	Gram-negative bacterial cell surface binding|Gram-positive bacterial cell surface binding|lipid binding|lipopolysaccharide binding|lipoteichoic acid binding|receptor binding			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(16)|ovary(2)|prostate(1)|urinary_tract(1)	28		Myeloproliferative disorder(115;0.00878)				ACCCTCCTTGCTGCAGTCATG	0.488000													57	66					0	0	1	0	0
AGBL2	79841	broad.mit.edu	37	11	47731973	47731973	+	Missense_Mutation	SNP	T	T	C			TCGA-P5-A735-01A-11D-A32B-08	TCGA-P5-A735-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28480ed8-d453-475f-a928-b02e55a6cb6e	a23c762e-4fd9-4110-9ee0-405694453b4f	g.chr11:47731973T>C	ENST00000525123.1	-	4	473	c.188A>G	c.(187-189)aAa>aGa	p.K63R	AGBL2_ENST00000528244.1_Missense_Mutation_p.K63R|AGBL2_ENST00000357610.3_Missense_Mutation_p.K63R|AGBL2_ENST00000529712.1_5'UTR|AGBL2_ENST00000298861.4_Missense_Mutation_p.K63R	NM_024783.3	NP_079059.2	Q5U5Z8	CBPC2_HUMAN	ATP/GTP binding protein-like 2	63					proteolysis	cytosol	metallocarboxypeptidase activity|zinc ion binding			NS(1)|endometrium(5)|kidney(1)|large_intestine(8)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(1)	34						CAAATCATCTTTTTCCCCAAG	0.433000													7	120					0	0	1	0	0
USP6	9098	broad.mit.edu	37	17	5066179	5066179	+	Splice_Site	SNP	A	A	G			TCGA-P5-A735-01A-11D-A32B-08	TCGA-P5-A735-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28480ed8-d453-475f-a928-b02e55a6cb6e	a23c762e-4fd9-4110-9ee0-405694453b4f	g.chr17:5066179A>G	ENST00000574788.1	+	33	5146	c.2915_splice	c.e33-1	p.R972_splice	USP6_ENST00000332776.4_3'UTR|USP6_ENST00000304328.5_Splice_Site_p.R655_splice|USP6_ENST00000250066.6_Splice_Site_p.R972_splice			P35125	UBP6_HUMAN	ubiquitin specific peptidase 6 (Tre-2 oncogene)	972					protein deubiquitination|regulation of vesicle-mediated transport|ubiquitin-dependent protein catabolic process	lysosome|plasma membrane|recycling endosome	calmodulin binding|cysteine-type endopeptidase activity|nucleic acid binding|protein binding|Rab GTPase activator activity|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	34						CCCTTTTTAGATTTTGCAGAG	0.388000			T	"""COL1A1, CDH11, ZNF9, OMD"""	aneurysmal bone cysts								5	159					0	0	1	0	0
TMEM19	55266	broad.mit.edu	37	12	72094726	72094726	+	Missense_Mutation	SNP	T	T	C			TCGA-P5-A735-01A-11D-A32B-08	TCGA-P5-A735-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28480ed8-d453-475f-a928-b02e55a6cb6e	a23c762e-4fd9-4110-9ee0-405694453b4f	g.chr12:72094726T>C	ENST00000266673.5	+	6	1556	c.962T>C	c.(961-963)aTt>aCt	p.I321T		NM_018279.3	NP_060749.2	Q96HH6	TMM19_HUMAN	transmembrane protein 19	321						integral to membrane				large_intestine(1)|lung(8)	9		Breast(359;0.0889)		GBM - Glioblastoma multiforme(134;0.044)		TCTGTTCTTATTGCCCTCTTG	0.463000													94	111					0	0	1	0	0
MEX3A	92312	broad.mit.edu	37	1	156046687	156046689	+	In_Frame_Del	DEL	GAG	GAG	-			TCGA-P5-A735-01A-11D-A32B-08	TCGA-P5-A735-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28480ed8-d453-475f-a928-b02e55a6cb6e	a23c762e-4fd9-4110-9ee0-405694453b4f	g.chr1:156046687_156046689delGAG	ENST00000532414.2	-	2	1238_1240	c.1239_1241delCTC	c.(1237-1242)tct>tc	p.SS413del		NM_001093725.1	NP_001087194.1	A1L020	MEX3A_HUMAN	mex-3 RNA binding family member A	413	Poly-Ser.					cytoplasmic mRNA processing body|nucleus	RNA binding|zinc ion binding			endometrium(2)|kidney(1)|large_intestine(3)|lung(3)	9	Hepatocellular(266;0.158)|all_neural(408;0.195)					CTTGGCggaagaggaggaggagg	0.744													2	4	---	---	---	---					
COLQ	8292	broad.mit.edu	37	3	15516986	15516986	+	Frame_Shift_Del	DEL	T	T	-			TCGA-P5-A735-01A-11D-A32B-08	TCGA-P5-A735-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28480ed8-d453-475f-a928-b02e55a6cb6e	a23c762e-4fd9-4110-9ee0-405694453b4f	g.chr3:15516986delT	ENST00000383785.2	-	7	599	c.474delA	c.(472-474)aafs	p.K158fs	COLQ_ENST00000383781.4_Frame_Shift_Del_p.K148fs|COLQ_ENST00000603808.1_Frame_Shift_Del_p.K158fs|COLQ_ENST00000435459.2_Frame_Shift_Del_p.K148fs|COLQ_ENST00000383786.5_Frame_Shift_Del_p.K124fs|COLQ_ENST00000383787.2_Frame_Shift_Del_p.K149fs|COLQ_ENST00000383788.5_Frame_Shift_Del_p.K158fs			Q9Y215	COLQ_HUMAN	collagen-like tail subunit (single strand of homotrimer) of asymmetric acetylcholinesterase	158	Collagen-like 1.				acetylcholine catabolic process in synaptic cleft|asymmetric protein localization	basal lamina|cell junction|collagen|extracellular space|synaptic cleft				endometrium(2)|large_intestine(4)|lung(10)|skin(3)	19						CCAGGTCACCTTTTTCACCCT	0.507													2	4	---	---	---	---					
KIFC1	3833	broad.mit.edu	37	6	33372952	33372953	+	Frame_Shift_Del	DEL	GA	GA	-			TCGA-P5-A735-01A-11D-A32B-08	TCGA-P5-A735-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28480ed8-d453-475f-a928-b02e55a6cb6e	a23c762e-4fd9-4110-9ee0-405694453b4f	g.chr6:33372952_33372953delGA	ENST00000428849.2	+	7	1530_1531	c.1080_1081delGA	c.(1078-1083)ctgtfs	p.LS360fs		NM_002263.3	NP_002254.2	Q9BW19	KIFC1_HUMAN	kinesin family member C1	360	Kinesin-motor.				blood coagulation|cell division|microtubule-based movement|mitotic sister chromatid segregation	early endosome|microtubule|microtubule associated complex|microtubule organizing center|nucleus|spindle	ATP binding|microtubule motor activity			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(3)|skin(1)	13						GTGGGACCCTGAGTGGGGCACC	0.609													55	60	---	---	---	---					
INSIG1	3638	broad.mit.edu	37	7	155090103	155090105	+	In_Frame_Del	DEL	GAT	GAT	-			TCGA-P5-A735-01A-11D-A32B-08	TCGA-P5-A735-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28480ed8-d453-475f-a928-b02e55a6cb6e	a23c762e-4fd9-4110-9ee0-405694453b4f	g.chr7:155090103_155090105delGAT	ENST00000340368.4	+	2	319_321	c.108_110delGAT	c.(106-111)gag>ga	p.EM36del	INSIG1_ENST00000344756.4_Intron|INSIG1_ENST00000342407.5_In_Frame_Del_p.EM36del	NM_005542.4	NP_005533.2	O15503	INSI1_HUMAN	insulin induced gene 1	36					cell proliferation|ER-nuclear sterol response pathway	endoplasmic reticulum membrane|integral to membrane	protein binding			endometrium(2)|kidney(2)|large_intestine(1)|lung(11)|prostate(1)|upper_aerodigestive_tract(2)	19	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.011)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		AGGTTGGGGAGATGATCAACGTT	0.744													4	3	---	---	---	---					
SPON1	10418	broad.mit.edu	37	11	14284600	14284600	+	RNA	DEL	A	A	-	rs79477301		TCGA-P5-A735-01A-11D-A32B-08	TCGA-P5-A735-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28480ed8-d453-475f-a928-b02e55a6cb6e	a23c762e-4fd9-4110-9ee0-405694453b4f	g.chr11:14284600delA	ENST00000310358.7	+	0	2795				RP11-21L19.1_ENST00000534587.1_RNA			Q9HCB6	SPON1_HUMAN	spondin 1, extracellular matrix protein						cell adhesion	extracellular space|proteinaceous extracellular matrix	protein binding			NS(1)|endometrium(1)|large_intestine(5)|lung(11)|prostate(2)|upper_aerodigestive_tract(1)	21				Epithelial(150;0.00898)		GGACCTGTTTaaaaaaaaaaa	0.463													3	4	---	---	---	---					
MKRN3	7681	broad.mit.edu	37	15	23811405	23811405	+	Frame_Shift_Del	DEL	C	C	-			TCGA-P5-A735-01A-11D-A32B-08	TCGA-P5-A735-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28480ed8-d453-475f-a928-b02e55a6cb6e	a23c762e-4fd9-4110-9ee0-405694453b4f	g.chr15:23811405delC	ENST00000314520.3	+	1	952	c.476delC	c.(475-477)gcfs	p.A159fs	MKRN3_ENST00000568252.1_Intron|MKRN3_ENST00000564592.1_Intron	NM_005664.3	NP_005655.1	Q13064	MKRN3_HUMAN	makorin ring finger protein 3	159						ribonucleoprotein complex	ligase activity|nucleic acid binding|zinc ion binding			breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(33)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		all_cancers(20;8.44e-25)|all_epithelial(15;3.69e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000353)|Colorectal(260;0.14)		all cancers(64;3.02e-06)|Epithelial(43;1.94e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0012)		GTGGCGGAAGCCCCCCCGGCT	0.642													8	14	---	---	---	---					
FCGBP	8857	broad.mit.edu	37	19	40368644	40368644	+	Frame_Shift_Del	DEL	A	A	-			TCGA-P5-A735-01A-11D-A32B-08	TCGA-P5-A735-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28480ed8-d453-475f-a928-b02e55a6cb6e	a23c762e-4fd9-4110-9ee0-405694453b4f	g.chr19:40368644delA	ENST00000221347.6	-	28	12711	c.12704delT	c.(12703-12705)cgfs	p.L4235fs		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	4235	VWFD 10.					extracellular region	protein binding			NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			GGAGGGAGCCAGTGTGCCATT	0.642													28	81	---	---	---	---					
SEZ6L	23544	broad.mit.edu	37	22	26688782	26688783	+	Frame_Shift_Ins	INS	-	-	ACCCGGACCCC			TCGA-P5-A735-01A-11D-A32B-08	TCGA-P5-A735-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28480ed8-d453-475f-a928-b02e55a6cb6e	a23c762e-4fd9-4110-9ee0-405694453b4f	g.chr22:26688782_26688783insACCCGGACCCC	ENST00000529632.2	+	2	701_702	c.505_506insACCCGGACCCC	c.(505-507)cccfs	p.-168fs	SEZ6L_ENST00000402979.1_5'UTR|SEZ6L_ENST00000248933.6_Frame_Shift_Ins_p.-168fs|SEZ6L_ENST00000404234.3_Frame_Shift_Ins_p.-168fs|SEZ6L_ENST00000343706.4_Frame_Shift_Ins_p.-168fs|SEZ6L_ENST00000403121.1_5'UTR|SEZ6L_ENST00000360929.3_Frame_Shift_Ins_p.-168fs	NM_001184774.1|NM_001184775.1|NM_001184777.1	NP_001171703.1|NP_001171704.1|NP_001171706.1	Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like							endoplasmic reticulum membrane|integral to membrane				breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(35)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	80						CCCACCGGGGGACCCGGACCCC	0.668													11	40	---	---	---	---					
ATRX	546	broad.mit.edu	37	X	76940492	76940493	+	Frame_Shift_Ins	INS	-	-	G			TCGA-P5-A735-01A-11D-A32B-08	TCGA-P5-A735-10A-01D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28480ed8-d453-475f-a928-b02e55a6cb6e	a23c762e-4fd9-4110-9ee0-405694453b4f	g.chrX:76940492_76940493insG	ENST00000373344.5	-	8	814_815	c.600_601insC	c.(598-603)tgttaafs	p.*201fs	ATRX_ENST00000480283.1_5'UTR|ATRX_ENST00000395603.3_Frame_Shift_Ins_p.*163fs	NM_000489.3	NP_000480.2	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	201	ADD.				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	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)	TAATACTTAAAGCAATTCTATT	0.292			"""Mis, F, N"""		"""Pancreatic neuroendocrine tumors, paediatric GBM"""		ATR-X (alpha thalassemia/mental retardation) syndrome						63	78	---	---	---	---					
