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
KIAA0562	9731	broad.mit.edu	37	1	3768869	3768869	+	Missense_Mutation	SNP	G	A	A			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08									Somatic	Phase_I	Capture				Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr1:3768869G>A	uc001aky.2	-	2	462	c.103C>T	c.(103-105)CGG>TGG	p.R35W	KIAA0562_uc010nzm.1_RNA|KIAA0562_uc001akz.2_Missense_Mutation_p.R35W	NM_014704	NP_055519	O60308	CE104_HUMAN	glycine-, glutamate-,	35						centriole	binding				0	all_cancers(77;0.0395)|Ovarian(185;0.0634)|all_lung(157;0.222)|Lung NSC(156;0.227)	all_epithelial(116;3.96e-21)|all_lung(118;2.74e-08)|Lung NSC(185;6.4e-06)|Breast(487;0.00066)|Renal(390;0.00121)|Hepatocellular(190;0.00335)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.031)|Lung SC(97;0.0548)|Medulloblastoma(700;0.212)		Epithelial(90;6.85e-39)|OV - Ovarian serous cystadenocarcinoma(86;1.59e-22)|GBM - Glioblastoma multiforme(42;3.16e-16)|Colorectal(212;2.01e-05)|COAD - Colon adenocarcinoma(227;7.99e-05)|BRCA - Breast invasive adenocarcinoma(365;0.000389)|Kidney(185;0.000513)|STAD - Stomach adenocarcinoma(132;0.00709)|KIRC - Kidney renal clear cell carcinoma(229;0.00714)|Lung(427;0.137)		CTAGGTGACCGCCACCCACTG	0.622000													3	21					0	0	0.009096	0	0
ITLN1	55600	broad.mit.edu	37	1	160850421	160850421	+	Silent	SNP	G	A	A			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08									Somatic	Phase_I	Capture				Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr1:160850421G>A	uc001fxc.2	-	6	758	c.642C>T	c.(640-642)GGC>GGT	p.G214G		NM_017625	NP_060095	Q8WWA0	ITLN1_HUMAN	intelectin precursor	214	Fibrinogen C-terminal.				positive regulation of glucose import|positive regulation of protein phosphorylation|response to nematode|signal transduction	anchored to membrane|brush border membrane|extracellular region|membrane raft	receptor binding|sugar binding			ovary(2)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)|central_nervous_system(1)	7	all_cancers(52;2.99e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00737)			TCTGGGCGTCGCCAAAATCAT	0.443000													7	261					0	0	0.029380	0	0
NOS1	4842	broad.mit.edu	37	12	117669890	117669890	+	Silent	SNP	G	A	A			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08									Somatic	Phase_I	Capture				Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr12:117669890G>A	uc001twm.1	-	22	3968	c.3282C>T	c.(3280-3282)ACC>ACT	p.T1094T		NM_000620	NP_000611	P29475	NOS1_HUMAN	nitric oxide synthase 1, neuronal	1094	FAD-binding FR-type.				multicellular organismal response to stress|myoblast fusion|negative regulation of calcium ion transport into cytosol|neurotransmitter biosynthetic process|nitric oxide biosynthetic process|platelet activation|positive regulation of vasodilation|regulation of cardiac muscle contraction|response to heat|response to hypoxia	cytoskeleton|cytosol|dendritic spine|perinuclear region of cytoplasm|photoreceptor inner segment|sarcolemma|sarcoplasmic reticulum	arginine binding|cadmium ion binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|tetrahydrobiopterin binding			ovary(3)|skin(3)|pancreas(1)	7	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)	L-Citrulline(DB00155)	CCTGGAAGATGGTGCAGGGCG	0.592000													19	19					0	0	0.049695	0	0
SFRS9	8683	broad.mit.edu	37	12	120903592	120903592	+	Splice_Site	SNP	T	A	A			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08									Somatic	Phase_I	Capture				Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr12:120903592T>A	uc001tyi.2	-	2	335	c.189_splice	c.e2-1	p.R63_splice	SFRS9_uc009zwy.2_Intron	NM_003769	NP_003760	Q13242	SRSF9_HUMAN	splicing factor, arginine/serine-rich 9						mRNA 3'-end processing|mRNA export from nucleus|mRNA splice site selection|termination of RNA polymerase II transcription	nucleoplasm	nucleotide binding|RNA binding				0	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					TCTGCATCTCTAAAAAAAACA	0.453000													3	33					0	0	0.115264	0	0
NPAS3	64067	broad.mit.edu	37	14	34263252	34263252	+	Splice_Site	SNP	T	G	G			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08									Somatic	Phase_I	Capture				Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr14:34263252T>G	uc001wru.2	+	10	1365	c.1301_splice	c.e10+2	p.S434_splice	NPAS3_uc001wrs.2_Splice_Site_p.S421_splice|NPAS3_uc001wrt.2_Splice_Site_p.S402_splice|NPAS3_uc001wrv.2_Splice_Site_p.S404_splice	NM_173159	NP_071406	Q8IXF0	NPAS3_HUMAN	neuronal PAS domain protein 3 isoform 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity			ovary(1)|skin(1)	2	Breast(36;0.0102)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00968)	GBM - Glioblastoma multiforme(1;1.31e-09)|all cancers(1;0.000112)|OV - Ovarian serous cystadenocarcinoma(311;0.115)		CCTTCTTAGGTATATTTTCTA	0.333000													25	39					0	0	0.099896	0	0
JAG2	3714	broad.mit.edu	37	14	105615619	105615619	+	Silent	SNP	G	A	A			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08									Somatic	Phase_I	Capture				Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr14:105615619G>A	uc001yqg.2	-	13	2045	c.1641C>T	c.(1639-1641)AAC>AAT	p.N547N	JAG2_uc010axf.2_5'Flank|JAG2_uc001yqf.2_Translation_Start_Site|JAG2_uc001yqh.2_Silent_p.N509N	NM_002226	NP_002217	Q9Y219	JAG2_HUMAN	jagged 2 isoform a precursor	547	EGF-like 9.|Extracellular (Potential).				auditory receptor cell fate commitment|cell communication|cell cycle|Notch receptor processing|Notch signaling pathway|regulation of cell migration|regulation of cell proliferation|spermatogenesis|thymic T cell selection	integral to plasma membrane	calcium ion binding|growth factor activity|Notch binding			lung(3)|breast(2)	5		all_cancers(154;0.0336)|all_epithelial(191;0.0729)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00989)|all cancers(16;0.0114)|Epithelial(46;0.0272)	Epithelial(152;0.047)|OV - Ovarian serous cystadenocarcinoma(161;0.148)|all cancers(159;0.208)		AGCGAGCGCCGTTCCGGCAGG	0.662000													44	70					0	0	0.139131	0	0
ADAM6	8755	broad.mit.edu	37	14	107062359	107062359	+	RNA	SNP	G	T	T			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08									Somatic	Phase_I	Capture				Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr14:107062359G>T	uc010tyt.1	-	131		c.6236C>A								Parts of antibodies, mostly variable regions.												0						AGACAGCGCAGATGAGGGACA	0.607000													3	47					2.56e-06	2.90595e-06	0.009096	1	0
C16orf48	84080	broad.mit.edu	37	16	67700039	67700039	+	Missense_Mutation	SNP	C	T	T			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08									Somatic	Phase_I	Capture				Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr16:67700039C>T	uc002etw.1	-	2	498	c.215G>A	c.(214-216)CGC>CAC	p.R72H	C16orf48_uc002etv.1_5'Flank|C16orf48_uc010cem.1_Missense_Mutation_p.R72H|C16orf86_uc002etx.1_5'Flank|C16orf86_uc002ety.2_5'Flank|C16orf86_uc002etz.2_5'Flank	NM_032140	NP_115516	Q9H0I2	CP048_HUMAN	hypothetical protein LOC84080	72						microtubule cytoskeleton	protein binding				0		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0143)|Epithelial(162;0.047)|all cancers(182;0.228)		CCCGACGCCGCGCTGGCCGCG	0.662000													8	44					0	0	0.038147	0	0
NF1	4763	broad.mit.edu	37	17	29553697	29553697	+	Nonsense_Mutation	SNP	C	A	A			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08									Somatic	Phase_I	Capture				Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr17:29553697C>A	uc002hgg.2	+	18	2579	c.2246C>A	c.(2245-2247)TCA>TAA	p.S749*	NF1_uc002hgh.2_Nonsense_Mutation_p.S749*|NF1_uc010csn.1_Nonsense_Mutation_p.S609*|NF1_uc002hgi.1_5'UTR	NM_001042492	NP_001035957	P21359	NF1_HUMAN	neurofibromin isoform 1	749					actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity	p.?(2)|p.S749*(1)		soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	330		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		AATATGATGTCAACAGGTAAA	0.403000			D|Mis|N|F|S|O		neurofibroma|glioma	neurofibroma|glioma			Neurofibromatosis_type_1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			7	162					0.00198382	0.00213642	0.029380	1	0
NF1	4763	broad.mit.edu	37	17	29670155	29670155	+	Splice_Site	SNP	T	A	A			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08									Somatic	Phase_I	Capture				Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr17:29670155T>A	uc002hgg.2	+	48	7522	c.7189_splice	c.e48+2	p.G2397_splice	NF1_uc002hgh.2_Splice_Site_p.G2376_splice|NF1_uc010cso.2_Splice_Site_p.G585_splice|NF1_uc010wbt.1_Splice_Site|NF1_uc010wbu.1_Splice_Site	NM_001042492	NP_001035957	P21359	NF1_HUMAN	neurofibromin isoform 1						actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity			soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	330		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		TTTTAAAAGGTAAAAAAGCCT	0.318000			D|Mis|N|F|S|O		neurofibroma|glioma	neurofibroma|glioma			Neurofibromatosis_type_1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			6	34					0	0	0.021553	0	0
NT5C	30833	broad.mit.edu	37	17	73126675	73126675	+	Missense_Mutation	SNP	C	A	A			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08									Somatic	Phase_I	Capture				Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr17:73126675C>A	uc002jmx.2	-	5	589	c.514G>T	c.(514-516)GTC>TTC	p.V172F	NT5C_uc002jmy.2_RNA	NM_014595	NP_055410	Q8TCD5	NT5C_HUMAN	5',3'-nucleotidase, cytosolic	172					purine base metabolic process|purine nucleotide catabolic process|pyrimidine base metabolic process|pyrimidine deoxyribonucleotide catabolic process|pyrimidine nucleoside catabolic process	cytosol|nucleus	5'-nucleotidase activity|metal ion binding|pyrimidine nucleotide binding				0	all_lung(278;0.14)|Lung NSC(278;0.168)		LUSC - Lung squamous cell carcinoma(166;0.162)|Lung(188;0.235)			GGGGGCAGGACCAGGTGCCGA	0.607000											OREG0024728	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	25	42					9.93527e-08	1.19223e-07	0.054565	1	0
NPTX1	4884	broad.mit.edu	37	17	78444660	78444660	+	Missense_Mutation	SNP	C	T	T			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08									Somatic	Phase_I	Capture				Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr17:78444660C>T	uc002jyp.1	-	5	1410	c.1252G>A	c.(1252-1254)GGA>AGA	p.G418R		NM_002522	NP_002513	Q15818	NPTX1_HUMAN	neuronal pentraxin I precursor	418	Pentaxin.				central nervous system development|synaptic transmission|transport	transport vesicle	metal ion binding				0	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0487)			GTGGCCCCTCCGTAGATCTCG	0.662000													7	48					0	0	0.038147	0	0
FKBP8	23770	broad.mit.edu	37	19	18650228	18650228	+	Silent	SNP	C	T	T			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08									Somatic	Phase_I	Capture				Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr19:18650228C>T	uc002njk.1	-	4	617	c.504G>A	c.(502-504)ACG>ACA	p.T168T	FKBP8_uc002nji.1_Silent_p.T6T|FKBP8_uc010xqi.1_Silent_p.T197T|FKBP8_uc002njj.1_Silent_p.T168T|FKBP8_uc002njl.1_Silent_p.T168T|FKBP8_uc002njm.1_Silent_p.T168T|FKBP8_uc010ebr.1_Silent_p.T6T|FKBP8_uc002njn.2_RNA	NM_012181	NP_036313	Q14318	FKBP8_HUMAN	FK506-binding protein 8	168	PPIase FKBP-type.				apoptosis|interspecies interaction between organisms|intracellular signal transduction|protein folding	integral to endoplasmic reticulum membrane|mitochondrial membrane	FK506 binding|peptidyl-prolyl cis-trans isomerase activity|protein binding			ovary(1)	1						TGACCATGGCCGTCTCCCCCA	0.637000													49	48					0	0	0.139131	0	0
IRF2BP1	26145	broad.mit.edu	37	19	46387378	46387378	+	Missense_Mutation	SNP	C	A	A			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08									Somatic	Phase_I	Capture				Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr19:46387378C>A	uc002pds.1	-	1	1999	c.1655G>T	c.(1654-1656)TGC>TTC	p.C552F		NM_015649	NP_056464	Q8IU81	I2BP1_HUMAN	interferon regulatory factor 2 binding protein	552					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.00442)|GBM - Glioblastoma multiforme(486;0.0402)|Epithelial(262;0.231)		GACCAGCGGGCACTTGTCTCC	0.642000													13	4					7.93312e-07	9.25531e-07	0.119110	1	0
IDH1	3417	broad.mit.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	T	T	rs121913500		TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08									Somatic	Phase_I	Capture				Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	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 								22	51					0	0	0.099896	0	0
PHACTR3	116154	broad.mit.edu	37	20	58381107	58381107	+	Missense_Mutation	SNP	C	T	T			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08									Somatic	Phase_I	Capture				Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr20:58381107C>T	uc002yau.2	+	8	1653	c.1186C>T	c.(1186-1188)CGG>TGG	p.R396W	PHACTR3_uc002yat.2_Missense_Mutation_p.R393W|PHACTR3_uc010zzw.1_Missense_Mutation_p.R355W|PHACTR3_uc002yav.2_Missense_Mutation_p.R355W|PHACTR3_uc002yaw.2_Missense_Mutation_p.R355W|PHACTR3_uc002yax.2_Missense_Mutation_p.R285W	NM_080672	NP_542403	Q96KR7	PHAR3_HUMAN	phosphatase and actin regulator 3 isoform 1	396						nuclear matrix	actin binding|protein phosphatase inhibitor activity			ovary(2)|pancreas(1)	3	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;2.76e-09)			AACACTGCCACGGAAATGCAA	0.547000													61	249					0	0	0.139131	0	0
C21orf99	149992	broad.mit.edu	37	21	14439185	14439185	+	RNA	SNP	C	A	A	rs112098339		TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08									Somatic	Phase_I	Capture				Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr21:14439185C>A	uc002yja.3	+	10		c.2703C>A				NR_026916				Homo sapiens C21orf99 protein (C21orf99) mRNA, complete cds.												0						TGACTTTAAACCAAGAAGAAG	0.269000													4	20					1.23904e-05	1.36947e-05	0.014758	1	0
C21orf99	149992	broad.mit.edu	37	21	14439208	14439208	+	RNA	SNP	A	G	G			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08									Somatic	Phase_I	Capture				Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr21:14439208A>G	uc002yja.3	+	10		c.2726A>G				NR_026916				Homo sapiens C21orf99 protein (C21orf99) mRNA, complete cds.												0						AAGAGAAGAAATGCCAATATA	0.299000													4	21					0	0	0.009096	0	0
KRTAP13-1	140258	broad.mit.edu	37	21	31768834	31768834	+	Missense_Mutation	SNP	G	A	A			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08									Somatic	Phase_I	Capture				Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr21:31768834G>A	uc002yoa.2	+	1	443	c.430G>A	c.(430-432)GTT>ATT	p.V144I		NM_181599	NP_853630	Q8IUC0	KR131_HUMAN	keratin associated protein 13-1	144						intermediate filament				ovary(1)	1						GGGCTATGGCGTTGGATTCTG	0.542000													15	16					0	0	0.033300	0	0
PWP2	5822	broad.mit.edu	37	21	45540355	45540355	+	Missense_Mutation	SNP	G	A	A			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08									Somatic	Phase_I	Capture				Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr21:45540355G>A	uc002zeb.2	+	11	1405	c.1315G>A	c.(1315-1317)GTG>ATG	p.V439M		NM_005049	NP_005040	Q15269	PWP2_HUMAN	PWP2 periodic tryptophan protein homolog	439	WD 9.					cytoplasm|nucleolus	signal transducer activity			pancreas(1)	1				STAD - Stomach adenocarcinoma(101;0.172)|Colorectal(79;0.2)		GGACGGGACCGTGCGAGCCTT	0.597000													67	80					0	0	0.139131	0	0
SMC4	10051	broad.mit.edu	37	3	160137299	160137299	+	Missense_Mutation	SNP	T	A	A			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08									Somatic	Phase_I	Capture				Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr3:160137299T>A	uc003fdh.2	+	12	1938	c.1825T>A	c.(1825-1827)TCT>ACT	p.S609T	IFT80_uc003fda.2_Intron|SMC4_uc010hwc.1_Missense_Mutation_p.S373T|SMC4_uc003fdi.2_Missense_Mutation_p.S584T|SMC4_uc003fdj.2_Missense_Mutation_p.S609T|SMC4_uc010hwd.2_Missense_Mutation_p.S609T|SMC4_uc003fdl.2_Missense_Mutation_p.S312T	NM_001002800	NP_001002800	Q9NTJ3	SMC4_HUMAN	SMC4 structural maintenance of chromosomes	609	Flexible hinge.				cell division|mitotic chromosome condensation	condensin complex|cytoplasm|nucleus	ATP binding|protein heterodimerization activity			ovary(1)|breast(1)	2			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			AGAAAAAAAATCTGGCAGGAT	0.343000													35	53					0	0	0.074837	0	0
TXK	7294	broad.mit.edu	37	4	48114404	48114404	+	Silent	SNP	A	G	G			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08									Somatic	Phase_I	Capture				Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr4:48114404A>G	uc003gxx.3	-	4	386	c.300T>C	c.(298-300)AAT>AAC	p.N100N	TXK_uc003gxy.1_Silent_p.N100N	NM_003328	NP_003319	P42681	TXK_HUMAN	TXK tyrosine kinase	100	SH3.					cytoplasm	ATP binding|non-membrane spanning protein tyrosine kinase activity				0						TTAAGGCTAAATTACAGGGTT	0.468000													26	136					0	0	0.091800	0	0
NPY1R	4886	broad.mit.edu	37	4	164247119	164247119	+	Silent	SNP	G	A	A			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08									Somatic	Phase_I	Capture				Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr4:164247119G>A	uc003iqm.1	-	2	854	c.588C>T	c.(586-588)TAC>TAT	p.Y196Y	NPY1R_uc011cjj.1_Intron	NM_000909	NP_000900	P25929	NPY1R_HUMAN	neuropeptide Y receptor Y1	196	Extracellular (Potential).				inhibition of adenylate cyclase activity by G-protein signaling pathway|outflow tract morphogenesis	integral to plasma membrane	protein binding			lung(1)|pancreas(1)	2	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				CAAAGCACACGTATTTGTCTT	0.408000													35	35					0	0	0.059317	0	0
IRF2	3660	broad.mit.edu	37	4	185339801	185339801	+	Silent	SNP	G	A	A	rs148758064	byFrequency	TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08									Somatic	Phase_I	Capture				Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr4:185339801G>A	uc003iwf.3	-	4	449	c.249C>T	c.(247-249)TGC>TGT	p.C83C		NM_002199	NP_002190	P14316	IRF2_HUMAN	interferon regulatory factor 2	83	IRF tryptophan pentad repeat.				blood coagulation|cell proliferation|interferon-gamma-mediated signaling pathway|negative regulation of transcription from RNA polymerase II promoter|type I interferon-mediated signaling pathway	focal adhesion|nucleoplasm	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		all_lung(41;7.86e-14)|Lung NSC(41;1.87e-13)|Colorectal(36;0.00146)|Hepatocellular(41;0.00826)|Renal(120;0.00992)|Prostate(90;0.0115)|all_neural(102;0.0573)|all_hematologic(60;0.0592)		all cancers(43;3.94e-27)|Epithelial(43;5.3e-24)|OV - Ovarian serous cystadenocarcinoma(60;1.06e-10)|Colorectal(24;7.98e-07)|STAD - Stomach adenocarcinoma(60;3.95e-05)|GBM - Glioblastoma multiforme(59;8.3e-05)|COAD - Colon adenocarcinoma(29;0.000106)|BRCA - Breast invasive adenocarcinoma(30;0.000311)|LUSC - Lung squamous cell carcinoma(40;0.0128)|READ - Rectum adenocarcinoma(43;0.0419)		AATTCATGGCGCATCTGAAAT	0.398000													4	45					0	0	0.009096	0	0
PLEKHG4B	153478	broad.mit.edu	37	5	143249	143249	+	Missense_Mutation	SNP	G	A	A	rs115149634	byFrequency	TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08									Somatic	Phase_I	Capture				Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr5:143249G>A	uc003jak.2	+	2	547	c.497G>A	c.(496-498)CGG>CAG	p.R166Q		NM_052909	NP_443141	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G	166					regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			skin(2)	2			all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)		GTGCCTGCCCGGCAGCCACAC	0.647000													18	52					0	0	0.069288	0	0
ZDHHC11	79844	broad.mit.edu	37	5	814876	814876	+	Missense_Mutation	SNP	C	G	G	rs138424733		TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08									Somatic	Phase_I	Capture				Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr5:814876C>G	uc011cma.1	-	11	1565	c.1181G>C	c.(1180-1182)GGG>GCG	p.G394A	ZDHHC11_uc010itc.2_RNA|ZDHHC11_uc003jbj.2_RNA	NM_024786	NP_079062	Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11	394						integral to membrane	acyltransferase activity|zinc ion binding			skin(1)|pancreas(1)	2			Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)			ACGAACTTACCCAAGTGTAGA	0.378000													25	31					0	0	0.099896	0	0
HLA-J	3137	broad.mit.edu	37	6	29977359	29977359	+	Missense_Mutation	SNP	G	A	A	rs146982767	by1000genomes	TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08									Somatic	Phase_I	Capture				Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr6:29977359G>A	uc003rtl.3	+	5	740	c.378G>A	c.(376-378)ATG>ATA	p.M126I	HLA-G_uc011dmb.1_3'UTR|NCRNA00171_uc011dme.1_Intron|HLA-J_uc003nou.3_RNA|HLA-J_uc003nov.3_RNA					Homo sapiens major histocompatibility complex, class I, J (pseudogene), mRNA (cDNA clone IMAGE:4694038).												0						ATTTGTTCATGCCTTCCCTTT	0.453000													8	43					0	0	0.069234	0	0
THEMIS	387357	broad.mit.edu	37	6	128135074	128135074	+	Nonsense_Mutation	SNP	G	A	A			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08									Somatic	Phase_I	Capture				Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr6:128135074G>A	uc003qbi.2	-	5	1031	c.712C>T	c.(712-714)CGA>TGA	p.R238*	THEMIS_uc010kfa.2_Nonsense_Mutation_p.R141*|THEMIS_uc011ebt.1_Nonsense_Mutation_p.R238*|THEMIS_uc010kfb.2_Nonsense_Mutation_p.R203*	NM_001010923	NP_001010923	Q8N1K5	THMS1_HUMAN	thymocyte selection pathway associated isoform	238	CABIT 1.				negative T cell selection|positive T cell selection|T cell receptor signaling pathway	cytoplasm|nucleus				ovary(2)|skin(2)	4						ATATCTTTTCGAACTAAAAAG	0.333000													37	53					0	0	0.086207	0	0
GTF2IRD1	9569	broad.mit.edu	37	7	74016720	74016720	+	Missense_Mutation	SNP	C	T	T			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08									Somatic	Phase_I	Capture				Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr7:74016720C>T	uc003uaq.2	+	27	3233	c.2840C>T	c.(2839-2841)GCC>GTC	p.A947V	GTF2IRD1_uc010lbq.2_Missense_Mutation_p.A964V|GTF2IRD1_uc003uap.2_Missense_Mutation_p.A932V|GTF2IRD1_uc003uar.1_3'UTR	NM_016328	NP_057412	Q9UHL9	GT2D1_HUMAN	GTF2I repeat domain containing 1 isoform 1	947				Missing: Cytoplasmic localization.		nucleus	DNA binding|protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			ovary(4)	4						GTGGACTATGCCGGCCTGAAC	0.468000													3	80					0	0	0.009096	0	0
ZNF782	158431	broad.mit.edu	37	9	99581580	99581580	+	Missense_Mutation	SNP	G	C	C			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08									Somatic	Phase_I	Capture				Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr9:99581580G>C	uc004awp.1	-	6	1006	c.725C>G	c.(724-726)TCT>TGT	p.S242C	ZNF782_uc011lup.1_Missense_Mutation_p.S110C	NM_001001662	NP_001001662	Q6ZMW2	ZN782_HUMAN	zinc finger protein 782	242					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Acute lymphoblastic leukemia(62;0.0527)				GAAATTGTAAGATTTTCCTTT	0.333000													7	85					0	0	0.029380	0	0
FRMPD4	9758	broad.mit.edu	37	X	12701668	12701668	+	Missense_Mutation	SNP	C	T	T			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08									Somatic	Phase_I	Capture				Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chrX:12701668C>T	uc004cuz.1	+	6	1041	c.535C>T	c.(535-537)CGC>TGC	p.R179C	FRMPD4_uc011mij.1_Missense_Mutation_p.R171C	NM_014728	NP_055543	Q14CM0	FRPD4_HUMAN	FERM and PDZ domain containing 4	179					positive regulation of synapse structural plasticity	cytoskeleton|dendritic spine	phosphatidylinositol-4,5-bisphosphate binding|protein binding			central_nervous_system(5)|ovary(3)|skin(2)|large_intestine(1)|lung(1)|pancreas(1)	13						TGTCAAAGTACGCTTCTCTGA	0.423000													24	3					0	0	0.099896	0	0
FUBP1	8880	broad.mit.edu	37	1	78433848	78433851	+	Splice_Site	DEL	CAGT	-	-			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08									Somatic	Phase_I	Capture				Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr1:78433848_78433851delCAGT	uc001dii.2	-	3	339	c.250_splice	c.e3+1	p.S84_splice	FUBP1_uc001dih.3_Splice_Site|FUBP1_uc010orm.1_Splice_Site_p.S105_splice	NM_003902	NP_003893	Q96AE4	FUBP1_HUMAN	far upstream element-binding protein						transcription from RNA polymerase II promoter	nucleus	protein binding|RNA binding|sequence-specific DNA binding transcription factor activity|single-stranded DNA binding	p.?(1)		central_nervous_system(2)|lung(1)	3						GGAATACTTACAGTCATTTTGAGG	0.319													20	11	---	---	---	---					
PHLPP2	23035	broad.mit.edu	37	16	71692597	71692599	+	In_Frame_Del	DEL	TGT	-	-	rs145938775		TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08									Somatic	Phase_I	Capture				Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr16:71692597_71692599delTGT	uc002fax.2	-	13	2111_2113	c.2105_2107delACA	c.(2104-2109)AACATC>ATC	p.N702del	PHLPP2_uc002fav.2_RNA|PHLPP2_uc010cgf.2_In_Frame_Del_p.N635del	NM_015020	NP_055835	Q6ZVD8	PHLP2_HUMAN	PH domain and leucine rich repeat protein	702	LRR 20.					cytoplasm|membrane|nucleus	metal ion binding|phosphoprotein phosphatase activity			ovary(1)|central_nervous_system(1)	2						AAAATGCTGATGTTGTTGGAGTG	0.458													25	135	---	---	---	---					
NF1	4763	broad.mit.edu	37	17	29546036	29546037	+	Frame_Shift_Del	DEL	AG	-	-			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08									Somatic	Phase_I	Capture				Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr17:29546036_29546037delAG	uc002hgg.2	+	14	1874_1875	c.1541_1542delAG	c.(1540-1542)CAGfs	p.Q514fs	NF1_uc002hge.1_Frame_Shift_Del_p.Q514fs|NF1_uc002hgf.1_Frame_Shift_Del_p.Q514fs|NF1_uc002hgh.2_Frame_Shift_Del_p.Q514fs|NF1_uc010csn.1_Frame_Shift_Del_p.Q374fs	NM_001042492	NP_001035957	P21359	NF1_HUMAN	neurofibromin isoform 1	514					actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity	p.?(3)|p.Q514fs*43(2)|p.N510_E547del(1)		soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	330		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		CCAAGAAAACAGGGGCCCGAAA	0.351			D|Mis|N|F|S|O		neurofibroma|glioma	neurofibroma|glioma			Neurofibromatosis_type_1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			7	13	---	---	---	---					
NF1	4763	broad.mit.edu	37	17	29652976	29652979	+	Frame_Shift_Del	DEL	TCTC	-	-			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08									Somatic	Phase_I	Capture				Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr17:29652976_29652979delTCTC	uc002hgg.2	+	37	5307_5310	c.4974_4977delTCTC	c.(4972-4977)TTTCTCfs	p.F1658fs	NF1_uc002hgh.2_Frame_Shift_Del_p.F1637fs|NF1_uc002hgi.1_Frame_Shift_Del_p.F670fs|NF1_uc010cso.2_5'UTR	NM_001042492	NP_001035957	P21359	NF1_HUMAN	neurofibromin isoform 1	1658_1659	CRAL-TRIO.				actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity	p.S1660fs*37(2)		soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	330		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		AAACAGACTTTCTCTCTAAGTGGT	0.422			D|Mis|N|F|S|O		neurofibroma|glioma	neurofibroma|glioma			Neurofibromatosis_type_1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			11	168	---	---	---	---					
PLIN4	729359	broad.mit.edu	37	19	4510914	4510916	+	In_Frame_Del	DEL	TGG	-	-			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08									Somatic	Phase_I	Capture				Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr19:4510914_4510916delTGG	uc002mar.1	-	3	3014_3016	c.3014_3016delCCA	c.(3013-3018)ACCAAG>AAG	p.T1005del	PLIN4_uc010dub.1_In_Frame_Del_p.T29del	NM_001080400	NP_001073869	Q96Q06	PLIN4_HUMAN	plasma membrane associated protein, S3-12	1005						lipid particle|plasma membrane					0						AGCACTGTCTTGGTGGTGTCCAG	0.626													22	28	---	---	---	---					
HGD	3081	broad.mit.edu	37	3	120357338	120357338	+	Frame_Shift_Del	DEL	C	-	-			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08									Somatic	Phase_I	Capture				Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr3:120357338delC	uc003edw.2	-	12	1340	c.970delG	c.(970-972)GTTfs	p.V324fs	HGD_uc003edv.2_Frame_Shift_Del_p.V183fs	NM_000187	NP_000178	Q93099	HGD_HUMAN	homogentisate 1,2-dioxygenase	324					L-phenylalanine catabolic process|tyrosine catabolic process	cytosol	homogentisate 1,2-dioxygenase activity|metal ion binding				0				GBM - Glioblastoma multiforme(114;0.158)		TTATCAGCAACCCCCCATCGA	0.483													23	94	---	---	---	---					
WDFY3	23001	broad.mit.edu	37	4	85731329	85731331	+	In_Frame_Del	DEL	GAA	-	-			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08									Somatic	Phase_I	Capture				Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr4:85731329_85731331delGAA	uc003hpd.2	-	14	2462_2464	c.2054_2056delTTC	c.(2053-2058)CTTCAC>CAC	p.L685del	WDFY3_uc003hpf.2_In_Frame_Del_p.L685del	NM_014991	NP_055806	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3 isoform	685						cytoplasmic part|extrinsic to membrane|nuclear envelope	1-phosphatidylinositol binding|metal ion binding|protein binding			ovary(2)|central_nervous_system(1)	3		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		AACACAGTGTGAAGAAGTTCAAA	0.448													28	51	---	---	---	---					
FAM149A	25854	broad.mit.edu	37	4	187084676	187084678	+	In_Frame_Del	DEL	CTT	-	-			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08									Somatic	Phase_I	Capture				Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr4:187084676_187084678delCTT	uc003iyt.3	+	10	1511_1513	c.932_934delCTT	c.(931-936)CCTTCT>CCT	p.S312del	FAM149A_uc011cla.1_In_Frame_Del_p.S312del|FAM149A_uc003iyu.3_In_Frame_Del_p.S312del|FAM149A_uc010isl.2_In_Frame_Del_p.S312del|FAM149A_uc011clb.1_In_Frame_Del_p.S312del	NM_015398	NP_056213	A5PLN7	F149A_HUMAN	hypothetical protein LOC25854	603										breast(1)	1		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.19e-10)|BRCA - Breast invasive adenocarcinoma(30;1.22e-05)|GBM - Glioblastoma multiforme(59;0.000122)|STAD - Stomach adenocarcinoma(60;0.000288)|LUSC - Lung squamous cell carcinoma(40;0.00241)|READ - Rectum adenocarcinoma(43;0.166)		GGATTATCACCTTCTGCAAAGAA	0.532													10	76	---	---	---	---					
PIK3R1	5295	broad.mit.edu	37	5	67591105	67591107	+	In_Frame_Del	DEL	TAA	-	-			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08									Somatic	Phase_I	Capture				Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr5:67591105_67591107delTAA	uc003jva.2	+	13	2258_2260	c.1698_1700delTAA	c.(1696-1701)ATTAAA>ATA	p.K567del	PIK3R1_uc003jvb.2_In_Frame_Del_p.K567del|PIK3R1_uc003jvc.2_In_Frame_Del_p.K267del|PIK3R1_uc003jvd.2_In_Frame_Del_p.K297del|PIK3R1_uc003jve.2_In_Frame_Del_p.K246del|PIK3R1_uc011crb.1_In_Frame_Del_p.K237del	NM_181523	NP_852664	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1	567					epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|growth hormone receptor signaling pathway|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|interspecies interaction between organisms|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol phosphorylation|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|T cell costimulation|T cell receptor signaling pathway	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex	1-phosphatidylinositol binding|ErbB-3 class receptor binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase regulator activity|protein phosphatase binding	p.?(1)		endometrium(34)|central_nervous_system(27)|large_intestine(20)|breast(7)|ovary(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|urinary_tract(1)|skin(1)|pancreas(1)	101		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoproterenol(DB01064)	TGAACAGCATTAAACCAGACCTT	0.369			Mis|F|O		gliobastoma|ovarian|colorectal					TCGA GBM(4;<1E-08)			16	108	---	---	---	---					
MAN2A1	4124	broad.mit.edu	37	5	109049430	109049433	+	Frame_Shift_Del	DEL	CTGT	-	-			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08									Somatic	Phase_I	Capture				Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr5:109049430_109049433delCTGT	uc003kou.1	+	2	1308_1311	c.345_348delCTGT	c.(343-348)GACTGTfs	p.D115fs		NM_002372	NP_002363	Q16706	MA2A1_HUMAN	mannosidase, alpha, class 2A, member 1	115_116	Lumenal (Potential).				mannose metabolic process|post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-mannosidase activity|carbohydrate binding|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity|zinc ion binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3		all_cancers(142;8.66e-07)|all_epithelial(76;7.73e-09)|Prostate(80;0.000303)|Lung NSC(167;0.0186)|all_lung(232;0.0241)|Ovarian(225;0.0444)|Colorectal(57;0.0959)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;2.17e-10)|Epithelial(69;1.37e-09)|COAD - Colon adenocarcinoma(37;0.141)		ACACTGCAGACTGTCTGTTTGCTT	0.407													38	135	---	---	---	---					
COL11A2	1302	broad.mit.edu	37	6	33159977	33159979	+	In_Frame_Del	DEL	AGG	-	-			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08									Somatic	Phase_I	Capture				Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr6:33159977_33159979delAGG	uc003ocx.1	-	1	267_269	c.39_41delCCT	c.(37-42)CTCCTA>CTA	p.13_14LL>L	COL11A2_uc003ocy.1_In_Frame_Del_p.13_14LL>L|COL11A2_uc003ocz.1_In_Frame_Del_p.13_14LL>L|COL11A2_uc003oda.2_In_Frame_Del_p.13_14LL>L	NM_080680	NP_542411	P13942	COBA2_HUMAN	collagen, type XI, alpha 2 isoform 1	13_14					cartilage development|cell adhesion|collagen fibril organization|sensory perception of sound|soft palate development	collagen type XI	extracellular matrix structural constituent conferring tensile strength|protein binding, bridging			ovary(3)|skin(2)	5						CACCAGAGGTAGGAGGAGGAGGA	0.675													3	3	---	---	---	---					
HDAC2	3066	broad.mit.edu	37	6	114277842	114277844	+	In_Frame_Del	DEL	TCT	-	-			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08									Somatic	Phase_I	Capture				Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr6:114277842_114277844delTCT	uc003pwd.1	-	4	579_581	c.579_581delAGA	c.(577-582)GAAGAT>GAT	p.E193del	HDAC2_uc003pwc.1_In_Frame_Del_p.E69del|HDAC2_uc003pwe.1_In_Frame_Del_p.E69del	NM_001527	NP_001518	Q92769	HDAC2_HUMAN	histone deacetylase 2	99	Histone deacetylase.				blood coagulation|dendrite development|embryonic digit morphogenesis|epidermal cell differentiation|eyelid development in camera-type eye|fungiform papilla formation|hair follicle placode formation|maintenance of chromatin silencing|negative regulation of apoptosis|negative regulation of cell cycle|negative regulation of neuron projection development|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|odontogenesis of dentine-containing tooth|positive regulation of cell proliferation|positive regulation of proteolysis|positive regulation of receptor biosynthetic process|positive regulation of transcription from RNA polymerase II promoter	cytoplasm|ESC/E(Z) complex|NuRD complex|Sin3 complex	chromatin binding|enzyme binding|histone deacetylase activity (H3-K16 specific)|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|sequence-specific DNA binding|transcription factor binding			skin(2)|ovary(1)|central_nervous_system(1)	4		all_cancers(87;0.000629)|all_epithelial(87;0.00274)|Colorectal(196;0.0317)|all_lung(197;0.24)		all cancers(137;0.00318)|OV - Ovarian serous cystadenocarcinoma(136;0.00569)|Epithelial(106;0.0112)|GBM - Glioblastoma multiforme(226;0.0832)	Vorinostat(DB02546)	CACTGGACAATCTTCTCCAACAT	0.350													15	16	---	---	---	---					
MAPK15	225689	broad.mit.edu	37	8	144801230	144801230	+	Frame_Shift_Del	DEL	T	-	-	rs139710965	byFrequency	TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08									Somatic	Phase_I	Capture				Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr8:144801230delT	uc003yzj.2	+	6	526	c.485delT	c.(484-486)CTGfs	p.L162fs		NM_139021	NP_620590	Q8TD08	MK15_HUMAN	mitogen-activated protein kinase 15	162	Protein kinase.				protein autophosphorylation	extracellular region	ATP binding|MAP kinase activity|SH3 domain binding			lung(2)	2	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			GCCCGCTCCCTGGGCGACCTC	0.667													2	4	---	---	---	---					
NOTCH1	4851	broad.mit.edu	37	9	139391997	139391998	+	Frame_Shift_Del	DEL	AG	-	-			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08									Somatic	Phase_I	Capture				Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr9:139391997_139391998delAG	uc004chz.2	-	34	6193_6194	c.6193_6194delCT	c.(6193-6195)CTGfs	p.L2065fs		NM_017617	NP_060087	P46531	NOTC1_HUMAN	notch1 preproprotein	2065	ANK 5.|Cytoplasmic (Potential).				aortic valve morphogenesis|immune response|negative regulation of BMP signaling pathway|negative regulation of cell-substrate adhesion|negative regulation of myoblast differentiation|negative regulation of osteoblast differentiation|negative regulation of transcription, DNA-dependent|Notch receptor processing	cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane	calcium ion binding|protein binding|receptor activity			haematopoietic_and_lymphoid_tissue(791)|upper_aerodigestive_tract(29)|lung(13)|central_nervous_system(10)|breast(9)|large_intestine(1)|skin(1)|oesophagus(1)|pancreas(1)	856	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		GGCCAGAAACAGGGGTGTCTCC	0.683			T|Mis|O	TRB@	T-ALL					HNSCC(8;0.001)			17	14	---	---	---	---					
NOTCH1	4851	broad.mit.edu	37	9	139395163	139395166	+	Frame_Shift_Del	DEL	GTCT	-	-			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08									Somatic	Phase_I	Capture				Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr9:139395163_139395166delGTCT	uc004chz.2	-	31	5772_5775	c.5772_5775delAGAC	c.(5770-5775)ACAGACfs	p.T1924fs		NM_017617	NP_060087	P46531	NOTC1_HUMAN	notch1 preproprotein	1924_1925	Cytoplasmic (Potential).				aortic valve morphogenesis|immune response|negative regulation of BMP signaling pathway|negative regulation of cell-substrate adhesion|negative regulation of myoblast differentiation|negative regulation of osteoblast differentiation|negative regulation of transcription, DNA-dependent|Notch receptor processing	cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane	calcium ion binding|protein binding|receptor activity			haematopoietic_and_lymphoid_tissue(791)|upper_aerodigestive_tract(29)|lung(13)|central_nervous_system(10)|breast(9)|large_intestine(1)|skin(1)|oesophagus(1)|pancreas(1)	856	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		CGCCCGTGCGGTCTGTCTGGTTGT	0.686			T|Mis|O	TRB@	T-ALL					HNSCC(8;0.001)			41	137	---	---	---	---					
BCORL1	63035	broad.mit.edu	37	X	129147257	129147259	+	In_Frame_Del	DEL	AGA	-	-			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08									Somatic	Phase_I	Capture				Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chrX:129147257_129147259delAGA	uc004evb.1	+	4	623_625	c.509_511delAGA	c.(508-513)GAGAAG>GAG	p.K171del	BCORL1_uc010nrd.1_In_Frame_Del_p.K73del	NM_021946	NP_068765	Q5H9F3	BCORL_HUMAN	BCL6 co-repressor-like 1	171					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus				ovary(4)|breast(2)|lung(1)	7						GGTGTTGGAGAGAAGAATACTTT	0.552													9	21	---	---	---	---					
