#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
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	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_Annotation_Transcript	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_Translocation_Partner	i_CGC_Tumor_Types_Germline	i_CGC_Tumor_Types_Somatic	i_COSMIC_fusion_genes	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_mutations	i_COSMIC_overlapping_primary_sites	i_COSMIC_tissue_types_affected	i_COSMIC_total_alterations_in_gene	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Codon_Change	i_DNARepairGenes_Role	i_Description	i_DrugBank	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_FamilialCancerDatabase_Syndromes	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GO_Biological_Process	i_GO_Cellular_Component	i_GO_Molecular_Function	i_Genome_Change	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_MUTSIG_Published_Results	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_AApos	i_UniProt_Experimental_Info	i_UniProt_Natural_Variations	i_UniProt_Region	i_UniProt_Site	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_cDNA_Change	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_ref_count_full	isArtifactMode	oxoGCut	pox	pox_cutoff	qox	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample
CEP104	9731	broad.mit.edu	37	1	3768869	3768869	+	Missense_Mutation	SNP	G	G	A			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr1:3768869G>A	ENST00000378230.3	-	2	427	c.103C>T	c.(103-105)Cgg>Tgg	p.R35W	CEP104_ENST00000378223.3_Missense_Mutation_p.R35W	NM_014704.3	NP_055519.1	O60308	CE104_HUMAN	centrosomal protein 104kDa	35						centriole (GO:0005814)	glutamate binding (GO:0016595)|glycine binding (GO:0016594)|thienylcyclohexylpiperidine binding (GO:0016596)			breast(2)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(14)|lung(8)|prostate(1)|skin(3)	39						CTAGGTGACCGCCACCCACTG	0.622																																						ENST00000378230.3																			0				breast(2)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(14)|lung(8)|prostate(1)|skin(3)	39						c.(103-105)Cgg>Tgg		centrosomal protein 104kDa							48.0	44.0	45.0					1																	3768869		2203	4300	6503	SO:0001583	missense	9731					centriole	binding	g.chr1:3768869G>A	AB011134	CCDS30571.1	1p36.32	2014-02-20	2011-05-06	2011-05-06	ENSG00000116198	ENSG00000116198			24866	protein-coding gene	gene with protein product	"""glycine, glutamate, thienylcyclohexylpiperidine binding protein"""		"""KIAA0562"""	KIAA0562		7488117, 21399614	Standard	NM_014704		Approved	GlyBP, RP1-286D6.4	uc001aky.2	O60308	OTTHUMG00000003507	ENST00000378230.3:c.103C>T	1.37:g.3768869G>A	ENSP00000367476:p.Arg35Trp					CEP104_ENST00000378223.3_Missense_Mutation_p.R35W	p.R35W	NM_014704.3	NP_055519.1	O60308	CE104_HUMAN			2	427	-			35					Q5JSQ3|Q5SR24|Q5SR25|Q6PKF5|Q86W32|Q86X14	Missense_Mutation	SNP	ENST00000378230.3	37	c.103C>T	CCDS30571.1	.	.	.	.	.	.	.	.	.	.	G	13.78	2.340128	0.41398	.	.	ENSG00000116198	ENST00000378230;ENST00000428079;ENST00000378223	T;T	0.80480	-1.38;-1.38	5.2	-0.339	0.12647	Galactose-binding domain-like (1);	0.000000	0.85682	D	0.000000	D	0.88373	0.6419	M	0.79258	2.445	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.91635	0.985;0.999	D	0.87820	0.2637	10	0.62326	D	0.03	.	15.8672	0.79074	0.0:0.0:0.6615:0.3385	.	35;35	O60308-3;O60308	.;CE104_HUMAN	W	35	ENSP00000367476:R35W;ENSP00000367468:R35W	ENSP00000367468:R35W	R	-	1	2	CEP104	3758729	1.000000	0.71417	0.989000	0.46669	0.023000	0.10783	1.818000	0.39012	-0.329000	0.08527	-0.518000	0.04402	CGG		0.622	CEP104-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009747.3	NM_014704		3	21	0	0	0	1	0	3	21				
TSSC2	650368	broad.mit.edu	37	11	3427845	3427845	+	RNA	SNP	C	C	T			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr11:3427845C>T	ENST00000529482.1	+	0	962									tumor suppressing subtransferable candidate 2 pseudogene																		CTTCAAGTGGCAGGAGCAGAA	0.587																																						ENST00000529482.1																			0																																																			0							g.chr11:3427845C>T			11p15.4	2014-06-05	2008-06-30		ENSG00000223756	ENSG00000223756			12384	pseudogene	pseudogene	"""tumor-supressing STF cDNA 2"", ""asparagine-linked glycosylation 1 homolog (yeast, beta-1,4-mannosyltransferase) (ALG1) pseudogene"""	608999	"""tumor suppressing subtransferable candidate 2"""			9403053	Standard	NR_024248		Approved				OTTHUMG00000011705		11.37:g.3427845C>T														0	962	+									RNA	SNP	ENST00000529482.1	37																																																																																						0.587	TSSC2-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000392020.1			4	32	0	0	0	1	0	4	32				
IGHV1OR16-3	28313	broad.mit.edu	37	16	32070612	32070612	+	RNA	SNP	A	A	C	rs368458790		TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr16:32070612A>C	ENST00000566806.1	-	0	499																											GGTCTCCTGCAAGGCTTCTGG	0.552																																						ENST00000566806.1																			0																																																			0							g.chr16:32070612A>C																													16.37:g.32070612A>C														0	499	-									RNA	SNP	ENST00000566806.1	37																																																																																						0.552	RP11-1166P10.6-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000432459.1			3	59	0	0	0	1	0	3	59				
NF1	4763	broad.mit.edu	37	17	29670155	29670155	+	Splice_Site	SNP	T	T	A			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr17:29670155T>A	ENST00000358273.4	+	48	7572		c.e48+2		NF1_ENST00000444181.2_Splice_Site|NF1_ENST00000356175.3_Splice_Site|NF1_ENST00000417592.2_Splice_Site	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1						actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(3)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		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	0.318			"""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)																												ENST00000358273.4			yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	"""D, Mis, N, F, S, O"""	neurofibromatosis type 1 gene			O		"""neurofibroma, glioma"""	"""neurofibroma, glioma"""	NF1/ACCN1(2)	11	Whole gene deletion(8)|Unknown(3)	p.0?(8)|p.?(3)	soft_tissue(7)|autonomic_ganglia(2)|lung(1)|central_nervous_system(1)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599						c.e48+2		neurofibromin 1							58.0	59.0	58.0					17																	29670155		2203	4300	6503	SO:0001630	splice_region_variant	4763	Neurofibromatosis, type 1	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	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	g.chr17:29670155T>A		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"""neurofibromatosis"", ""von Recklinghausen disease"", ""Watson disease"""	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.7189+2T>A	17.37:g.29670155T>A		TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)				NF1_ENST00000356175.3_Splice_Site|NF1_ENST00000444181.2_Splice_Site|NF1_ENST00000417592.2_Splice_Site		NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN		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)	48	7572	+		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)						O00662|Q14284|Q14930|Q14931|Q9UMK3	Splice_Site	SNP	ENST00000358273.4	37		CCDS42292.1	.	.	.	.	.	.	.	.	.	.	T	20.1	3.938687	0.73557	.	.	ENSG00000196712	ENST00000358273;ENST00000356175;ENST00000456735;ENST00000444181;ENST00000417592	.	.	.	5.32	5.32	0.75619	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.2798	0.73773	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	NF1	26694281	1.000000	0.71417	0.996000	0.52242	0.851000	0.48451	7.254000	0.78329	2.022000	0.59522	0.460000	0.39030	.		0.318	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267	Intron	6	34	0	0	0	1	0	6	34				
ENKD1	84080	broad.mit.edu	37	16	67700039	67700039	+	Missense_Mutation	SNP	C	C	T			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr16:67700039C>T	ENST00000243878.4	-	2	536	c.215G>A	c.(214-216)cGc>cAc	p.R72H	C16orf86_ENST00000403458.4_5'Flank|ENKD1_ENST00000602644.1_Missense_Mutation_p.R72H|ENKD1_ENST00000602409.1_5'Flank	NM_032140.1	NP_115516.1	Q9H0I2	ENKD1_HUMAN	enkurin domain containing 1	72						cytoplasmic microtubule (GO:0005881)|microtubule cytoskeleton (GO:0015630)											CCCGACGCCGCGCTGGCCGCG	0.662																																						ENST00000243878.4																			0											c.(214-216)cGc>cAc		enkurin domain containing 1							35.0	39.0	37.0					16																	67700039		2195	4292	6487	SO:0001583	missense	84080							g.chr16:67700039C>T	BC008284	CCDS10844.1	16q22.1	2012-10-09	2012-10-09	2012-10-09	ENSG00000124074	ENSG00000124074			25246	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 48"""	C16orf48		11230166	Standard	NM_032140		Approved	DKFZP434A1319	uc002etw.1	Q9H0I2	OTTHUMG00000137550	ENST00000243878.4:c.215G>A	16.37:g.67700039C>T	ENSP00000243878:p.Arg72His					ENKD1_ENST00000602644.1_Missense_Mutation_p.R72H	p.R72H	NM_032140.1	NP_115516.1					2	536	-								Q6UWD7	Missense_Mutation	SNP	ENST00000243878.4	37	c.215G>A	CCDS10844.1	.	.	.	.	.	.	.	.	.	.	C	10.51	1.369173	0.24771	.	.	ENSG00000124074	ENST00000243878	.	.	.	4.84	-1.24	0.09435	.	0.660669	0.13981	N	0.349455	T	0.24586	0.0596	N	0.25890	0.77	0.09310	N	1	B	0.17038	0.02	B	0.10450	0.005	T	0.15037	-1.0451	9	0.56958	D	0.05	-4.5353	4.9973	0.14245	0.1498:0.3252:0.0:0.5251	.	72	Q9H0I2	CP048_HUMAN	H	72	.	ENSP00000243878:R72H	R	-	2	0	C16orf48	66257540	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.562000	0.05950	-0.253000	0.09514	0.462000	0.41574	CGC		0.662	ENKD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268884.1	NM_032140		8	44	0	0	0	1	0	8	44				
JAG2	3714	broad.mit.edu	37	14	105615619	105615619	+	Silent	SNP	G	G	A			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr14:105615619G>A	ENST00000331782.3	-	13	2044	c.1641C>T	c.(1639-1641)aaC>aaT	p.N547N	JAG2_ENST00000347004.2_Silent_p.N509N|RP11-44N21.4_ENST00000548203.1_RNA	NM_002226.4	NP_002217.3	Q9Y219	JAG2_HUMAN	jagged 2	547	EGF-like 9. {ECO:0000255|PROSITE- ProRule:PRU00076}.				auditory receptor cell fate commitment (GO:0009912)|cell cycle (GO:0007049)|cell differentiation (GO:0030154)|epithelial cell apoptotic process involved in palatal shelf morphogenesis (GO:1990134)|gamma-delta T cell differentiation (GO:0042492)|in utero embryonic development (GO:0001701)|morphogenesis of embryonic epithelium (GO:0016331)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|respiratory system process (GO:0003016)|skeletal system development (GO:0001501)|spermatogenesis (GO:0007283)|T cell differentiation (GO:0030217)|thymic T cell selection (GO:0045061)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|Notch binding (GO:0005112)			breast(2)|endometrium(2)|kidney(3)|large_intestine(1)|lung(7)|prostate(2)|skin(5)	22		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	0.662																																						ENST00000331782.3																			0				breast(2)|endometrium(2)|kidney(3)|large_intestine(1)|lung(7)|prostate(2)|skin(5)	22						c.(1639-1641)aaC>aaT		jagged 2							89.0	92.0	91.0					14																	105615619		2203	4299	6502	SO:0001819	synonymous_variant	3714				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	g.chr14:105615619G>A	AF020201	CCDS9998.1, CCDS9999.1	14q32	2008-08-01			ENSG00000184916	ENSG00000184916			6189	protein-coding gene	gene with protein product		602570				9315665, 10662552	Standard	NM_002226		Approved		uc001yqg.4	Q9Y219	OTTHUMG00000140172	ENST00000331782.3:c.1641C>T	14.37:g.105615619G>A						JAG2_ENST00000347004.2_Silent_p.N509N	p.N547N	NM_002226.4	NP_002217.3	Q9Y219	JAG2_HUMAN	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)	13	2044	-		all_cancers(154;0.0336)|all_epithelial(191;0.0729)|Melanoma(154;0.155)	547			EGF-like 9.		Q9UE17|Q9UE99|Q9UNK8|Q9Y6P9|Q9Y6Q0	Silent	SNP	ENST00000331782.3	37	c.1641C>T	CCDS9998.1																																																																																				0.662	JAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276506.2			44	70	0	0	0	1	0	44	70				
ITLN1	55600	broad.mit.edu	37	1	160850421	160850421	+	Silent	SNP	G	G	A	rs201111955		TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr1:160850421G>A	ENST00000326245.3	-	6	757	c.642C>T	c.(640-642)ggC>ggT	p.G214G	ITLN1_ENST00000487531.1_5'UTR	NM_017625.2	NP_060095.2	Q8WWA0	ITLN1_HUMAN	intelectin 1 (galactofuranose binding)	214	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				positive regulation of glucose import (GO:0046326)|positive regulation of protein phosphorylation (GO:0001934)|response to nematode (GO:0009624)	anchored component of membrane (GO:0031225)|brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(6)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	21	all_cancers(52;2.99e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00737)			TCTGGGCGTCGCCAAAATCAT	0.443																																						ENST00000326245.3																			0				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(6)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	21						c.(640-642)ggC>ggT		intelectin 1 (galactofuranose binding)							181.0	181.0	181.0					1																	160850421		2203	4300	6503	SO:0001819	synonymous_variant	55600				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	g.chr1:160850421G>A	AB036706	CCDS1211.1	1q21.3	2008-02-05			ENSG00000179914	ENSG00000179914			18259	protein-coding gene	gene with protein product		609873				11313366, 11181563	Standard	NM_017625		Approved	ITLN, FLJ20022, LFR, HL-1, hIntL	uc001fxc.3	Q8WWA0	OTTHUMG00000028604	ENST00000326245.3:c.642C>T	1.37:g.160850421G>A						ITLN1_ENST00000487531.1_5'UTR	p.G214G	NM_017625.2	NP_060095.2	Q8WWA0	ITLN1_HUMAN	BRCA - Breast invasive adenocarcinoma(70;0.00737)		6	757	-	all_cancers(52;2.99e-17)|all_hematologic(112;0.093)		214			Fibrinogen C-terminal.		Q5IWS4|Q5VYI4|Q6YDJ3|Q9NP67	Silent	SNP	ENST00000326245.3	37	c.642C>T	CCDS1211.1																																																																																				0.443	ITLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071462.1	NM_017625		7	261	0	0	0	1	0	7	261				
ZNRD1-AS1	80862	broad.mit.edu	37	6	29977359	29977359	+	RNA	SNP	G	G	A	rs367861986|rs3831361|rs370297731	byFrequency	TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr6:29977359G>A	ENST00000376797.3	-	0	731				ZNRD1-AS1_ENST00000448093.1_RNA|ZNRD1-AS1_ENST00000444051.1_RNA|ZNRD1-AS1_ENST00000420251.1_RNA|HLA-J_ENST00000462773.1_RNA|ZNRD1-AS1_ENST00000425604.1_RNA			Q2KJ03	ZRAS1_HUMAN	ZNRD1 antisense RNA 1																		ATTTGTTCATGCCTTCCCTTT	0.453																																						ENST00000376797.3																			0																																																			0							g.chr6:29977359G>A	AF032110		6p21.33	2014-08-14	2012-08-15	2010-11-25	ENSG00000204623	ENSG00000204623		"""Long non-coding RNAs"""	13924	non-coding RNA	RNA, long non-coding		615714	"""chromosome 6 open reading frame 12"", ""non-protein coding RNA 171"", ""ZNRD1 antisense RNA (non-protein coding)"", ""ZNRD1 antisense RNA 1 (non-protein coding)"""	C6orf12, NCRNA00171, ZNRD1AS, ZNRD1-AS		9553157, 11130983, 25110835	Standard	NR_026751		Approved	HTEX4, Em:AB023056.3	uc003rto.3	Q2KJ03	OTTHUMG00000031109		6.37:g.29977359G>A						ZNRD1-AS1_ENST00000420251.1_RNA|ZNRD1-AS1_ENST00000425604.1_RNA|HLA-J_ENST00000462773.1_RNA|ZNRD1-AS1_ENST00000448093.1_RNA								0	731	-									RNA	SNP	ENST00000376797.3	37																																																																																						0.453	ZNRD1-AS1-006	KNOWN	basic|exp_conf	antisense	antisense	OTTHUMT00000253083.1	NR_026751		8	43	0	0	0	1	0	8	43				
TRBV7-6	28592	broad.mit.edu	37	7	142139349	142139349	+	RNA	SNP	G	G	A			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr7:142139349G>A	ENST00000390374.3	-	0	320									T cell receptor beta variable 7-6																		GAGTGGAGACGGATCCCTCAG	0.567																																						ENST00000390374.3																			0																				89.0	87.0	88.0					7																	142139349		1990	4163	6153			0							g.chr7:142139349G>A	L36092		7q34	2012-02-07			ENSG00000211727	ENSG00000211727		"""T cell receptors / TRB locus"""	12240	other	T cell receptor gene						8650574	Standard	NG_001333		Approved	TRBV76, TCRBV6S3A1N1T, TCRBV7S6			OTTHUMG00000158882		7.37:g.142139349G>A														0	320	-									RNA	SNP	ENST00000390374.3	37																																																																																						0.567	TRBV7-6-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	TR_V_gene	TR_V_gene	OTTHUMT00000352490.2	NG_001333		27	94	0	0	0	1	0	27	94				
NPY1R	4886	broad.mit.edu	37	4	164247119	164247119	+	Silent	SNP	G	G	A	rs189884361		TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr4:164247119G>A	ENST00000296533.2	-	2	1119	c.588C>T	c.(586-588)taC>taT	p.Y196Y	NPY1R_ENST00000509586.1_Intron	NM_000909.5	NP_000900.1	P25929	NPY1R_HUMAN	neuropeptide Y receptor Y1	196					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glucose metabolic process (GO:0006006)|locomotory behavior (GO:0007626)|neuropeptide signaling pathway (GO:0007218)|outflow tract morphogenesis (GO:0003151)|regulation of blood pressure (GO:0008217)|regulation of multicellular organism growth (GO:0040014)|sensory perception of pain (GO:0019233)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neuropeptide Y receptor activity (GO:0004983)|pancreatic polypeptide receptor activity (GO:0001602)|peptide YY receptor activity (GO:0001601)			breast(1)|cervix(1)|large_intestine(4)|lung(18)|pancreas(1)|skin(1)|upper_aerodigestive_tract(4)	30	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				CAAAGCACACGTATTTGTCTT	0.408													G|||	1	0.000199681	0.0008	0.0	5008	,	,		21046	0.0		0.0	False		,,,				2504	0.0					ENST00000296533.2																			0				breast(1)|cervix(1)|large_intestine(4)|lung(18)|pancreas(1)|skin(1)|upper_aerodigestive_tract(4)	30						c.(586-588)taC>taT		neuropeptide Y receptor Y1							110.0	96.0	101.0					4																	164247119		2203	4300	6503	SO:0001819	synonymous_variant	0				inhibition of adenylate cyclase activity by G-protein signaling pathway|outflow tract morphogenesis	integral to plasma membrane	protein binding	g.chr4:164247119G>A		CCDS34089.1	4q31.3-q32	2012-08-08				ENSG00000164128		"""GPCR / Class A : Neuropeptide receptors : Y"""	7956	protein-coding gene	gene with protein product		162641		NPYR		8095935	Standard	NM_000909		Approved		uc003iqm.2	P25929		ENST00000296533.2:c.588C>T	4.37:g.164247119G>A						NPY1R_ENST00000509586.1_Intron	p.Y196Y	NM_000909.5	NP_000900.1	P25929	NPY1R_HUMAN			2	1119	-	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)	196					B2R6H5	Silent	SNP	ENST00000296533.2	37	c.588C>T	CCDS34089.1																																																																																				0.408	NPY1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364685.1			35	35	0	0	0	1	0	35	35				
OR1J2	26740	broad.mit.edu	37	9	125273992	125273992	+	Silent	SNP	C	C	A			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr9:125273992C>A	ENST00000335302.5	+	1	912	c.912C>A	c.(910-912)ctC>ctA	p.L304L		NM_054107.1	NP_473448.1	Q8NGS2	OR1J2_HUMAN	olfactory receptor, family 1, subfamily J, member 2	304						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(8)|pancreas(1)|skin(7)|stomach(1)	26						TTGGGAAACTCTTCAGTAGAG	0.383																																						ENST00000335302.5																			0				NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(8)|pancreas(1)|skin(7)|stomach(1)	26						c.(910-912)ctC>ctA		olfactory receptor, family 1, subfamily J, member 2							57.0	60.0	59.0					9																	125273992		2203	4300	6503	SO:0001819	synonymous_variant	26740				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr9:125273992C>A		CCDS35121.1	9q33.2	2013-09-20			ENSG00000197233	ENSG00000197233		"""GPCR / Class A : Olfactory receptors"""	8209	protein-coding gene	gene with protein product				OR1J3, OR1J5			Standard	XM_005251920		Approved	OST044	uc011lyv.2	Q8NGS2	OTTHUMG00000020604	ENST00000335302.5:c.912C>A	9.37:g.125273992C>A							p.L304L	NM_054107.1	NP_473448.1	Q8NGS2	OR1J2_HUMAN			1	912	+			304					A3KFL9|Q6IF14|Q96R90|Q9NZP1	Silent	SNP	ENST00000335302.5	37	c.912C>A	CCDS35121.1																																																																																				0.383	OR1J2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053932.1			5	77	1	0	0.217242	1	0.22218	5	77				
ZNRD1-AS1	80862	broad.mit.edu	37	6	29977358	29977358	+	RNA	SNP	T	T	C			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr6:29977358T>C	ENST00000376797.3	-	0	731				ZNRD1-AS1_ENST00000448093.1_RNA|ZNRD1-AS1_ENST00000444051.1_RNA|ZNRD1-AS1_ENST00000420251.1_RNA|HLA-J_ENST00000462773.1_RNA|ZNRD1-AS1_ENST00000425604.1_RNA			Q2KJ03	ZRAS1_HUMAN	ZNRD1 antisense RNA 1																		GATTTGTTCATGCCTTCCCTT	0.448																																						ENST00000376797.3																			0																																																			0							g.chr6:29977358T>C	AF032110		6p21.33	2014-08-14	2012-08-15	2010-11-25	ENSG00000204623	ENSG00000204623		"""Long non-coding RNAs"""	13924	non-coding RNA	RNA, long non-coding		615714	"""chromosome 6 open reading frame 12"", ""non-protein coding RNA 171"", ""ZNRD1 antisense RNA (non-protein coding)"", ""ZNRD1 antisense RNA 1 (non-protein coding)"""	C6orf12, NCRNA00171, ZNRD1AS, ZNRD1-AS		9553157, 11130983, 25110835	Standard	NR_026751		Approved	HTEX4, Em:AB023056.3	uc003rto.3	Q2KJ03	OTTHUMG00000031109		6.37:g.29977358T>C						ZNRD1-AS1_ENST00000420251.1_RNA|ZNRD1-AS1_ENST00000425604.1_RNA|HLA-J_ENST00000462773.1_RNA|ZNRD1-AS1_ENST00000448093.1_RNA								0	731	-									RNA	SNP	ENST00000376797.3	37																																																																																						0.448	ZNRD1-AS1-006	KNOWN	basic|exp_conf	antisense	antisense	OTTHUMT00000253083.1	NR_026751		7	43	0	0	0	1	0	7	43				
THEMIS	387357	broad.mit.edu	37	6	128135074	128135074	+	Nonsense_Mutation	SNP	G	G	A			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr6:128135074G>A	ENST00000368248.2	-	4	860	c.712C>T	c.(712-714)Cga>Tga	p.R238*	THEMIS_ENST00000543064.1_Nonsense_Mutation_p.R238*|THEMIS_ENST00000368250.1_Nonsense_Mutation_p.R159*|THEMIS_ENST00000537166.1_Nonsense_Mutation_p.R203*	NM_001010923.2	NP_001010923.1	Q8N1K5	THMS1_HUMAN	thymocyte selection associated	238	CABIT 1.				negative T cell selection (GO:0043383)|positive T cell selection (GO:0043368)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(3)	60						ATATCTTTTCGAACTAAAAAG	0.333																																						ENST00000368250.1																			0				breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(3)	60						c.(475-477)Cga>Tga		thymocyte selection associated							58.0	63.0	61.0					6																	128135074		2128	4283	6411	SO:0001587	stop_gained	387357				negative T cell selection|positive T cell selection|T cell receptor signaling pathway	cytoplasm|nucleus		g.chr6:128135074G>A	AK094863	CCDS34534.1, CCDS55055.1	6q22.33	2012-02-08	2009-06-25	2009-06-25	ENSG00000172673	ENSG00000172673			21569	protein-coding gene	gene with protein product	"""thymocyte expressed molecule involved in selection"""	613607	"""chromosome 6 open reading frame 207"", ""chromosome 6 open reading frame 190"", ""thymocyte selection pathway associated"""	C6orf207, C6orf190, TSEPA		19597499, 19597498, 19597497	Standard	NM_001010923		Approved	bA325O24.4, FLJ40584, bA325O24.3	uc011ebt.2	Q8N1K5	OTTHUMG00000015534	ENST00000368248.2:c.712C>T	6.37:g.128135074G>A	ENSP00000357231:p.Arg238*					THEMIS_ENST00000368248.2_Nonsense_Mutation_p.R238*|THEMIS_ENST00000537166.1_Nonsense_Mutation_p.R203*|THEMIS_ENST00000543064.1_Nonsense_Mutation_p.R238*	p.R159*			Q8N1K5	THMS1_HUMAN			5	973	-			238			CABIT 1.		A1L4F0|A8K7N1|B3KT31|B3KW32|B3KY07|F5H1J9|Q5T3C4|Q5T3C5|Q6MZT7	Nonsense_Mutation	SNP	ENST00000368248.2	37	c.475C>T	CCDS34534.1	.	.	.	.	.	.	.	.	.	.	G	37	6.242014	0.97408	.	.	ENSG00000172673	ENST00000368250;ENST00000543064;ENST00000368248;ENST00000537166;ENST00000434358	.	.	.	5.73	1.82	0.25136	.	0.466331	0.22107	N	0.064531	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.6297	16.0043	0.80349	0.0:0.0:0.6002:0.3998	.	.	.	.	X	159;238;238;203;6	.	ENSP00000357231:R238X	R	-	1	2	THEMIS	128176767	0.924000	0.31332	0.030000	0.17652	0.941000	0.58515	2.332000	0.43903	0.042000	0.15717	0.557000	0.71058	CGA		0.333	THEMIS-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_001010923		37	53	0	0	0	1	0	37	53				
SRSF9	8683	broad.mit.edu	37	12	120903592	120903592	+	Splice_Site	SNP	T	T	A	rs201316560		TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr12:120903592T>A	ENST00000229390.3	-	2	372		c.e2-2			NM_003769.2	NP_003760.1	Q13242	SRSF9_HUMAN	serine/arginine-rich splicing factor 9						gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splice site selection (GO:0006376)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1)|urinary_tract(1)	9						TCTGCATCTCTAAAAAAAACA	0.453																																						ENST00000229390.3																			0				cervix(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1)|urinary_tract(1)	9						c.e2-2		serine/arginine-rich splicing factor 9							34.0	35.0	35.0					12																	120903592		2203	4300	6503	SO:0001630	splice_region_variant	8683				mRNA 3'-end processing|mRNA export from nucleus|mRNA splice site selection|termination of RNA polymerase II transcription	nucleoplasm	nucleotide binding|RNA binding	g.chr12:120903592T>A	U30825	CCDS9199.1	12q24.31	2013-02-12	2010-06-22	2010-06-22	ENSG00000111786	ENSG00000111786		"""Serine/arginine-rich splicing factors"", ""RNA binding motif (RRM) containing"""	10791	protein-coding gene	gene with protein product	"""SR splicing factor 9"""	601943	"""splicing factor, arginine/serine-rich 9"""	SFRS9		7556075, 20516191	Standard	NM_003769		Approved	SRp30c	uc001tyi.3	Q13242	OTTHUMG00000047790	ENST00000229390.3:c.189-2A>T	12.37:g.120903592T>A								NM_003769.2	NP_003760.1	Q13242	SRSF9_HUMAN			2	372	-								Q52LD1	Splice_Site	SNP	ENST00000229390.3	37		CCDS9199.1	.	.	.	.	.	.	.	.	.	.	T	18.09	3.547009	0.65198	.	.	ENSG00000111786	ENST00000229390;ENST00000550458	.	.	.	5.18	5.18	0.71444	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.1505	0.65381	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	SRSF9	119387975	1.000000	0.71417	0.997000	0.53966	0.906000	0.53458	7.103000	0.77014	2.185000	0.69588	0.528000	0.53228	.		0.453	SRSF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108983.2	NM_003769	Intron	3	33	0	0	0	1	0	3	33				
IDH1	3417	broad.mit.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	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	NM_001282387.1	NP_001269316.1	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). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:19117336}.|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation). {ECO:0000269|PubMed:19117336}.|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). {ECO:0000269|PubMed:18772396}.|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). {ECO:0000269|PubMed:19117336}.|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). {ECO:0000269|PubMed:18772396}.		2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	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	0.393			Mis		gliobastoma																																Pancreas(158;264 1958 3300 35450 36047)	ENST00000415913.1				Dom	yes		2	2q33.3	3417	Mis	"""isocitrate dehydrogenase 1 (NADP+), soluble"""			O			gliobastoma		2835	Substitution - Missense(2834)|Complex - compound substitution(1)	p.R132H(2774)|p.R132L(59)|p.R132V(1)|p.G131_R132>VL(1)	central_nervous_system(2579)|haematopoietic_and_lymphoid_tissue(205)|bone(43)|prostate(4)|biliary_tract(2)|urinary_tract(1)|skin(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						c.(394-396)cGt>cAt		isocitrate dehydrogenase 1 (NADP+), soluble							79.0	73.0	75.0					2																	209113112		2203	4300	6503	SO:0001583	missense	3417				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	g.chr2:209113112C>T		CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.395G>A	2.37:g.209113112C>T	ENSP00000390265:p.Arg132His					IDH1_ENST00000446179.1_Missense_Mutation_p.R132H|IDH1_ENST00000345146.2_Missense_Mutation_p.R132H	p.R132H			O75874	IDHC_HUMAN		Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)	4	776	-			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).			Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	37	c.395G>A	CCDS2381.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.657324	0.88154	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913;ENST00000415282	D;D;D;D	0.86956	-2.19;-2.19;-2.19;-2.19	5.57	4.69	0.59074	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.93145	0.7817	H	0.99379	4.54	0.80722	D	1	B	0.25486	0.127	B	0.25405	0.06	D	0.92324	0.5868	10	0.87932	D	0	-20.0399	14.3783	0.66895	0.0:0.9288:0.0:0.0712	.	132	O75874	IDHC_HUMAN	H	132	ENSP00000260985:R132H;ENSP00000410513:R132H;ENSP00000390265:R132H;ENSP00000391075:R132H	ENSP00000260985:R132H	R	-	2	0	IDH1	208821357	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	6.088000	0.71371	1.356000	0.45884	0.555000	0.69702	CGT		0.393	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1			22	51	0	0	0	1	0	22	51				
IRF2	3660	broad.mit.edu	37	4	185339801	185339801	+	Silent	SNP	G	G	A	rs148758064	byFrequency	TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr4:185339801G>A	ENST00000393593.3	-	4	456	c.249C>T	c.(247-249)tgC>tgT	p.C83C	IRF2_ENST00000512020.1_5'UTR	NM_002199.3	NP_002190.2	P14316	IRF2_HUMAN	interferon regulatory factor 2	83					blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|ovary(2)|prostate(1)|skin(3)|stomach(1)|urinary_tract(2)	22		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	0.398													G|||	7	0.00139776	0.0	0.0043	5008	,	,		21467	0.0		0.001	False		,,,				2504	0.0031					ENST00000393593.3																			0				cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|ovary(2)|prostate(1)|skin(3)|stomach(1)|urinary_tract(2)	22						c.(247-249)tgC>tgT		interferon regulatory factor 2		G		1,4405	2.1+/-5.4	0,1,2202	108.0	104.0	106.0		249	-0.7	1.0	4	dbSNP_134	106	26,8574	18.5+/-59.3	0,26,4274	no	coding-synonymous	IRF2	NM_002199.3		0,27,6476	AA,AG,GG		0.3023,0.0227,0.2076		83/350	185339801	27,12979	2203	4300	6503	SO:0001819	synonymous_variant	3660				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	g.chr4:185339801G>A		CCDS3835.1	4q34.1-q35.1	2008-07-29				ENSG00000168310			6117	protein-coding gene	gene with protein product		147576				2475256	Standard	NM_002199		Approved		uc003iwf.4	P14316		ENST00000393593.3:c.249C>T	4.37:g.185339801G>A						IRF2_ENST00000512020.1_5'UTR	p.C83C	NM_002199.3	NP_002190.2	P14316	IRF2_HUMAN		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)	4	456	-		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)	83					D6RCK5|H0Y8S3|Q6IAS7|Q96B99	Silent	SNP	ENST00000393593.3	37	c.249C>T	CCDS3835.1																																																																																				0.398	IRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361393.1			4	45	0	0	0	1	0	4	45				
PGLYRP2	114770	broad.mit.edu	37	19	15582755	15582755	+	Missense_Mutation	SNP	C	C	A			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr19:15582755C>A	ENST00000340880.4	-	3	1769	c.1289G>T	c.(1288-1290)cGc>cTc	p.R430L	PGLYRP2_ENST00000292609.4_Missense_Mutation_p.R430L	NM_052890.3	NP_443122.3	Q96PD5	PGRP2_HUMAN	peptidoglycan recognition protein 2	430					defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|growth of symbiont in host (GO:0044117)|innate immune response (GO:0045087)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of natural killer cell differentiation involved in immune response (GO:0032827)|pattern recognition receptor signaling pathway (GO:0002221)|peptide amidation (GO:0001519)|peptidoglycan catabolic process (GO:0009253)|regulation of inflammatory response (GO:0050727)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	N-acetylmuramoyl-L-alanine amidase activity (GO:0008745)|peptidoglycan binding (GO:0042834)|peptidoglycan receptor activity (GO:0016019)|zinc ion binding (GO:0008270)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(3)|prostate(2)|skin(3)|stomach(2)|urinary_tract(1)	28						CTGCATGGAGCGCATGTTGGC	0.672																																						ENST00000292609.4																			0				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(3)|prostate(2)|skin(3)|stomach(2)|urinary_tract(1)	28						c.(1288-1290)cGc>cTc		peptidoglycan recognition protein 2							60.0	50.0	53.0					19																	15582755		2203	4300	6503	SO:0001583	missense	114770				defense response to Gram-positive bacterium|detection of bacterium|innate immune response|peptide amidation|peptidoglycan catabolic process	extracellular region|intracellular|membrane	N-acetylmuramoyl-L-alanine amidase activity|peptidoglycan receptor activity|zinc ion binding	g.chr19:15582755C>A	AY358156	CCDS12330.2	19p13.12	2010-04-27			ENSG00000161031	ENSG00000161031	3.5.1.28		30013	protein-coding gene	gene with protein product	"""peptidoglycan recognition protein L precursor"", ""peptidoglycan recognition protein-like"", ""N-acetylmuramoyl-L-alanine amidase"""	608199				11461926, 12669421, 14506276	Standard	NM_052890		Approved	PGRP-L, PGLYRPL, TAGL-like, tagL, tagL-alpha, tagl-beta, PGRPL	uc002nbf.4	Q96PD5	OTTHUMG00000150690	ENST00000340880.4:c.1289G>T	19.37:g.15582755C>A	ENSP00000345968:p.Arg430Leu					PGLYRP2_ENST00000340880.4_Missense_Mutation_p.R430L	p.R430L			Q96PD5	PGRP2_HUMAN			3	1418	-			430					A8K050|A8K8C7|B2RMZ2|B7ZM33|Q68CK1|Q96N74|Q9UC60	Missense_Mutation	SNP	ENST00000340880.4	37	c.1289G>T	CCDS12330.2	.	.	.	.	.	.	.	.	.	.	C	22.5	4.298386	0.81025	.	.	ENSG00000161031	ENST00000340880;ENST00000292609	T;T	0.23348	1.91;1.91	4.62	2.4	0.29515	Peptidoglycan recognition protein family domain, metazoa/bacteria (1);N-acetylmuramoyl-L-alanine amidase domain (4);	0.133333	0.44902	N	0.000418	T	0.53110	0.1776	M	0.92555	3.32	0.39536	D	0.968742	P;D	0.71674	0.857;0.998	P;D	0.69307	0.744;0.963	T	0.59783	-0.7389	10	0.87932	D	0	-11.5315	7.4635	0.27308	0.1639:0.7434:0.0:0.0927	.	430;430	Q96PD5-2;Q96PD5	.;PGRP2_HUMAN	L	430	ENSP00000345968:R430L;ENSP00000292609:R430L	ENSP00000292609:R430L	R	-	2	0	PGLYRP2	15443755	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	4.154000	0.58125	0.900000	0.36469	0.561000	0.74099	CGC		0.672	PGLYRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319626.1	NM_052890		3	45	1	0	0.150653	1	0.157661	3	45				
GTF2IRD1	9569	broad.mit.edu	37	7	74016720	74016720	+	Missense_Mutation	SNP	C	C	T			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr7:74016720C>T	ENST00000265755.3	+	27	3233	c.2840C>T	c.(2839-2841)gCc>gTc	p.A947V	GTF2IRD1_ENST00000476977.1_3'UTR|GTF2IRD1_ENST00000455841.2_Missense_Mutation_p.A964V|GTF2IRD1_ENST00000424337.2_Missense_Mutation_p.A932V	NM_005685.3|NM_016328.2	NP_005676.3|NP_057412.1	Q9UHL9	GT2D1_HUMAN	GTF2I repeat domain containing 1	947					multicellular organismal development (GO:0007275)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transition between slow and fast fiber (GO:0014886)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(19)|ovary(6)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						GTGGACTATGCCGGCCTGAAC	0.468																																						ENST00000265755.3																			0				NS(1)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(19)|ovary(6)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						c.(2839-2841)gCc>gTc		GTF2I repeat domain containing 1							141.0	130.0	133.0					7																	74016720		2203	4300	6503	SO:0001583	missense	9569					nucleus	DNA binding|protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity	g.chr7:74016720C>T	AF151354	CCDS5571.1, CCDS47613.1, CCDS56492.1	7q11.23	2008-04-18	2002-01-14		ENSG00000006704	ENSG00000006704			4661	protein-coding gene	gene with protein product	"""binding factor for early enhancer"""	604318	"""GTF2I repeat domain-containing 1"""	WBSCR11		9774679, 10198167	Standard	NM_016328		Approved	MusTRD1, RBAP2, GTF3, WBSCR12, BEN, Cream1	uc010lbq.3	Q9UHL9	OTTHUMG00000023782	ENST00000265755.3:c.2840C>T	7.37:g.74016720C>T	ENSP00000265755:p.Ala947Val					GTF2IRD1_ENST00000424337.2_Missense_Mutation_p.A932V|GTF2IRD1_ENST00000476977.1_3'UTR|GTF2IRD1_ENST00000455841.2_Missense_Mutation_p.A964V	p.A947V	NM_005685.3|NM_016328.2	NP_005676.3|NP_057412.1	Q9UHL9	GT2D1_HUMAN			27	3233	+			947					O95444|Q6DSU6|Q75MX7|Q86UM3|Q8WVC4|Q9UHK8|Q9UI91	Missense_Mutation	SNP	ENST00000265755.3	37	c.2840C>T	CCDS5571.1	.	.	.	.	.	.	.	.	.	.	C	17.48	3.400046	0.62177	.	.	ENSG00000006704	ENST00000265755;ENST00000455841;ENST00000424337	T;T;T	0.32515	1.45;1.45;1.45	5.66	4.76	0.60689	.	0.376195	0.29660	N	0.011538	T	0.21347	0.0514	N	0.22421	0.69	0.80722	D	1	B;B;B	0.26845	0.1;0.1;0.161	B;B;B	0.23852	0.024;0.036;0.049	T	0.04005	-1.0985	10	0.46703	T	0.11	-9.9402	12.4513	0.55679	0.0:0.6433:0.3567:0.0	.	964;947;932	Q6DSU6;Q9UHL9;Q9UHL9-2	.;GT2D1_HUMAN;.	V	947;964;932	ENSP00000265755:A947V;ENSP00000397566:A964V;ENSP00000408477:A932V	ENSP00000265755:A947V	A	+	2	0	GTF2IRD1	73654656	1.000000	0.71417	0.971000	0.41717	0.997000	0.91878	4.098000	0.57748	2.662000	0.90505	0.561000	0.74099	GCC		0.468	GTF2IRD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252654.2	NM_016328		3	80	0	0	0	1	0	3	80				
ZNF782	158431	broad.mit.edu	37	9	99581580	99581580	+	Missense_Mutation	SNP	G	G	C			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr9:99581580G>C	ENST00000481138.1	-	6	1386	c.725C>G	c.(724-726)tCt>tGt	p.S242C	ZNF782_ENST00000466833.1_5'Flank|ZNF782_ENST00000535338.1_Missense_Mutation_p.S110C	NM_001001662.1	NP_001001662.1	Q6ZMW2	ZN782_HUMAN	zinc finger protein 782	242					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(8)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)	33		Acute lymphoblastic leukemia(62;0.0527)				GAAATTGTAAGATTTTCCTTT	0.333																																						ENST00000481138.1																			0				NS(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(8)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)	33						c.(724-726)tCt>tGt		zinc finger protein 782							68.0	74.0	72.0					9																	99581580		2200	4298	6498	SO:0001583	missense	158431				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr9:99581580G>C	AK131468	CCDS35075.1	9q22.33	2013-01-08			ENSG00000196597	ENSG00000196597		"""Zinc fingers, C2H2-type"", ""-"""	33110	protein-coding gene	gene with protein product							Standard	NM_001001662		Approved	FLJ16636	uc004awp.1	Q6ZMW2	OTTHUMG00000020310	ENST00000481138.1:c.725C>G	9.37:g.99581580G>C	ENSP00000419397:p.Ser242Cys					ZNF782_ENST00000535338.1_Missense_Mutation_p.S110C	p.S242C	NM_001001662.1	NP_001001662.1	Q6ZMW2	ZN782_HUMAN			6	1386	-		Acute lymphoblastic leukemia(62;0.0527)	242					B2RNR0	Missense_Mutation	SNP	ENST00000481138.1	37	c.725C>G	CCDS35075.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.02|15.02	2.708803|2.708803	0.48517|0.48517	.|.	.|.	ENSG00000196597|ENSG00000196597	ENST00000289032|ENST00000481138;ENST00000535338	.|T;T	.|0.07216	.|3.39;3.21	3.43|3.43	0.311|0.311	0.15831|0.15831	.|.	.|0.861944	.|0.09457	.|U	.|0.799601	T|T	0.07369|0.07369	0.0186|0.0186	L|L	0.27053|0.27053	0.805|0.805	0.09310|0.09310	N|N	0.999994|0.999994	.|D	.|0.58620	.|0.983	.|P	.|0.46975	.|0.533	T|T	0.31752|0.31752	-0.9932|-0.9932	5|10	.|0.72032	.|D	.|0.01	.|.	3.9335|3.9335	0.09296|0.09296	0.2375:0.0:0.5753:0.1871|0.2375:0.0:0.5753:0.1871	.|.	.|242	.|Q6ZMW2	.|ZN782_HUMAN	M|C	230|242;110	.|ENSP00000419397:S242C;ENSP00000440624:S110C	.|ENSP00000419397:S242C	I|S	-|-	3|2	3|0	ZNF782|ZNF782	98621401|98621401	0.683000|0.683000	0.27633|0.27633	0.000000|0.000000	0.03702|0.03702	0.040000|0.040000	0.13550|0.13550	1.196000|1.196000	0.32198|0.32198	0.065000|0.065000	0.16485|0.16485	0.650000|0.650000	0.86243|0.86243	ATC|TCT		0.333	ZNF782-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356810.1	NM_001001662		7	85	0	0	0	1	0	7	85				
NF1	4763	broad.mit.edu	37	17	29553697	29553697	+	Nonsense_Mutation	SNP	C	C	A			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr17:29553697C>A	ENST00000358273.4	+	18	2629	c.2246C>A	c.(2245-2247)tCa>tAa	p.S749*	NF1_ENST00000356175.3_Nonsense_Mutation_p.S749*	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	749					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(4)|p.S749*(1)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		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	0.403			"""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)																												ENST00000358273.4			yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	"""D, Mis, N, F, S, O"""	neurofibromatosis type 1 gene			O		"""neurofibroma, glioma"""	"""neurofibroma, glioma"""	NF1/ACCN1(2)	13	Whole gene deletion(8)|Unknown(4)|Substitution - Nonsense(1)	p.0?(8)|p.?(4)|p.S749*(1)	soft_tissue(8)|autonomic_ganglia(2)|central_nervous_system(2)|lung(1)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599	GRCh37	CM076343	NF1	M		c.(2245-2247)tCa>tAa		neurofibromin 1							122.0	108.0	113.0					17																	29553697		2203	4300	6503	SO:0001587	stop_gained	4763	Neurofibromatosis, type 1	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	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	g.chr17:29553697C>A		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"""neurofibromatosis"", ""von Recklinghausen disease"", ""Watson disease"""	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.2246C>A	17.37:g.29553697C>A	ENSP00000351015:p.Ser749*	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)				NF1_ENST00000356175.3_Nonsense_Mutation_p.S749*	p.S749*	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN		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)	18	2629	+		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)	749					O00662|Q14284|Q14930|Q14931|Q9UMK3	Nonsense_Mutation	SNP	ENST00000358273.4	37	c.2246C>A	CCDS42292.1	.	.	.	.	.	.	.	.	.	.	C	37	6.597138	0.97692	.	.	ENSG00000196712	ENST00000358273;ENST00000356175;ENST00000456735	.	.	.	5.78	5.78	0.91487	.	0.397887	0.25912	N	0.027490	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.11485	T	0.65	.	20.0278	0.97529	0.0:1.0:0.0:0.0	.	.	.	.	X	749;749;415	.	ENSP00000348498:S749X	S	+	2	0	NF1	26577823	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.724000	0.68500	2.717000	0.92951	0.650000	0.86243	TCA		0.403	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		7	162	1	0	0.00198382	1	0.00212552	7	162				
NOS1	4842	broad.mit.edu	37	12	117669890	117669890	+	Silent	SNP	G	G	A			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr12:117669890G>A	ENST00000338101.4	-	22	3388	c.3384C>T	c.(3382-3384)acC>acT	p.T1128T	NOS1_ENST00000344089.3_3'UTR|NOS1_ENST00000317775.6_Silent_p.T1094T			Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	0					cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		CCTGGAAGATGGTGCAGGGCG	0.592																																					Esophageal Squamous(162;1748 2599 51982 52956)	ENST00000317775.6																			0				NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						c.(3280-3282)acC>acT		nitric oxide synthase 1 (neuronal)	L-Citrulline(DB00155)						74.0	83.0	80.0					12																	117669890		2170	4271	6441	SO:0001819	synonymous_variant	4842				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	g.chr12:117669890G>A		CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS		1385308, 7682706	Standard	NM_001204213		Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000338101.4:c.3384C>T	12.37:g.117669890G>A						NOS1_ENST00000344089.3_3'UTR|NOS1_ENST00000338101.4_Silent_p.T1128T	p.T1094T	NM_000620.4|NM_001204218.1	NP_000611.1|NP_001191147.1	P29475	NOS1_HUMAN		BRCA - Breast invasive adenocarcinoma(302;0.0561)	22	3967	-	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)		1094			FAD-binding FR-type.			Silent	SNP	ENST00000338101.4	37	c.3282C>T	CCDS55890.1																																																																																				0.592	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000268053.1			19	19	0	0	0	1	0	19	19				
PHACTR3	116154	broad.mit.edu	37	20	58381107	58381107	+	Missense_Mutation	SNP	C	C	T			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr20:58381107C>T	ENST00000371015.1	+	8	1653	c.1186C>T	c.(1186-1188)Cgg>Tgg	p.R396W	PHACTR3_ENST00000355648.4_Missense_Mutation_p.R355W|PHACTR3_ENST00000395639.4_Missense_Mutation_p.R285W|PHACTR3_ENST00000361300.4_Missense_Mutation_p.R285W|PHACTR3_ENST00000359926.3_Missense_Mutation_p.R393W|PHACTR3_ENST00000395636.2_Missense_Mutation_p.R355W|PHACTR3_ENST00000541461.1_Missense_Mutation_p.R355W	NM_001281507.1|NM_080672.3	NP_001268436.1|NP_542403.1	Q96KR7	PHAR3_HUMAN	phosphatase and actin regulator 3	396						nucleus (GO:0005634)	protein phosphatase inhibitor activity (GO:0004864)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|liver(2)|lung(32)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	59	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;2.76e-09)			AACACTGCCACGGAAATGCAA	0.547																																						ENST00000371015.1																			0				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|liver(2)|lung(32)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	59						c.(1186-1188)Cgg>Tgg		phosphatase and actin regulator 3							193.0	208.0	203.0					20																	58381107		2203	4300	6503	SO:0001583	missense	116154					nuclear matrix	actin binding|protein phosphatase inhibitor activity	g.chr20:58381107C>T	AJ311122	CCDS13480.1, CCDS13481.1, CCDS42895.1, CCDS56202.1	20q13.32-q13.33	2014-06-13	2004-05-20	2004-05-20	ENSG00000087495	ENSG00000087495		"""Phosphatase and actin regulators"""	15833	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 123"""	608725	"""chromosome 20 open reading frame 101"""	C20orf101		15107502	Standard	NM_001199505		Approved	PPP1R123	uc002yau.3	Q96KR7	OTTHUMG00000032869	ENST00000371015.1:c.1186C>T	20.37:g.58381107C>T	ENSP00000360054:p.Arg396Trp					PHACTR3_ENST00000355648.4_Missense_Mutation_p.R355W|PHACTR3_ENST00000361300.4_Missense_Mutation_p.R285W|PHACTR3_ENST00000395636.2_Missense_Mutation_p.R355W|PHACTR3_ENST00000395639.4_Missense_Mutation_p.R285W|PHACTR3_ENST00000359926.3_Missense_Mutation_p.R393W|PHACTR3_ENST00000541461.1_Missense_Mutation_p.R355W	p.R396W	NM_080672.3	NP_542403.1	Q96KR7	PHAR3_HUMAN	BRCA - Breast invasive adenocarcinoma(7;2.76e-09)		8	1653	+	all_lung(29;0.00344)		396					B1AKX0|B1AN68|B1AN69|B2RB46|Q32P33|Q707P6|Q9H4T4	Missense_Mutation	SNP	ENST00000371015.1	37	c.1186C>T	CCDS13480.1	.	.	.	.	.	.	.	.	.	.	C	12.73	2.024513	0.35701	.	.	ENSG00000087495	ENST00000359926;ENST00000371015;ENST00000395639;ENST00000541461;ENST00000355648;ENST00000395636;ENST00000361300	T;T;T;T;T;T;T	0.34072	1.74;1.75;1.38;1.76;1.76;1.76;1.38	5.07	2.77	0.32553	.	0.000000	0.85682	D	0.000000	T	0.57431	0.2053	M	0.74258	2.255	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.982;0.982	T	0.58233	-0.7672	10	0.87932	D	0	-25.6526	11.567	0.50811	0.5299:0.4701:0.0:0.0	.	285;396;393	Q96KR7-3;Q96KR7;B1AKX0	.;PHAR3_HUMAN;.	W	393;396;285;355;355;355;285	ENSP00000353002:R393W;ENSP00000360054:R396W;ENSP00000379001:R285W;ENSP00000442483:R355W;ENSP00000347866:R355W;ENSP00000378998:R355W;ENSP00000354555:R285W	ENSP00000347866:R355W	R	+	1	2	PHACTR3	57814502	0.954000	0.32549	0.573000	0.28510	0.168000	0.22595	2.287000	0.43505	0.259000	0.21709	-0.271000	0.10264	CGG		0.547	PHACTR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079923.3	NM_080672		61	249	0	0	0	1	0	61	249				
KRTAP13-1	140258	broad.mit.edu	37	21	31768834	31768834	+	Missense_Mutation	SNP	G	G	A	rs374257240		TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr21:31768834G>A	ENST00000355459.2	+	1	443	c.430G>A	c.(430-432)Gtt>Att	p.V144I		NM_181599.2	NP_853630.2	Q8IUC0	KR131_HUMAN	keratin associated protein 13-1	144						intermediate filament (GO:0005882)				endometrium(1)|kidney(2)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						GGGCTATGGCGTTGGATTCTG	0.542																																						ENST00000355459.2																			0				endometrium(1)|kidney(2)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						c.(430-432)Gtt>Att		keratin associated protein 13-1		G	ILE/VAL	0,4406		0,0,2203	61.0	57.0	59.0		430	1.8	0.0	21		59	1,8599	1.2+/-3.3	0,1,4299	no	missense	KRTAP13-1	NM_181599.2	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	144/173	31768834	1,13005	2203	4300	6503	SO:0001583	missense	140258					intermediate filament		g.chr21:31768834G>A	AJ457066	CCDS13590.2	21q22.11	2013-06-20			ENSG00000198390	ENSG00000198390		"""Keratin associated proteins"""	18924	protein-coding gene	gene with protein product		608718				12359730	Standard	NM_181599		Approved	KAP13.1	uc002yoa.3	Q8IUC0	OTTHUMG00000057800	ENST00000355459.2:c.430G>A	21.37:g.31768834G>A	ENSP00000347635:p.Val144Ile						p.V144I	NM_181599.2	NP_853630.2	Q8IUC0	KR131_HUMAN			1	443	+			144					Q14D20|Q3LI79	Missense_Mutation	SNP	ENST00000355459.2	37	c.430G>A	CCDS13590.2	.	.	.	.	.	.	.	.	.	.	G	11.60	1.685832	0.29962	0.0	1.16E-4	ENSG00000198390	ENST00000355459	T	0.03035	4.07	4.41	1.76	0.24704	.	0.557606	0.14727	N	0.301981	T	0.02848	0.0085	N	0.24115	0.695	0.09310	N	1	B	0.11235	0.004	B	0.08055	0.003	T	0.41324	-0.9515	10	0.66056	D	0.02	.	5.945	0.19213	0.0:0.0984:0.1624:0.7392	.	144	Q8IUC0	KR131_HUMAN	I	144	ENSP00000347635:V144I	ENSP00000347635:V144I	V	+	1	0	KRTAP13-1	30690705	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.068000	0.14531	0.372000	0.24591	-0.272000	0.10252	GTT		0.542	KRTAP13-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128252.3			15	16	0	0	0	1	0	15	16				
ZDHHC11	79844	broad.mit.edu	37	5	814876	814876	+	Splice_Site	SNP	C	C	G	rs370784284		TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr5:814876C>G	ENST00000283441.8	-	11	1564	c.1181G>C	c.(1180-1182)gGg>gCg	p.G394A	ZDHHC11_ENST00000424784.2_Splice_Site_p.G394A|ZDHHC11_ENST00000503758.2_5'UTR	NM_024786.2	NP_079062.1	Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11	394						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|liver(1)|lung(10)|pancreas(1)|prostate(5)|skin(2)|urinary_tract(1)	21			Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)			ACGAACTTACCCAAGTGTAGA	0.378																																						ENST00000283441.8																			0				haematopoietic_and_lymphoid_tissue(1)|liver(1)|lung(10)|pancreas(1)|prostate(5)|skin(2)|urinary_tract(1)	21						c.e11+1		zinc finger, DHHC-type containing 11							135.0	92.0	107.0					5																	814876		2203	4290	6493	SO:0001630	splice_region_variant	79844					integral to membrane	acyltransferase activity|zinc ion binding	g.chr5:814876C>G	AK023215	CCDS3857.1	5p15.2	2011-02-09			ENSG00000188818	ENSG00000188818		"""Zinc fingers, DHHC-type"""	19158	protein-coding gene	gene with protein product							Standard	NM_024786		Approved	ZNF399, FLJ13153	uc011cma.1	Q9H8X9	OTTHUMG00000090319	ENST00000283441.8:c.1181+1G>C	5.37:g.814876C>G						ZDHHC11_ENST00000424784.2_Splice_Site_p.G394_splice|ZDHHC11_ENST00000503758.2_5'UTR	p.G394_splice	NM_024786.2	NP_079062.1	Q9H8X9	ZDH11_HUMAN	Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)		11	1564	-			394					Q6UWR9	Splice_Site	SNP	ENST00000283441.8	37	c.1181_splice	CCDS3857.1	.	.	.	.	.	.	.	.	.	.	c	0.573	-0.840121	0.02692	.	.	ENSG00000188818	ENST00000424784;ENST00000283441	T;T	0.56444	0.46;0.46	1.23	1.23	0.21249	.	.	.	.	.	T	0.22475	0.0542	N	0.08118	0	0.09310	N	1	P	0.36535	0.557	B	0.23150	0.044	T	0.07214	-1.0784	8	.	.	.	.	5.8228	0.18536	0.0:1.0:0.0:0.0	.	394	Q9H8X9	ZDH11_HUMAN	A	394	ENSP00000397719:G394A;ENSP00000283441:G394A	.	G	-	2	0	ZDHHC11	867876	0.009000	0.17119	0.013000	0.15412	0.025000	0.11179	1.314000	0.33597	0.966000	0.38159	0.195000	0.17529	GGG		0.378	ZDHHC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206681.3	NM_024786	Missense_Mutation	25	31	0	0	0	1	0	25	31				
KIF26A	26153	broad.mit.edu	37	14	104643666	104643666	+	Nonsense_Mutation	SNP	C	C	A			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr14:104643666C>A	ENST00000423312.2	+	12	4541	c.4541C>A	c.(4540-4542)tCg>tAg	p.S1514*	KIF26A_ENST00000315264.7_Nonsense_Mutation_p.S1375*	NM_015656.1	NP_056471.1	Q9ULI4	KI26A_HUMAN	kinesin family member 26A	1514					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|blood coagulation (GO:0007596)|enteric nervous system development (GO:0048484)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of signal transduction (GO:0009968)|regulation of cell growth by extracellular stimulus (GO:0001560)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	21		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0767)	Epithelial(46;0.152)	Epithelial(152;0.161)		CTGGGGCCTTCGGTGAAGCTG	0.736																																						ENST00000315264.7																			0				autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	21						c.(4123-4125)tCg>tAg		kinesin family member 26A							8.0	12.0	11.0					14																	104643666		1805	3942	5747	SO:0001587	stop_gained	26153				blood coagulation|enteric nervous system development|microtubule-based movement|negative regulation of signal transduction|regulation of cell growth by extracellular stimulus	cytosol|microtubule	ATP binding|microtubule binding|microtubule motor activity	g.chr14:104643666C>A	AB033062	CCDS45171.1	14q32.33	2009-03-19			ENSG00000066735	ENSG00000066735		"""Kinesins"""	20226	protein-coding gene	gene with protein product		613231				10574462, 11416179	Standard	NM_015656		Approved	KIAA1236, DKFZP434N178	uc001yos.4	Q9ULI4	OTTHUMG00000154986	ENST00000423312.2:c.4541C>A	14.37:g.104643666C>A	ENSP00000388241:p.Ser1514*					KIF26A_ENST00000423312.2_Nonsense_Mutation_p.S1514*	p.S1375*			Q9ULI4	KI26A_HUMAN	Epithelial(46;0.152)	Epithelial(152;0.161)	11	4502	+		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0767)	1514					Q8TAZ7|Q96GK3|Q9UFL3	Nonsense_Mutation	SNP	ENST00000423312.2	37	c.4124C>A	CCDS45171.1	.	.	.	.	.	.	.	.	.	.	C	42	9.773959	0.99260	.	.	ENSG00000066735	ENST00000423312;ENST00000315264	.	.	.	3.57	2.67	0.31697	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.4395	0.44457	0.0:0.9025:0.0:0.0975	.	.	.	.	X	1514;1375	.	ENSP00000325452:S1375X	S	+	2	0	KIF26A	103713419	0.990000	0.36364	0.001000	0.08648	0.004000	0.04260	4.409000	0.59768	0.689000	0.31550	0.462000	0.41574	TCG		0.736	KIF26A-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414356.1			2	4	1	0	1	1	1	2	4				
IRF2BP1	26145	broad.mit.edu	37	19	46387378	46387378	+	Missense_Mutation	SNP	C	C	A			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr19:46387378C>A	ENST00000302165.3	-	1	1998	c.1655G>T	c.(1654-1656)tGc>tTc	p.C552F		NM_015649.1	NP_056464.1	Q8IU81	I2BP1_HUMAN	interferon regulatory factor 2 binding protein 1	552					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)			cervix(1)|kidney(1)|lung(2)	4		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	0.642																																						ENST00000302165.3																			0				cervix(1)|kidney(1)|lung(2)	4						c.(1654-1656)tGc>tTc		interferon regulatory factor 2 binding protein 1							46.0	45.0	45.0					19																	46387378		2202	4300	6502	SO:0001583	missense	26145				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus		g.chr19:46387378C>A	AY278022	CCDS12678.1	19q13.32	2008-02-05							21728	protein-coding gene	gene with protein product		615331				12799427	Standard	NM_015649		Approved	DKFZP434M154, IRF-2BP1	uc002pds.1	Q8IU81		ENST00000302165.3:c.1655G>T	19.37:g.46387378C>A	ENSP00000307265:p.Cys552Phe						p.C552F	NM_015649.1	NP_056464.1	Q8IU81	I2BP1_HUMAN		OV - Ovarian serous cystadenocarcinoma(262;0.00442)|GBM - Glioblastoma multiforme(486;0.0402)|Epithelial(262;0.231)	1	1998	-		all_neural(266;0.113)|Ovarian(192;0.127)	552					Q53EL7|Q6DC95|Q9BRZ9|Q9Y4P4	Missense_Mutation	SNP	ENST00000302165.3	37	c.1655G>T	CCDS12678.1	.	.	.	.	.	.	.	.	.	.	C	19.24	3.789761	0.70337	.	.	ENSG00000170604	ENST00000302165	D	0.84298	-1.83	4.58	4.58	0.56647	.	0.000000	0.64402	D	0.000001	D	0.90335	0.6976	L	0.60455	1.87	0.80722	D	1	D	0.71674	0.998	D	0.79784	0.993	D	0.91344	0.5099	10	0.87932	D	0	.	14.914	0.70781	0.0:1.0:0.0:0.0	.	552	Q8IU81	I2BP1_HUMAN	F	552	ENSP00000307265:C552F	ENSP00000307265:C552F	C	-	2	0	IRF2BP1	51079218	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	7.645000	0.83430	2.362000	0.80069	0.563000	0.77884	TGC		0.642	IRF2BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461683.1	NM_015649		13	4	1	0	7.93312e-07	1	8.92476e-07	13	4				
PWP2	5822	broad.mit.edu	37	21	45540355	45540355	+	Missense_Mutation	SNP	G	G	A			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr21:45540355G>A	ENST00000291576.7	+	11	1442	c.1315G>A	c.(1315-1317)Gtg>Atg	p.V439M		NM_005049.2	NP_005040.2	Q15269	PWP2_HUMAN	PWP2 periodic tryptophan protein homolog (yeast)	439					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|signal transducer activity (GO:0004871)			cervix(1)|endometrium(6)|large_intestine(6)|lung(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(1)	21				STAD - Stomach adenocarcinoma(101;0.172)|Colorectal(79;0.2)		GGACGGGACCGTGCGAGCCTT	0.597																																						ENST00000291576.7																			0				cervix(1)|endometrium(6)|large_intestine(6)|lung(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(1)	21						c.(1315-1317)Gtg>Atg		PWP2 periodic tryptophan protein homolog (yeast)							182.0	157.0	166.0					21																	45540355		2203	4300	6503	SO:0001583	missense	5822					cytoplasm|nucleolus	signal transducer activity	g.chr21:45540355G>A		CCDS33579.1	21q22.3	2013-01-10	2001-11-28	2006-11-24	ENSG00000241945	ENSG00000241945		"""WD repeat domain containing"""	9711	protein-coding gene	gene with protein product		601475	"""PWP2 (periodic tryptophan protein, yeast) homolog"""	PWP2H		8893822	Standard	NM_005049		Approved	EHOC-17, UTP1	uc002zeb.3	Q15269	OTTHUMG00000086893	ENST00000291576.7:c.1315G>A	21.37:g.45540355G>A	ENSP00000291576:p.Val439Met						p.V439M	NM_005049.2	NP_005040.2	Q15269	PWP2_HUMAN		STAD - Stomach adenocarcinoma(101;0.172)|Colorectal(79;0.2)	11	1442	+			439					B2RAG8|Q96A77	Missense_Mutation	SNP	ENST00000291576.7	37	c.1315G>A	CCDS33579.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.394784	0.83011	.	.	ENSG00000241945	ENST00000291576	T	0.67345	-0.26	4.89	4.89	0.63831	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.83390	0.5244	M	0.84511	2.7	0.58432	D	0.999999	D	0.89917	1.0	D	0.81914	0.995	D	0.86497	0.1801	10	0.87932	D	0	-16.228	16.6196	0.84926	0.0:0.0:1.0:0.0	.	439	Q15269	PWP2_HUMAN	M	439	ENSP00000291576:V439M	ENSP00000291576:V439M	V	+	1	0	PWP2	44364783	1.000000	0.71417	0.773000	0.31616	0.712000	0.41017	8.503000	0.90509	2.425000	0.82216	0.655000	0.94253	GTG		0.597	PWP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195736.3	NM_005049		67	80	0	0	0	1	0	67	80				
NT5C	30833	broad.mit.edu	37	17	73126675	73126675	+	Missense_Mutation	SNP	C	C	A			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr17:73126675C>A	ENST00000245552.2	-	5	601	c.514G>T	c.(514-516)Gtc>Ttc	p.V172F	NT5C_ENST00000579082.1_5'Flank|NT5C_ENST00000578337.1_3'UTR|NT5C_ENST00000582170.1_Missense_Mutation_p.G170V|NT5C_ENST00000582160.1_Missense_Mutation_p.V86F	NM_014595.2	NP_055410.1	Q8TCD5	NT5C_HUMAN	5', 3'-nucleotidase, cytosolic	172					dephosphorylation (GO:0016311)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|pyrimidine deoxyribonucleotide catabolic process (GO:0009223)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	5'-nucleotidase activity (GO:0008253)|metal ion binding (GO:0046872)|nucleotidase activity (GO:0008252)|pyrimidine nucleotide binding (GO:0019103)					all_lung(278;0.14)|Lung NSC(278;0.168)		LUSC - Lung squamous cell carcinoma(166;0.162)|Lung(188;0.235)		Lamivudine(DB00709)	GGGGGCAGGACCAGGTGCCGA	0.607											OREG0024728	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										ENST00000245552.2																			0											c.(514-516)Gtc>Ttc		5', 3'-nucleotidase, cytosolic							70.0	66.0	67.0					17																	73126675		2203	4300	6503	SO:0001583	missense	30833				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	g.chr17:73126675C>A	AF154829	CCDS11715.1	17q25	2011-03-29	2002-05-23		ENSG00000125458	ENSG00000125458	3.1.3.5		17144	protein-coding gene	gene with protein product		191720	"""5' nucleotidase, deoxy (pyrimidine), cytosolic type C"", ""uridine 5-prime monophosphate hydrolase 2"""	UMPH2		10899995	Standard	NM_014595		Approved	DNT1, DNT-1, PN-I, cdN, dNT-1	uc002jmx.3	Q8TCD5		ENST00000245552.2:c.514G>T	17.37:g.73126675C>A	ENSP00000245552:p.Val172Phe		OREG0024728	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	1142	NT5C_ENST00000578337.1_3'UTR|NT5C_ENST00000582170.1_Missense_Mutation_p.G170V|NT5C_ENST00000582160.1_Missense_Mutation_p.V86F	p.V172F	NM_014595.2	NP_055410.1	Q8TCD5	NT5C_HUMAN	LUSC - Lung squamous cell carcinoma(166;0.162)|Lung(188;0.235)		5	601	-	all_lung(278;0.14)|Lung NSC(278;0.168)		172					Q96HS6|Q9NP82	Missense_Mutation	SNP	ENST00000245552.2	37	c.514G>T	CCDS11715.1	.	.	.	.	.	.	.	.	.	.	C	11.57	1.677664	0.29783	.	.	ENSG00000125458	ENST00000245552	T	0.42513	0.97	4.74	3.75	0.43078	HAD-like domain (2);	0.998287	0.08109	N	0.996414	T	0.22589	0.0545	N	0.08118	0	0.80722	D	1	B	0.33883	0.43	B	0.31495	0.131	T	0.08994	-1.0695	10	0.56958	D	0.05	-7.6615	4.9349	0.13935	0.0:0.6401:0.189:0.1709	.	172	Q8TCD5	NT5C_HUMAN	F	172	ENSP00000245552:V172F	ENSP00000245552:V172F	V	-	1	0	NT5C	70638270	0.161000	0.22892	0.994000	0.49952	0.911000	0.54048	0.107000	0.15375	1.318000	0.45170	0.561000	0.74099	GTC		0.607	NT5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445853.1			25	42	1	0	9.93527e-08	1	1.14638e-07	25	42				
NPTX1	4884	broad.mit.edu	37	17	78444660	78444660	+	Missense_Mutation	SNP	C	C	T			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr17:78444660C>T	ENST00000306773.4	-	5	1409	c.1252G>A	c.(1252-1254)Gga>Aga	p.G418R	NPTX1_ENST00000575212.1_5'Flank	NM_002522.3	NP_002513.2	Q15818	NPTX1_HUMAN	neuronal pentraxin I	418	Pentaxin.				axonogenesis involved in innervation (GO:0060385)|cellular response to glucose stimulus (GO:0071333)|cellular response to potassium ion (GO:0035865)|central nervous system development (GO:0007417)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrial transport (GO:0006839)|synaptic transmission (GO:0007268)|transport (GO:0006810)	cytoplasmic vesicle (GO:0031410)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			kidney(1)|large_intestine(2)|liver(1)|lung(4)|prostate(2)|upper_aerodigestive_tract(1)	11	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0487)			GTGGCCCCTCCGTAGATCTCG	0.662																																						ENST00000306773.4																			0				kidney(1)|large_intestine(2)|liver(1)|lung(4)|prostate(2)|upper_aerodigestive_tract(1)	11						c.(1252-1254)Gga>Aga		neuronal pentraxin I							71.0	64.0	66.0					17																	78444660		2203	4300	6503	SO:0001583	missense	4884				central nervous system development|synaptic transmission|transport	transport vesicle	metal ion binding	g.chr17:78444660C>T	U61849	CCDS32762.1	17q25.3	2008-05-14				ENSG00000171246			7952	protein-coding gene	gene with protein product		602367				8884281	Standard	NM_002522		Approved		uc002jyp.1	Q15818		ENST00000306773.4:c.1252G>A	17.37:g.78444660C>T	ENSP00000307549:p.Gly418Arg						p.G418R	NM_002522.3	NP_002513.2	Q15818	NPTX1_HUMAN	BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0487)		5	1409	-	all_neural(118;0.0538)		418			Pentaxin.		B3KXH3|Q5FWE6	Missense_Mutation	SNP	ENST00000306773.4	37	c.1252G>A	CCDS32762.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.351706	0.82132	.	.	ENSG00000171246	ENST00000306773;ENST00000535681	T	0.66815	-0.23	5.55	5.55	0.83447	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.000000	0.85682	D	0.000000	D	0.88288	0.6396	H	0.96111	3.77	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.91661	0.5342	10	0.87932	D	0	-15.3641	19.0994	0.93268	0.0:1.0:0.0:0.0	.	418	Q15818	NPTX1_HUMAN	R	418;180	ENSP00000307549:G418R	ENSP00000307549:G418R	G	-	1	0	NPTX1	76059255	1.000000	0.71417	0.122000	0.21767	0.404000	0.30871	7.749000	0.85096	2.607000	0.88179	0.561000	0.74099	GGA		0.662	NPTX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438051.1			7	48	0	0	0	1	0	7	48				
TXK	7294	broad.mit.edu	37	4	48114404	48114404	+	Silent	SNP	A	A	G	rs369849027		TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr4:48114404A>G	ENST00000264316.4	-	4	385	c.300T>C	c.(298-300)aaT>aaC	p.N100N	RNU6-868P_ENST00000517241.1_RNA|TXK_ENST00000510457.1_5'UTR	NM_003328.2	NP_003319.2	P42681	TXK_HUMAN	TXK tyrosine kinase	100	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				activation of phospholipase C activity (GO:0007202)|adaptive immune response (GO:0002250)|cytokine production (GO:0001816)|interferon-gamma production (GO:0032609)|interleukin-4 production (GO:0032633)|NK T cell differentiation (GO:0001865)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|T cell receptor signaling pathway (GO:0050852)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|RNA polymerase II regulatory region DNA binding (GO:0001012)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|prostate(2)	25						TTAAGGCTAAATTACAGGGTT	0.468																																						ENST00000264316.4																			0				breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|prostate(2)	25						c.(298-300)aaT>aaC		TXK tyrosine kinase		A		2,4404	4.2+/-10.8	0,2,2201	185.0	190.0	188.0		300	-7.7	0.0	4		188	0,8600		0,0,4300	no	coding-synonymous	TXK	NM_003328.2		0,2,6501	GG,GA,AA		0.0,0.0454,0.0154		100/528	48114404	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	7294					cytoplasm	ATP binding|non-membrane spanning protein tyrosine kinase activity	g.chr4:48114404A>G	L27071	CCDS3480.1	4p12	2013-02-14	2003-04-01		ENSG00000074966	ENSG00000074966	2.7.10.1	"""SH2 domain containing"""	12434	protein-coding gene	gene with protein product		600058	"""PTK4 protein tyrosine kinase 4"""	PTK4		7951233, 7528718	Standard	NM_003328		Approved	TKL, PSCTK5, BTKL, RLK	uc003gxx.4	P42681	OTTHUMG00000102065	ENST00000264316.4:c.300T>C	4.37:g.48114404A>G						TXK_ENST00000510457.1_5'UTR	p.N100N	NM_003328.2	NP_003319.2	P42681	TXK_HUMAN			4	385	-			100			SH3.		Q14220	Silent	SNP	ENST00000264316.4	37	c.300T>C	CCDS3480.1																																																																																				0.468	TXK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219869.7	NM_003328		26	136	0	0	0	1	0	26	136				
DNAH8	1769	broad.mit.edu	37	6	38690599	38690599	+	5'Flank	SNP	C	C	T			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr6:38690599C>T	ENST00000359357.3	+	0	0				DNAH8_ENST00000449981.2_Missense_Mutation_p.A5V			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8						cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						GAGAAGGATGCTGAAGATGGC	0.532																																						ENST00000449981.2																			0				NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						c.(13-15)gCt>gTt		dynein, axonemal, heavy chain 8							29.0	29.0	29.0					6																	38690599		876	1991	2867	SO:0001631	upstream_gene_variant	1769							g.chr6:38690599C>T	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"""Axonemal dyneins"""	2952	protein-coding gene	gene with protein product		603337	"""dynein, axonemal, heavy polypeptide 8"""			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253		6.37:g.38690599C>T	Exception_encountered						p.A5V							2	123	+								O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	37	c.14C>T		.	.	.	.	.	.	.	.	.	.	C	13.67	2.307703	0.40795	.	.	ENSG00000124721	ENST00000373278	.	.	.	4.66	3.78	0.43462	.	.	.	.	.	T	0.10723	0.0262	N	0.08118	0	0.31108	N	0.710241	B	0.32829	0.386	B	0.34242	0.178	T	0.14811	-1.0459	8	0.30854	T	0.27	.	11.6843	0.51476	0.1776:0.8223:0.0:0.0	.	5	Q8IU65	.	V	5	.	ENSP00000362375:A5V	A	+	2	0	DNAH8	38798577	0.002000	0.14202	0.001000	0.08648	0.004000	0.04260	0.235000	0.17948	1.064000	0.40671	0.591000	0.81541	GCT		0.532	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		9	13	0	0	0	1	0	9	13				
FKBP8	23770	broad.mit.edu	37	19	18650228	18650228	+	Silent	SNP	C	C	T	rs376393547		TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr19:18650228C>T	ENST00000596558.2	-	4	613	c.504G>A	c.(502-504)acG>acA	p.T168T	FKBP8_ENST00000608443.1_Silent_p.T168T|FKBP8_ENST00000610101.1_Intron|FKBP8_ENST00000453489.2_Silent_p.T197T|FKBP8_ENST00000222308.4_Silent_p.T168T|FKBP8_ENST00000597960.3_Silent_p.T168T			Q14318	FKBP8_HUMAN	FK506 binding protein 8, 38kDa	168	PPIase FKBP-type. {ECO:0000255|PROSITE- ProRule:PRU00277}.				apoptotic process (GO:0006915)|camera-type eye development (GO:0043010)|cell fate specification (GO:0001708)|chaperone-mediated protein folding (GO:0061077)|dorsal/ventral neural tube patterning (GO:0021904)|intracellular signal transduction (GO:0035556)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|positive regulation of BMP signaling pathway (GO:0030513)|protein peptidyl-prolyl isomerization (GO:0000413)|regulation of gene expression (GO:0010468)|smoothened signaling pathway (GO:0007224)|viral process (GO:0016032)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|mitochondrial envelope (GO:0005740)	FK506 binding (GO:0005528)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)	15						TGACCATGGCCGTCTCCCCCA	0.637																																						ENST00000597960.2																			0				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)	15						c.(502-504)acG>acA		FK506 binding protein 8, 38kDa		C		0,4406		0,0,2203	115.0	86.0	95.0		504	-2.7	1.0	19		95	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	FKBP8	NM_012181.3		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		168/414	18650228	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	23770				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	g.chr19:18650228C>T	L37033	CCDS32961.1	19p12	2013-01-10	2002-08-29		ENSG00000105701	ENSG00000105701		"""Tetratricopeptide (TTC) repeat domain containing"""	3724	protein-coding gene	gene with protein product	"""FK506-binding protein 8 (38kD)"""	604840	"""FK506-binding protein 8 (38kD)"""			7543869	Standard	NM_012181		Approved	FKBP38, FKBPr38	uc002njj.1	Q14318		ENST00000596558.2:c.504G>A	19.37:g.18650228C>T						FKBP8_ENST00000453489.2_Silent_p.T197T|FKBP8_ENST00000222308.3_Silent_p.T168T|FKBP8_ENST00000544835.2_Intron|FKBP8_ENST00000596558.1_Silent_p.T168T	p.T168T			Q14318	FKBP8_HUMAN			4	624	-			168			PPIase FKBP-type.		C8C9T5|Q53GU3|Q7Z349|Q86YK6	Silent	SNP	ENST00000596558.2	37	c.504G>A																																																																																					0.637	FKBP8-002	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000466374.3	NM_012181		49	48	0	0	0	1	0	49	48				
FRMPD4	9758	broad.mit.edu	37	X	12701668	12701668	+	Missense_Mutation	SNP	C	C	T			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chrX:12701668C>T	ENST00000380682.1	+	6	1041	c.535C>T	c.(535-537)Cgc>Tgc	p.R179C		NM_014728.3	NP_055543.2	Q14CM0	FRPD4_HUMAN	FERM and PDZ domain containing 4	179					positive regulation of synapse structural plasticity (GO:0051835)	cytoskeleton (GO:0005856)|dendritic spine (GO:0043197)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			breast(1)|central_nervous_system(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)	22						TGTCAAAGTACGCTTCTCTGA	0.423																																						ENST00000380682.1																			0				breast(1)|central_nervous_system(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)	22						c.(535-537)Cgc>Tgc		FERM and PDZ domain containing 4							125.0	95.0	105.0					X																	12701668		2203	4300	6503	SO:0001583	missense	9758				positive regulation of synapse structural plasticity	cytoskeleton|dendritic spine	phosphatidylinositol-4,5-bisphosphate binding|protein binding	g.chrX:12701668C>T	AB002314	CCDS35201.1	Xp22.31	2006-02-09	2006-02-09	2006-02-09	ENSG00000169933	ENSG00000169933			29007	protein-coding gene	gene with protein product		300838	"""PDZ domain containing 10"""	PDZK10, PDZD10		9205841	Standard	NM_014728		Approved	KIAA0316	uc004cuz.2	Q14CM0	OTTHUMG00000021138	ENST00000380682.1:c.535C>T	X.37:g.12701668C>T	ENSP00000370057:p.Arg179Cys						p.R179C	NM_014728.3	NP_055543.2	Q14CM0	FRPD4_HUMAN			6	1041	+			179					A8K0X9|O15032	Missense_Mutation	SNP	ENST00000380682.1	37	c.535C>T	CCDS35201.1	.	.	.	.	.	.	.	.	.	.	C	27.6	4.847936	0.91277	.	.	ENSG00000169933	ENST00000380682;ENST00000429478;ENST00000304087	T	0.09073	3.02	5.11	5.11	0.69529	.	0.000000	0.85682	D	0.000000	T	0.28333	0.0700	M	0.64997	1.995	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.995	T	0.01386	-1.1368	10	0.87932	D	0	.	17.9703	0.89111	0.0:1.0:0.0:0.0	.	171;179	B7ZLE1;Q14CM0	.;FRPD4_HUMAN	C	179;170;168	ENSP00000370057:R179C	ENSP00000304583:R168C	R	+	1	0	FRMPD4	12611589	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.370000	0.79589	2.264000	0.75181	0.600000	0.82982	CGC		0.423	FRMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055771.1	XM_045712		24	3	0	0	0	1	0	24	3				
PLEKHG4B	153478	broad.mit.edu	37	5	143249	143249	+	Missense_Mutation	SNP	G	G	A	rs115149634	byFrequency	TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr5:143249G>A	ENST00000283426.6	+	2	547	c.497G>A	c.(496-498)cGg>cAg	p.R166Q	Y_RNA_ENST00000362670.1_RNA	NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4B	166							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(1)|large_intestine(2)|lung(2)|prostate(3)|skin(3)	11			all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)		GTGCCTGCCCGGCAGCCACAC	0.647																																						ENST00000283426.6																			0				endometrium(1)|large_intestine(2)|lung(2)|prostate(3)|skin(3)	11						c.(496-498)cGg>cAg		pleckstrin homology domain containing, family G (with RhoGef domain) member 4B							60.0	74.0	69.0					5																	143249		2202	4298	6500	SO:0001583	missense	153478				regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity	g.chr5:143249G>A	BC008352	CCDS34124.1	5p15.33	2013-01-11			ENSG00000153404	ENSG00000153404		"""Pleckstrin homology (PH) domain containing"""	29399	protein-coding gene	gene with protein product						11572484	Standard	NM_052909		Approved	KIAA1909	uc003jak.2	Q96PX9	OTTHUMG00000161570	ENST00000283426.6:c.497G>A	5.37:g.143249G>A	ENSP00000283426:p.Arg166Gln						p.R166Q	NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)	2	547	+			166						Missense_Mutation	SNP	ENST00000283426.6	37	c.497G>A	CCDS34124.1	.	.	.	.	.	.	.	.	.	.	.	1.770	-0.484579	0.04352	.	.	ENSG00000153404	ENST00000283426;ENST00000502646	T;T	0.27402	1.67;3.09	2.85	-2.41	0.06562	.	.	.	.	.	T	0.08492	0.0211	N	0.02539	-0.55	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.29549	-1.0008	9	0.15066	T	0.55	.	1.1536	0.01791	0.5216:0.1755:0.1302:0.1728	.	166	Q96PX9	PKH4B_HUMAN	Q	166;80	ENSP00000283426:R166Q;ENSP00000422493:R80Q	ENSP00000283426:R166Q	R	+	2	0	PLEKHG4B	196249	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.352000	0.07701	-0.686000	0.05170	-2.195000	0.00310	CGG		0.647	PLEKHG4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365359.1	NM_052909		18	52	0	0	0	1	0	18	52				
SMC4	10051	broad.mit.edu	37	3	160137299	160137299	+	Missense_Mutation	SNP	T	T	A			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr3:160137299T>A	ENST00000357388.3	+	12	2276	c.1825T>A	c.(1825-1827)Tct>Act	p.S609T	SMC4_ENST00000344722.5_Missense_Mutation_p.S609T|SMC4_ENST00000360111.2_Missense_Mutation_p.S609T|SMC4_ENST00000462787.1_Missense_Mutation_p.S609T|SMC4_ENST00000469762.1_Missense_Mutation_p.S584T|RP11-432B6.3_ENST00000483754.1_Intron	NM_001002800.1	NP_001002800.1	Q9NTJ3	SMC4_HUMAN	structural maintenance of chromosomes 4	609	Flexible hinge.				kinetochore organization (GO:0051383)|meiotic chromosome condensation (GO:0010032)|meiotic chromosome segregation (GO:0045132)|mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)|mitotic sister chromatid segregation (GO:0000070)	condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein heterodimerization activity (GO:0046982)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(15)|lung(20)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	48			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			AGAAAAAAAATCTGGCAGGAT	0.343																																						ENST00000357388.3																			0				breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(15)|lung(20)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	48						c.(1825-1827)Tct>Act		structural maintenance of chromosomes 4							55.0	61.0	59.0					3																	160137299		2203	4295	6498	SO:0001583	missense	10051				cell division|mitotic chromosome condensation	condensin complex|cytoplasm|nucleus	ATP binding|protein heterodimerization activity	g.chr3:160137299T>A	AF092564	CCDS3189.1, CCDS75046.1	3q26.1	2006-07-06	2006-07-06	2006-07-06	ENSG00000113810	ENSG00000113810		"""Structural maintenance of chromosomes proteins"""	14013	protein-coding gene	gene with protein product		605575	"""SMC4 (structural maintenance of chromosomes 4, yeast)-like 1"", ""SMC4 structural maintenance of chromosomes 4-like 1 (yeast)"""	SMC4L1		9789013, 10319587	Standard	NM_005496		Approved	hCAP-C, CAP-C	uc003fdh.3	Q9NTJ3	OTTHUMG00000159006	ENST00000357388.3:c.1825T>A	3.37:g.160137299T>A	ENSP00000349961:p.Ser609Thr					SMC4_ENST00000469762.1_Missense_Mutation_p.S584T|SMC4_ENST00000344722.5_Missense_Mutation_p.S609T|SMC4_ENST00000360111.2_Missense_Mutation_p.S609T|RP11-432B6.3_ENST00000483754.1_Intron|SMC4_ENST00000462787.1_Missense_Mutation_p.S609T	p.S609T	NM_001002800.1	NP_001002800.1	Q9NTJ3	SMC4_HUMAN	Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)		12	2276	+			609			Flexible hinge.		A6NLT9|D3DNL8|O95752|Q8NDL4|Q9UNT9	Missense_Mutation	SNP	ENST00000357388.3	37	c.1825T>A	CCDS3189.1	.	.	.	.	.	.	.	.	.	.	T	16.01	3.001441	0.54254	.	.	ENSG00000113810	ENST00000357388;ENST00000360111;ENST00000469762;ENST00000462787;ENST00000344722;ENST00000545277	T;T;T;T;T	0.74842	-0.88;-0.87;-0.86;-0.87;-0.88	6.04	6.04	0.98038	SMCs flexible hinge (1);RecF/RecN/SMC (1);	0.100389	0.64402	D	0.000001	T	0.67933	0.2946	L	0.41961	1.31	0.50813	D	0.999895	B;B;B;B	0.22003	0.024;0.008;0.063;0.03	B;B;B;B	0.19946	0.009;0.023;0.027;0.007	T	0.62609	-0.6818	10	0.20519	T	0.43	-12.4382	16.5885	0.84745	0.0:0.0:0.0:1.0	.	609;584;584;609	Q9NTJ3-2;B3KXX5;E9PD53;Q9NTJ3	.;.;.;SMC4_HUMAN	T	609;609;584;609;609;203	ENSP00000349961:S609T;ENSP00000353225:S609T;ENSP00000417964:S584T;ENSP00000420734:S609T;ENSP00000341382:S609T	ENSP00000341382:S609T	S	+	1	0	SMC4	161619993	1.000000	0.71417	0.995000	0.50966	0.994000	0.84299	3.202000	0.51067	2.317000	0.78254	0.460000	0.39030	TCT		0.343	SMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352862.1			35	53	0	0	0	1	0	35	53				
NPAS3	64067	broad.mit.edu	37	14	34263252	34263252	+	Splice_Site	SNP	T	T	G			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr14:34263252T>G	ENST00000356141.4	+	10	1301		c.e10+2		NPAS3_ENST00000548645.1_Splice_Site|NPAS3_ENST00000357798.5_Splice_Site|NPAS3_ENST00000551492.1_Splice_Site|NPAS3_ENST00000346562.2_Splice_Site			Q8IXF0	NPAS3_HUMAN	neuronal PAS domain protein 3						locomotory behavior (GO:0007626)|maternal behavior (GO:0042711)|positive regulation of transcription, DNA-templated (GO:0045893)|startle response (GO:0001964)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(4)|endometrium(3)|kidney(1)|large_intestine(6)|liver(2)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	40	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	0.333																																						ENST00000346562.2																			0				breast(4)|endometrium(3)|kidney(1)|large_intestine(6)|liver(2)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	40						c.e9+2		neuronal PAS domain protein 3							90.0	80.0	83.0					14																	34263252		2203	4300	6503	SO:0001630	splice_region_variant	64067				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity	g.chr14:34263252T>G	AF164438	CCDS9645.1, CCDS53891.1, CCDS53892.1, CCDS55912.1	14q13.1	2013-08-23			ENSG00000151322	ENSG00000151322		"""Basic helix-loop-helix proteins"""	19311	protein-coding gene	gene with protein product		609430					Standard	NM_022123		Approved	MOP6, PASD6, bHLHe12	uc001wru.3	Q8IXF0	OTTHUMG00000140215	ENST00000356141.4:c.1301+2T>G	14.37:g.34263252T>G						NPAS3_ENST00000551492.1_Splice_Site|NPAS3_ENST00000548645.1_Splice_Site|NPAS3_ENST00000357798.5_Splice_Site|NPAS3_ENST00000356141.4_Splice_Site		NM_001164749.1|NM_001165893.1|NM_022123.2|NM_173159.2	NP_001158221.1|NP_001159365.1|NP_071406.1|NP_775182.1	Q8IXF0	NPAS3_HUMAN	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)	9	1279	+	Breast(36;0.0102)|Hepatocellular(127;0.133)							Q86US6|Q86US7|Q8IXF2|Q9BY81|Q9H323|Q9Y4L8	Splice_Site	SNP	ENST00000356141.4	37		CCDS53891.1	.	.	.	.	.	.	.	.	.	.	T	20.1	3.935159	0.73442	.	.	ENSG00000151322	ENST00000551634;ENST00000551492;ENST00000346562;ENST00000548645;ENST00000356141;ENST00000357798	.	.	.	5.94	5.94	0.96194	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.3939	0.83550	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	NPAS3	33333003	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	8.040000	0.89188	2.276000	0.75962	0.455000	0.32223	.		0.333	NPAS3-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276645.1		Intron	25	39	0	0	0	1	0	25	39				
FUBP1	8880	broad.mit.edu	37	1	78433848	78433851	+	Splice_Site	DEL	CAGT	CAGT	-			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr1:78433848_78433851delCAGT	ENST00000370768.2	-	3	329_332	c.248_251delACTG	c.(247-252)gactgt>gt	p.DC83fs	FUBP1_ENST00000370767.1_Splice_Site_p.DC83fs|FUBP1_ENST00000436586.2_Splice_Site_p.DC104fs	NM_003902.3	NP_003893.2	Q96AE4	FUBP1_HUMAN	far upstream element (FUSE) binding protein 1	83					positive regulation of gene expression (GO:0010628)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)	p.?(1)		central_nervous_system(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(1)|upper_aerodigestive_tract(3)	17						GGAATACTTACAGTCATTTTGAGG	0.319			"""F, N"""		oligodendroglioma																																	ENST00000370767.1				Rec	yes		1	1p13.1	8880	"""F, N"""	far upstream element (FUSE) binding protein 1			O			oligodendroglioma		1	Unknown(1)	p.?(1)	central_nervous_system(1)	central_nervous_system(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(1)|upper_aerodigestive_tract(3)	17						c.e3+1		far upstream element (FUSE) binding protein 1																																				SO:0001630	splice_region_variant	8880				transcription from RNA polymerase II promoter	nucleus	protein binding|RNA binding|sequence-specific DNA binding transcription factor activity|single-stranded DNA binding	g.chr1:78433848_78433851delCAGT	U05040	CCDS683.1	1p31.1	2008-02-05			ENSG00000162613	ENSG00000162613			4004	protein-coding gene	gene with protein product		603444		FUBP		8125259	Standard	XM_005271309		Approved	FBP	uc001dii.3	Q96AE4	OTTHUMG00000040799	ENST00000370768.2:c.250+1ACTG>-	1.37:g.78433848_78433851delCAGT						FUBP1_ENST00000436586.2_Splice_Site_p.104_splice|FUBP1_ENST00000370768.2_Splice_Site_p.83_splice	p.83_splice			Q96AE4	FUBP1_HUMAN			3	335_338	-			83					Q12828	Splice_Site	DEL	ENST00000370768.2	37	c.250_splice	CCDS683.1																																																																																				0.319	FUBP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098030.3	NM_003902	Frame_Shift_Del	20	11						20	11	---	---	---	---
HGD	3081	broad.mit.edu	37	3	120357338	120357338	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr3:120357338delC	ENST00000283871.5	-	12	1429	c.970delG	c.(970-972)gttfs	p.V324fs		NM_000187.3	NP_000178.2	Q93099	HGD_HUMAN	homogentisate 1,2-dioxygenase	324					cellular nitrogen compound metabolic process (GO:0034641)|L-phenylalanine catabolic process (GO:0006559)|small molecule metabolic process (GO:0044281)|tyrosine catabolic process (GO:0006572)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	homogentisate 1,2-dioxygenase activity (GO:0004411)|metal ion binding (GO:0046872)			cervix(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(2)	25				GBM - Glioblastoma multiforme(114;0.158)		TTATCAGCAACCCCCCATCGA	0.483																																						ENST00000283871.5																			0				cervix(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(2)	25						c.(970-972)ttfs		homogentisate 1,2-dioxygenase							120.0	115.0	117.0					3																	120357338		2203	4296	6499	SO:0001589	frameshift_variant	3081				L-phenylalanine catabolic process|tyrosine catabolic process	cytosol	homogentisate 1,2-dioxygenase activity|metal ion binding	g.chr3:120357338delC		CCDS3000.1	3q	2010-04-27	2010-04-27		ENSG00000113924	ENSG00000113924	1.13.11.5		4892	protein-coding gene	gene with protein product	"""homogentisate oxidase"""	607474	"""homogentisate 1,2-dioxygenase (homogentisate oxidase)"""	AKU		8188241	Standard	NM_000187		Approved	HGO	uc003edw.3	Q93099	OTTHUMG00000159441	ENST00000283871.5:c.970delG	3.37:g.120357338delC	ENSP00000283871:p.Val324fs						p.V324fs	NM_000187.3	NP_000178.2	Q93099	HGD_HUMAN		GBM - Glioblastoma multiforme(114;0.158)	12	1429	-			324					A8K417|B2R8Z0	Frame_Shift_Del	DEL	ENST00000283871.5	37	c.970delG	CCDS3000.1																																																																																				0.483	HGD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355410.1			23	94						23	94	---	---	---	---
WDFY3	23001	broad.mit.edu	37	4	85731329	85731331	+	In_Frame_Del	DEL	GAA	GAA	-			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr4:85731329_85731331delGAA	ENST00000295888.4	-	14	2461_2463	c.2054_2056delTTC	c.(2053-2058)cttcac>cac	p.L685del	WDFY3_ENST00000322366.6_In_Frame_Del_p.L685del|WDFY3-AS1_ENST00000510449.1_RNA	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	685					aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		AACACAGTGTGAAGAAGTTCAAA	0.448																																						ENST00000322366.6																			0				breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134						c.(2053-2058)cac>c		WD repeat and FYVE domain containing 3																																				SO:0001651	inframe_deletion	23001					cytoplasmic part|extrinsic to membrane|nuclear envelope	1-phosphatidylinositol binding|metal ion binding|protein binding	g.chr4:85731329_85731331delGAA	AB023210	CCDS3609.1	4q21.3	2013-01-09			ENSG00000163625	ENSG00000163625		"""Zinc fingers, FYVE domain containing"", ""WD repeat domain containing"""	20751	protein-coding gene	gene with protein product						10231032	Standard	NM_014991		Approved	KIAA0993, ALFY, ZFYVE25	uc003hpd.3	Q8IZQ1	OTTHUMG00000130424	ENST00000295888.4:c.2054_2056delTTC	4.37:g.85731332_85731334delGAA	ENSP00000295888:p.Leu685del					WDFY3-AS1_ENST00000510449.1_RNA|WDFY3_ENST00000295888.4_In_Frame_Del_p.LH685del	p.LH685del			Q8IZQ1	WDFY3_HUMAN		OV - Ovarian serous cystadenocarcinoma(123;0.000808)	14	2461_2463	-		Hepatocellular(203;0.114)	685					Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	In_Frame_Del	DEL	ENST00000295888.4	37	c.2054_2056delTTC	CCDS3609.1																																																																																				0.448	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991		28	51						28	51	---	---	---	---
FAM149A	25854	broad.mit.edu	37	4	187084676	187084678	+	In_Frame_Del	DEL	CTT	CTT	-			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr4:187084676_187084678delCTT	ENST00000356371.5	+	10	1805_1807	c.1805_1807delCTT	c.(1804-1809)ccttct>cct	p.S603del	FAM149A_ENST00000502970.1_In_Frame_Del_p.S312del|FAM149A_ENST00000514153.1_In_Frame_Del_p.S312del|FAM149A_ENST00000389354.5_In_Frame_Del_p.S312del|FAM149A_ENST00000503432.1_In_Frame_Del_p.S312del|FAM149A_ENST00000227065.4_In_Frame_Del_p.S312del			A5PLN7	F149A_HUMAN	family with sequence similarity 149, member A	603										breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(8)|lung(8)|pancreas(1)|prostate(1)|skin(2)	25		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																																						ENST00000356371.5																			0				breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(8)|lung(8)|pancreas(1)|prostate(1)|skin(2)	25						c.(1804-1809)cct>c		family with sequence similarity 149, member A																																				SO:0001651	inframe_deletion	25854							g.chr4:187084676_187084678delCTT	AK057166	CCDS34117.1	4q35.1	2012-04-19			ENSG00000109794	ENSG00000109794			24527	protein-coding gene	gene with protein product							Standard	NM_015398		Approved	DKFZP564J102, MST119, MSTP119	uc010isl.3	A5PLN7	OTTHUMG00000160565	ENST00000356371.5:c.1805_1807delCTT	4.37:g.187084676_187084678delCTT	ENSP00000348732:p.Ser603del					FAM149A_ENST00000514153.1_In_Frame_Del_p.PS311del|FAM149A_ENST00000503432.1_In_Frame_Del_p.PS311del|FAM149A_ENST00000502970.1_In_Frame_Del_p.PS311del|FAM149A_ENST00000389354.5_In_Frame_Del_p.PS311del|FAM149A_ENST00000227065.4_In_Frame_Del_p.PS311del	p.PS602del			A5PLN7	F149A_HUMAN		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)	10	1805_1807	+		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)	602					B5MDB8|Q2TAN6|Q7Z2S5|Q9Y4T9	In_Frame_Del	DEL	ENST00000356371.5	37	c.1805_1807delCTT																																																																																					0.532	FAM149A-201	KNOWN	basic	protein_coding	protein_coding		NM_001006655		10	76						10	76	---	---	---	---
PIK3R1	5295	broad.mit.edu	37	5	67591105	67591107	+	In_Frame_Del	DEL	TAA	TAA	-			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr5:67591105_67591107delTAA	ENST00000521381.1	+	13	2314_2316	c.1698_1700delTAA	c.(1696-1701)attaaa>ata	p.K567del	PIK3R1_ENST00000336483.5_In_Frame_Del_p.K297del|PIK3R1_ENST00000396611.1_In_Frame_Del_p.K567del|PIK3R1_ENST00000523872.1_In_Frame_Del_p.K204del|PIK3R1_ENST00000521657.1_In_Frame_Del_p.K567del|PIK3R1_ENST00000274335.5_In_Frame_Del_p.K567del|PIK3R1_ENST00000320694.8_In_Frame_Del_p.K267del	NM_181523.2	NP_852664.1	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	567					B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|growth hormone receptor signaling pathway (GO:0060396)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of osteoclast differentiation (GO:0045671)|neurotrophin TRK receptor signaling pathway (GO:0048011)|NFAT protein import into nucleus (GO:0051531)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|protein phosphorylation (GO:0006468)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|membrane (GO:0016020)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	ErbB-3 class receptor binding (GO:0043125)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.K267_L270delKPDL(1)|p.0?(1)|p.?(1)|p.K297E(1)|p.K567_L570delKPDL(1)|p.K567E(1)|p.K267E(1)|p.K297_L300delKPDL(1)		breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178		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)	Isoprenaline(DB01064)	TGAACAGCATTAAACCAGACCTT	0.369			"""Mis, F, O"""		"""gliobastoma, ovarian, colorectal"""					TCGA GBM(4;<1E-08)																												ENST00000521381.1				Rec	yes		5	5q13.1	5295	"""Mis, F, O"""	"""phosphoinositide-3-kinase, regulatory subunit 1 (alpha)"""			"""E, O"""			"""gliobastoma, ovarian, colorectal"""		8	Substitution - Missense(3)|Deletion - In frame(3)|Whole gene deletion(1)|Unknown(1)	p.K267_L270delKPDL(1)|p.0?(1)|p.?(1)|p.K297E(1)|p.K567_L570delKPDL(1)|p.K567E(1)|p.K267E(1)|p.K297_L300delKPDL(1)	breast(3)|endometrium(3)|large_intestine(1)|lung(1)	breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178						c.(1696-1701)ata>at		phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	Isoproterenol(DB01064)																																			SO:0001651	inframe_deletion	5295				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	g.chr5:67591105_67591107delTAA	M61906	CCDS3993.1, CCDS3994.1, CCDS3995.1, CCDS56374.1	5q13.1	2014-09-17	2008-02-04		ENSG00000145675	ENSG00000145675		"""SH2 domain containing"""	8979	protein-coding gene	gene with protein product		171833				1314371, 18387942	Standard	NM_181524		Approved	GRB1, p85-ALPHA, p85	uc003jva.3	P27986	OTTHUMG00000131251	ENST00000521381.1:c.1698_1700delTAA	5.37:g.67591105_67591107delTAA	ENSP00000428056:p.Lys567del	TCGA GBM(4;<1E-08)				PIK3R1_ENST00000521657.1_In_Frame_Del_p.IK566del|PIK3R1_ENST00000396611.1_In_Frame_Del_p.IK566del|PIK3R1_ENST00000320694.8_In_Frame_Del_p.IK266del|PIK3R1_ENST00000523872.1_In_Frame_Del_p.IK203del|PIK3R1_ENST00000336483.5_In_Frame_Del_p.IK296del|PIK3R1_ENST00000274335.5_In_Frame_Del_p.IK566del	p.IK566del	NM_181523.2	NP_852664.1	P27986	P85A_HUMAN		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	13	2314_2316	+		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)	566					B3KT19|D3DWA0|E7EX19|Q15747|Q4VBZ7|Q53EM6|Q8IXA2|Q8N1C5	In_Frame_Del	DEL	ENST00000521381.1	37	c.1698_1700delTAA	CCDS3993.1																																																																																				0.369	PIK3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254013.2	NM_181504		16	108						16	108	---	---	---	---
MAN2A1	4124	broad.mit.edu	37	5	109049430	109049433	+	Frame_Shift_Del	DEL	CTGT	CTGT	-			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr5:109049430_109049433delCTGT	ENST00000261483.4	+	2	1397_1400	c.345_348delCTGT	c.(343-348)gactgtfs	p.DC115fs		NM_002372.2	NP_002363.2	Q16706	MA2A1_HUMAN	mannosidase, alpha, class 2A, member 1	115					cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|lung alveolus development (GO:0048286)|mannose metabolic process (GO:0006013)|mitochondrion organization (GO:0007005)|N-glycan processing (GO:0006491)|positive regulation of neurogenesis (GO:0050769)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|respiratory gaseous exchange (GO:0007585)|retina morphogenesis in camera-type eye (GO:0060042)|vacuole organization (GO:0007033)	cis-Golgi network (GO:0005801)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity (GO:0004572)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		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																																						ENST00000261483.4																			0				breast(2)|central_nervous_system(2)|endometrium(7)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	55						c.(343-348)gafs		mannosidase, alpha, class 2A, member 1																																				SO:0001589	frameshift_variant	4124				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	g.chr5:109049430_109049433delCTGT		CCDS34209.1	5q21.3	2013-09-20			ENSG00000112893	ENSG00000112893	3.2.1.114		6824	protein-coding gene	gene with protein product	"""golgi integral membrane protein 7"""	154582		MANA2		1757461, 15004235	Standard	NM_002372		Approved	GOLIM7	uc003kou.1	Q16706	OTTHUMG00000162834	ENST00000261483.4:c.345_348delCTGT	5.37:g.109049434_109049437delCTGT	ENSP00000261483:p.Asp115fs						p.DC115fs	NM_002372.2	NP_002363.2	Q16706	MA2A1_HUMAN		OV - Ovarian serous cystadenocarcinoma(64;2.17e-10)|Epithelial(69;1.37e-09)|COAD - Colon adenocarcinoma(37;0.141)	2	1397_1400	+		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)	115					Q16767	Frame_Shift_Del	DEL	ENST00000261483.4	37	c.345_348delCTGT	CCDS34209.1																																																																																				0.407	MAN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370680.1			38	135						38	135	---	---	---	---
RXRB	6257	broad.mit.edu	37	6	33159977	33159979	+	IGR	DEL	AGG	AGG	-			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr6:33159977_33159979delAGG	ENST00000374680.3	-	0	2908				COL11A2_ENST00000374712.1_In_Frame_Del_p.13_14LL>L|COL11A2_ENST00000395194.1_In_Frame_Del_p.13_14LL>L|COL11A2_ENST00000361917.1_In_Frame_Del_p.13_14LL>L|COL11A2_ENST00000374714.1_In_Frame_Del_p.13_14LL>L|COL11A2_ENST00000341947.2_In_Frame_Del_p.13_14LL>L|COL11A2_ENST00000395197.1_In_Frame_Del_p.13_14LL>L|COL11A2_ENST00000374713.1_In_Frame_Del_p.13_14LL>L|COL11A2_ENST00000374708.4_In_Frame_Del_p.13_14LL>L|COL11A2_ENST00000357486.1_In_Frame_Del_p.13_14LL>L	NM_001270401.1|NM_021976.4	NP_001257330.1|NP_068811.1	P28702	RXRB_HUMAN	retinoid X receptor, beta						cardiac muscle cell proliferation (GO:0060038)|cellular response to retinoic acid (GO:0071300)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|maternal placenta development (GO:0001893)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular cardiac muscle cell differentiation (GO:0055012)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	9-cis retinoic acid receptor activity (GO:0004886)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|ovary(3)|prostate(1)|skin(2)	15					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Bexarotene(DB00307)|Tazarotene(DB00799)|Tretinoin(DB00755)	CACCAGAGGTAGGAGGAGGAGGA	0.675																																						ENST00000341947.2																			0				biliary_tract(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(27)|ovary(5)|prostate(5)|skin(6)	68						c.(37-42)cta>ct		collagen, type XI, alpha 2			,,,	11,3241		1,9,1616					,,,	-5.0	0.1			8	29,6129		0,29,3050	no	coding,coding,coding,coding	COL11A2	NM_080681.2,NM_080680.2,NM_080679.2,NM_001163771.1	,,,	1,38,4666	A1A1,A1R,RR		0.4709,0.3383,0.4251	,,,	,,,		40,9370				SO:0001628	intergenic_variant	1302				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	g.chr6:33159977_33159979delAGG	M84820	CCDS4768.1, CCDS59007.1	6p21.3	2013-01-16			ENSG00000204231	ENSG00000204231		"""Nuclear hormone receptors"""	10478	protein-coding gene	gene with protein product	"""nuclear receptor subfamily 2 group B member 2"""	180246				8257090	Standard	NM_021976		Approved	NR2B2, H-2RIIBP, RCoR-1	uc003odc.4	P28702	OTTHUMG00000031298		6.37:g.33159986_33159988delAGG						COL11A2_ENST00000357486.1_In_Frame_Del_p.LL13del|COL11A2_ENST00000361917.1_In_Frame_Del_p.LL13del|COL11A2_ENST00000395194.1_In_Frame_Del_p.LL13del|COL11A2_ENST00000374713.1_In_Frame_Del_p.LL13del|COL11A2_ENST00000374714.1_In_Frame_Del_p.LL13del|COL11A2_ENST00000374712.1_In_Frame_Del_p.LL13del|COL11A2_ENST00000374708.4_In_Frame_Del_p.LL13del|COL11A2_ENST00000395197.1_In_Frame_Del_p.LL13del	p.LL13del	NM_080680.2	NP_542411.2	P13942	COBA2_HUMAN			1	266_268	-			13					P28703|Q59G65|Q5JP92|Q5STQ1	In_Frame_Del	DEL	ENST00000374680.3	37	c.39_41delCCT	CCDS4768.1																																																																																				0.675	RXRB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076642.2	NM_021976		3	3						3	3	---	---	---	---
HDAC2	3066	broad.mit.edu	37	6	114277842	114277844	+	In_Frame_Del	DEL	TCT	TCT	-			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr6:114277842_114277844delTCT	ENST00000519065.1	-	4	673_675	c.297_299delAGA	c.(295-300)gaagat>gat	p.E99del	HDAC2_ENST00000519108.1_In_Frame_Del_p.E69del|HDAC2_ENST00000368632.2_In_Frame_Del_p.E69del|HDAC2_ENST00000398283.2_In_Frame_Del_p.E193del			Q92769	HDAC2_HUMAN	histone deacetylase 2	99	Histone deacetylase.				ATP-dependent chromatin remodeling (GO:0043044)|blood coagulation (GO:0007596)|cardiac muscle cell development (GO:0055013)|chromatin remodeling (GO:0006338)|circadian regulation of gene expression (GO:0032922)|dendrite development (GO:0016358)|embryonic digit morphogenesis (GO:0042733)|epidermal cell differentiation (GO:0009913)|eyelid development in camera-type eye (GO:0061029)|fungiform papilla formation (GO:0061198)|hair follicle placode formation (GO:0060789)|hippocampus development (GO:0021766)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|maintenance of chromatin silencing (GO:0006344)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of cell cycle (GO:0045786)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of MHC class II biosynthetic process (GO:0045347)|negative regulation of neuron projection development (GO:0010977)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of cell proliferation (GO:0008284)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of oligodendrocyte differentiation (GO:0048714)|positive regulation of proteolysis (GO:0045862)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of protein deacetylation (GO:0090311)|regulation of protein kinase B signaling (GO:0051896)|regulation of sarcomere organization (GO:0060297)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|ESC/E(Z) complex (GO:0035098)|heterochromatin (GO:0000792)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)|replication fork (GO:0005657)|Sin3 complex (GO:0016580)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|deacetylase activity (GO:0019213)|enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|poly(A) RNA binding (GO:0044822)|protein deacetylase activity (GO:0033558)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			biliary_tract(1)|central_nervous_system(5)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(1)|skin(2)	27		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)	Aminophylline(DB01223)|Lovastatin(DB00227)|Oxtriphylline(DB01303)|Theophylline(DB00277)|Valproic Acid(DB00313)|Vorinostat(DB02546)	CACTGGACAATCTTCTCCAACAT	0.35																																						ENST00000519065.1																			0				biliary_tract(1)|central_nervous_system(5)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(1)|skin(2)	27						c.(295-300)gat>ga		histone deacetylase 2	Vorinostat(DB02546)																																			SO:0001651	inframe_deletion	3066				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	g.chr6:114277842_114277844delTCT	U31814	CCDS43493.1, CCDS43493.2	6q21	2008-08-29			ENSG00000196591	ENSG00000196591			4853	protein-coding gene	gene with protein product		605164				9782097	Standard	NM_001527		Approved	RPD3, YAF1	uc003pwd.2	Q92769	OTTHUMG00000015411	ENST00000519065.1:c.297_299delAGA	6.37:g.114277845_114277847delTCT	ENSP00000430432:p.Glu99del					HDAC2_ENST00000398283.2_In_Frame_Del_p.ED193del|HDAC2_ENST00000519108.1_In_Frame_Del_p.ED69del|HDAC2_ENST00000368632.2_In_Frame_Del_p.ED69del	p.ED99del			Q92769	HDAC2_HUMAN		all cancers(137;0.00318)|OV - Ovarian serous cystadenocarcinoma(136;0.00569)|Epithelial(106;0.0112)|GBM - Glioblastoma multiforme(226;0.0832)	4	673_675	-		all_cancers(87;0.000629)|all_epithelial(87;0.00274)|Colorectal(196;0.0317)|all_lung(197;0.24)	99			Histone deacetylase.		B3KRS5|B4DL58|E1P561|Q5SRI8|Q5SZ86|Q8NEH4	In_Frame_Del	DEL	ENST00000519065.1	37	c.297_299delAGA	CCDS43493.2																																																																																				0.350	HDAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041909.2			15	16						15	16	---	---	---	---
ZAN	7455	broad.mit.edu	37	7	100369720	100369721	+	RNA	INS	-	-	T			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr7:100369720_100369721insT	ENST00000348028.3	+	0	5590				ZAN_ENST00000427578.1_RNA|ZAN_ENST00000349350.6_RNA|ZAN_ENST00000546213.1_RNA|ZAN_ENST00000421100.1_RNA|ZAN_ENST00000546292.1_RNA|ZAN_ENST00000449052.1_RNA|ZAN_ENST00000538115.1_RNA|ZAN_ENST00000443370.1_RNA|ZAN_ENST00000542585.1_RNA			Q9Y493	ZAN_HUMAN	zonadhesin (gene/pseudogene)						binding of sperm to zona pellucida (GO:0007339)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(2)|breast(3)|central_nervous_system(3)|endometrium(21)|kidney(6)|large_intestine(18)|lung(60)|ovary(4)|pancreas(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)	139	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)			cctctaaattcttttttttttt	0.535																																						ENST00000542585.1																			0				NS(2)|breast(3)|central_nervous_system(3)|endometrium(21)|kidney(6)|large_intestine(18)|lung(60)|ovary(4)|pancreas(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)	139								zonadhesin (gene/pseudogene)																																						7455				binding of sperm to zona pellucida|cell-cell adhesion	integral to membrane|plasma membrane		g.chr7:100369720_100369721insT	U83191		7q22.1	2013-10-10	2013-10-10		ENSG00000146839	ENSG00000146839			12857	protein-coding gene	gene with protein product		602372	"""zonadhesin"""			9799793, 17033959	Standard	NM_003386		Approved		uc003uwk.3	Q9Y493	OTTHUMG00000157037		7.37:g.100369731_100369731dupT						ZAN_ENST00000443370.1_RNA|ZAN_ENST00000421100.1_RNA|ZAN_ENST00000449052.1_RNA|ZAN_ENST00000348028.3_RNA|ZAN_ENST00000538115.1_RNA|ZAN_ENST00000546213.1_RNA|ZAN_ENST00000427578.1_RNA|ZAN_ENST00000349350.6_RNA|ZAN_ENST00000546292.1_RNA		NM_003386.1	NP_003377.1	Q9Y493	ZAN_HUMAN	STAD - Stomach adenocarcinoma(171;0.19)		0	5573	+	Lung NSC(181;0.041)|all_lung(186;0.0581)							A0FKC8|D6W5W4|O00218|Q96L85|Q96L86|Q96L87|Q96L88|Q96L89|Q96L90|Q9BXN9|Q9BZ83|Q9BZ84|Q9BZ85|Q9BZ86|Q9BZ87|Q9BZ88	RNA	INS	ENST00000348028.3	37																																																																																						0.535	ZAN-006	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000347214.1	NM_003386		4	7						4	7	---	---	---	---
MAPK15	225689	broad.mit.edu	37	8	144801230	144801230	+	Frame_Shift_Del	DEL	T	T	-	rs139710965	byFrequency	TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr8:144801230delT	ENST00000338033.4	+	6	604	c.485delT	c.(484-486)ctgfs	p.L162fs	MAPK15_ENST00000395108.2_Frame_Shift_Del_p.L162fs|MAPK15_ENST00000395107.4_Frame_Shift_Del_p.L179fs|RP11-429J17.5_ENST00000527908.1_RNA	NM_139021.2	NP_620590.2	Q8TD08	MK15_HUMAN	mitogen-activated protein kinase 15	162	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				MAPK cascade (GO:0000165)|negative regulation of DNA replication (GO:0008156)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|response to estradiol (GO:0032355)	extracellular region (GO:0005576)|intracellular (GO:0005622)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|SH3 domain binding (GO:0017124)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|skin(1)|stomach(1)	12	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																																						ENST00000338033.4																			0				endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|skin(1)|stomach(1)	12						c.(484-486)cgfs		mitogen-activated protein kinase 15							28.0	27.0	27.0					8																	144801230		2201	4297	6498	SO:0001589	frameshift_variant	225689				protein autophosphorylation	extracellular region	ATP binding|MAP kinase activity|SH3 domain binding	g.chr8:144801230delT	AY065978	CCDS6409.2	8q24.3	2011-06-09			ENSG00000181085	ENSG00000181085		"""Mitogen-activated protein kinase cascade / Kinases"""	24667	protein-coding gene	gene with protein product	"""extracellular signal regulated kinase 8"""					11875070	Standard	XM_006716528		Approved	ERK8, ERK7	uc003yzj.3	Q8TD08	OTTHUMG00000146450	ENST00000338033.4:c.485delT	8.37:g.144801230delT	ENSP00000337691:p.Leu162fs					MAPK15_ENST00000395108.2_Frame_Shift_Del_p.L162fs|MAPK15_ENST00000395107.4_Frame_Shift_Del_p.L179fs	p.L162fs	NM_139021.2	NP_620590.2	Q8TD08	MK15_HUMAN	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)		6	604	+	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)		162			Protein kinase.		Q2TCF9|Q8N362	Frame_Shift_Del	DEL	ENST00000338033.4	37	c.485delT	CCDS6409.2																																																																																				0.667	MAPK15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000300348.1	NM_139021		2	4						2	4	---	---	---	---
NOTCH1	4851	broad.mit.edu	37	9	139391997	139391998	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr9:139391997_139391998delAG	ENST00000277541.6	-	34	6268_6269	c.6193_6194delCT	c.(6193-6195)ctgfs	p.L2065fs		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	2065					anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	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)																												ENST00000277541.6				Dom	yes		9	9q34.3	4851	"""T, Mis, O"""	"""Notch homolog 1, translocation-associated (Drosophila) (TAN1)"""			L	TRB@		T-ALL		0				breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359						c.(6193-6195)gfs		notch 1																																				SO:0001589	frameshift_variant	4851				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	g.chr9:139391997_139391998delAG	AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"""Ankyrin repeat domain containing"""	7881	protein-coding gene	gene with protein product		190198	"""Notch (Drosophila) homolog 1 (translocation-associated)"", ""Notch homolog 1, translocation-associated (Drosophila)"""	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.6193_6194delCT	9.37:g.139391997_139391998delAG	ENSP00000277541:p.Leu2065fs	HNSCC(8;0.001)					p.L2065fs	NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)	34	6268_6269	-	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)	2065					Q59ED8|Q5SXM3	Frame_Shift_Del	DEL	ENST00000277541.6	37	c.6193_6194delCT	CCDS43905.1																																																																																				0.683	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617		17	14						17	14	---	---	---	---
NOTCH1	4851	broad.mit.edu	37	9	139395163	139395166	+	Frame_Shift_Del	DEL	GTCT	GTCT	-			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr9:139395163_139395166delGTCT	ENST00000277541.6	-	31	5847_5850	c.5772_5775delAGAC	c.(5770-5775)acagacfs	p.TD1924fs		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	1924					anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	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)																												ENST00000277541.6				Dom	yes		9	9q34.3	4851	"""T, Mis, O"""	"""Notch homolog 1, translocation-associated (Drosophila) (TAN1)"""			L	TRB@		T-ALL		0				breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359						c.(5770-5775)acfs		notch 1																																				SO:0001589	frameshift_variant	4851				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	g.chr9:139395163_139395166delGTCT	AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"""Ankyrin repeat domain containing"""	7881	protein-coding gene	gene with protein product		190198	"""Notch (Drosophila) homolog 1 (translocation-associated)"", ""Notch homolog 1, translocation-associated (Drosophila)"""	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.5772_5775delAGAC	9.37:g.139395167_139395170delGTCT	ENSP00000277541:p.Thr1924fs	HNSCC(8;0.001)					p.TD1924fs	NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)	31	5847_5850	-	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)	1924					Q59ED8|Q5SXM3	Frame_Shift_Del	DEL	ENST00000277541.6	37	c.5772_5775delAGAC	CCDS43905.1																																																																																				0.686	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617		41	137						41	137	---	---	---	---
PHLPP2	23035	broad.mit.edu	37	16	71692597	71692599	+	In_Frame_Del	DEL	TGT	TGT	-	rs145938775		TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr16:71692597_71692599delTGT	ENST00000568954.1	-	14	2483_2485	c.2105_2107delACA	c.(2104-2109)aacatc>atc	p.N702del	PHLPP2_ENST00000360429.3_In_Frame_Del_p.N702del|PHLPP2_ENST00000393524.2_In_Frame_Del_p.N635del|PHLPP2_ENST00000567016.1_In_Frame_Del_p.N737del|PHLPP2_ENST00000540628.1_5'UTR|RP11-432I5.6_ENST00000567077.1_RNA|PHLPP2_ENST00000356272.3_In_Frame_Del_p.N702del			Q6ZVD8	PHLP2_HUMAN	PH domain and leucine rich repeat protein phosphatase 2	702					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment membrane (GO:0042622)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(7)|lung(15)|ovary(1)|prostate(1)|skin(1)|stomach(1)	37						AAAATGCTGATGTTGTTGGAGTG	0.458																																						ENST00000393524.2																			0				central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(7)|lung(15)|ovary(1)|prostate(1)|skin(1)|stomach(1)	37						c.(1903-1908)atc>a		PH domain and leucine rich repeat protein phosphatase 2																																				SO:0001651	inframe_deletion	23035					cytoplasm|membrane|nucleus	metal ion binding|phosphoprotein phosphatase activity	g.chr16:71692597_71692599delTGT	BX647823	CCDS32479.1, CCDS73910.1	16q22.2	2013-01-11	2009-05-26	2009-05-26	ENSG00000040199	ENSG00000040199		"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"", ""Pleckstrin homology (PH) domain containing"""	29149	protein-coding gene	gene with protein product		611066	"""PH domain and leucine rich repeat protein phosphatase-like"""	PHLPPL		17386267	Standard	NM_001289003		Approved	KIAA0931	uc002fax.3	Q6ZVD8		ENST00000568954.1:c.2105_2107delACA	16.37:g.71692600_71692602delTGT	ENSP00000457991:p.Asn702del					PHLPP2_ENST00000568954.1_In_Frame_Del_p.NI702del|PHLPP2_ENST00000567016.1_In_Frame_Del_p.NI737del|RP11-432I5.6_ENST00000567077.1_RNA|PHLPP2_ENST00000356272.3_In_Frame_Del_p.NI702del|PHLPP2_ENST00000540628.1_5'UTR|PHLPP2_ENST00000360429.3_In_Frame_Del_p.NI702del	p.NI635del			Q6ZVD8	PHLP2_HUMAN			12	2637_2639	-			702					A1L374|Q9NV17|Q9Y2E3	In_Frame_Del	DEL	ENST00000568954.1	37	c.1904_1906delACA	CCDS32479.1																																																																																				0.458	PHLPP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000434139.1	NM_015020		25	135						25	135	---	---	---	---
NF1	4763	broad.mit.edu	37	17	29546036	29546037	+	Frame_Shift_Del	DEL	AG	AG	-	rs267606600		TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr17:29546036_29546037delAG	ENST00000358273.4	+	14	1924_1925	c.1541_1542delAG	c.(1540-1542)cagfs	p.Q514fs	NF1_ENST00000431387.4_Frame_Shift_Del_p.Q514fs|NF1_ENST00000356175.3_Frame_Shift_Del_p.Q514fs	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	514					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(6)|p.Q514fs*43(2)|p.N510_E547del(1)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		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	0.426			"""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)																												ENST00000358273.4			yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	"""D, Mis, N, F, S, O"""	neurofibromatosis type 1 gene			O		"""neurofibroma, glioma"""	"""neurofibroma, glioma"""	NF1/ACCN1(2)	17	Whole gene deletion(8)|Unknown(6)|Deletion - Frameshift(2)|Deletion - In frame(1)	p.0?(8)|p.?(6)|p.Q514fs*43(2)|p.N510_E547del(1)	soft_tissue(11)|autonomic_ganglia(3)|central_nervous_system(2)|lung(1)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599	GRCh37	CD962097	NF1	D		c.(1540-1542)cfs		neurofibromin 1																																				SO:0001589	frameshift_variant	4763	Neurofibromatosis, type 1	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	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	g.chr17:29546036_29546037delAG		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"""neurofibromatosis"", ""von Recklinghausen disease"", ""Watson disease"""	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.1541_1542delAG	17.37:g.29546036_29546037delAG	ENSP00000351015:p.Gln514fs	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)				NF1_ENST00000356175.3_Frame_Shift_Del_p.Q514fs|NF1_ENST00000431387.4_Frame_Shift_Del_p.Q514fs	p.Q514fs	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN		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)	14	1924_1925	+		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)	514					O00662|Q14284|Q14930|Q14931|Q9UMK3	Frame_Shift_Del	DEL	ENST00000358273.4	37	c.1541_1542delAG	CCDS42292.1																																																																																				0.426	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		7	13						7	13	---	---	---	---
NF1	4763	broad.mit.edu	37	17	29652976	29652979	+	Frame_Shift_Del	DEL	TCTC	TCTC	-			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr17:29652976_29652979delTCTC	ENST00000358273.4	+	37	5357_5360	c.4974_4977delTCTC	c.(4972-4977)tttctcfs	p.FL1658fs	NF1_ENST00000356175.3_Frame_Shift_Del_p.FL1637fs|NF1_ENST00000581113.2_3'UTR	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	1658	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.|Lipid binding.				actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(3)|p.S1660fs*37(2)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		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)																												ENST00000358273.4			yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	"""D, Mis, N, F, S, O"""	neurofibromatosis type 1 gene			O		"""neurofibroma, glioma"""	"""neurofibroma, glioma"""	NF1/ACCN1(2)	13	Whole gene deletion(8)|Unknown(3)|Deletion - Frameshift(2)	p.0?(8)|p.?(3)|p.S1660fs*37(2)	soft_tissue(7)|autonomic_ganglia(2)|central_nervous_system(2)|lung(1)|large_intestine(1)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599	GRCh37	CD972357	NF1	D		c.(4972-4977)ttfs		neurofibromin 1																																				SO:0001589	frameshift_variant	4763	Neurofibromatosis, type 1	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	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	g.chr17:29652976_29652979delTCTC		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"""neurofibromatosis"", ""von Recklinghausen disease"", ""Watson disease"""	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.4974_4977delTCTC	17.37:g.29652976_29652979delTCTC	ENSP00000351015:p.Phe1658fs	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)				NF1_ENST00000356175.3_Frame_Shift_Del_p.FL1637fs|NF1_ENST00000581113.2_3'UTR	p.FL1658fs	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN		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)	37	5357_5360	+		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)	1658			CRAL-TRIO.		O00662|Q14284|Q14930|Q14931|Q9UMK3	Frame_Shift_Del	DEL	ENST00000358273.4	37	c.4974_4977delTCTC	CCDS42292.1																																																																																				0.422	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		11	168						11	168	---	---	---	---
PLIN4	729359	broad.mit.edu	37	19	4510914	4510916	+	In_Frame_Del	DEL	TGG	TGG	-			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chr19:4510914_4510916delTGG	ENST00000301286.3	-	3	3013_3015	c.3014_3016delCCA	c.(3013-3018)accaag>aag	p.T1005del		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	1005						cytoplasm (GO:0005737)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)				NS(2)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|soft_tissue(1)|stomach(2)	41						AGCACTGTCTTGGTGGTGTCCAG	0.626																																						ENST00000301286.3																			0				NS(2)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|soft_tissue(1)|stomach(2)	41						c.(3013-3018)aag>a		perilipin 4																																				SO:0001651	inframe_deletion	729359					lipid particle|plasma membrane		g.chr19:4510914_4510916delTGG	AB067468	CCDS45927.1	19p13.3	2009-10-06	2009-08-12	2009-08-12	ENSG00000167676	ENSG00000167676		"""Perilipins"""	29393	protein-coding gene	gene with protein product		613247	"""KIAA1881"""	KIAA1881		11572484, 19638644	Standard	NM_001080400		Approved	S3-12	uc002mar.1	Q96Q06	OTTHUMG00000167571	ENST00000301286.3:c.3014_3016delCCA	19.37:g.4510917_4510919delTGG	ENSP00000301286:p.Thr1005del						p.TK1005del	NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN			3	3013_3015	-			1005					A6NEI2	In_Frame_Del	DEL	ENST00000301286.3	37	c.3014_3016delCCA	CCDS45927.1																																																																																				0.626	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901		22	28						22	28	---	---	---	---
BCORL1	63035	broad.mit.edu	37	X	129147257	129147259	+	In_Frame_Del	DEL	AGA	AGA	-			TCGA-DU-6394-01A-11D-1705-08	TCGA-DU-6394-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	611b0bd5-fb3a-4c10-999c-e4b3f6980d0b	d7371b5d-ee62-450e-bc22-082b1de3911b	g.chrX:129147257_129147259delAGA	ENST00000218147.7	+	4	706_708	c.509_511delAGA	c.(508-513)gagaag>gag	p.K171del	BCORL1_ENST00000540052.1_In_Frame_Del_p.K171del|BCORL1_ENST00000303743.5_In_Frame_Del_p.K171del|BCORL1_ENST00000359304.2_In_Frame_Del_p.K171del			Q5H9F3	BCORL_HUMAN	BCL6 corepressor-like 1	171					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|liver(3)|lung(30)|ovary(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	75						GGTGTTGGAGAGAAGAATACTTT	0.552																																						ENST00000540052.1																			0				breast(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|liver(3)|lung(30)|ovary(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	75						c.(508-513)gag>g		BCL6 corepressor-like 1																																				SO:0001651	inframe_deletion	63035				chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus		g.chrX:129147257_129147259delAGA	AL136450	CCDS14616.1	Xq25-q26.1	2014-09-17	2010-06-10		ENSG00000085185	ENSG00000085185		"""Ankyrin repeat domain containing"""	25657	protein-coding gene	gene with protein product		300688	"""chromosome X open reading frame 10"", ""BCL6 co-repressor-like 1"""	CXorf10			Standard	NM_021946		Approved	FLJ11362	uc022cdu.1	Q5H9F3	OTTHUMG00000022379	ENST00000218147.7:c.509_511delAGA	X.37:g.129147260_129147262delAGA	ENSP00000218147:p.Lys171del					BCORL1_ENST00000218147.7_In_Frame_Del_p.EK170del|BCORL1_ENST00000359304.2_In_Frame_Del_p.EK170del|BCORL1_ENST00000303743.5_In_Frame_Del_p.EK170del	p.EK170del	NM_021946.4	NP_068765.3	Q5H9F3	BCORL_HUMAN			3	553_555	+			170					B5MDQ8|Q5H9F2|Q5H9F4|Q6ZVE0|Q8TEN3|Q9Y528	In_Frame_Del	DEL	ENST00000218147.7	37	c.509_511delAGA	CCDS14616.1																																																																																				0.552	BCORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058223.1	NM_021946		9	21						9	21	---	---	---	---
