#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
MAP2	4133	broad.mit.edu	37	2	210560053	210560053	+	Silent	SNP	T	T	C			TCGA-DU-7011-01A-11D-2024-08	TCGA-DU-7011-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a998b8e9-3711-460c-8e4b-6597b6760a15	faf5593b-8173-4404-adef-379c03202b68	g.chr2:210560053T>C	ENST00000360351.4	+	7	3665	c.3159T>C	c.(3157-3159)ttT>ttC	p.F1053F	MAP2_ENST00000392194.1_Intron|MAP2_ENST00000361559.4_Intron|MAP2_ENST00000447185.1_Silent_p.F1049F|MAP2_ENST00000199940.6_Intron	NM_002374.3	NP_002365.3	P11137	MTAP2_HUMAN	microtubule-associated protein 2	1053					axonogenesis (GO:0007409)|cellular response to organic substance (GO:0071310)|central nervous system neuron development (GO:0021954)|dendrite morphogenesis (GO:0048813)|microtubule bundle formation (GO:0001578)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|nuclear periphery (GO:0034399)	dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(36)|liver(2)|lung(42)|ovary(11)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	124		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Docetaxel(DB01248)|Estramustine(DB01196)|Paclitaxel(DB01229)	TTAGTGACTTTGGACAGATGG	0.468																																					Pancreas(27;423 979 28787 29963)	ENST00000360351.4																			0				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(36)|liver(2)|lung(42)|ovary(11)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	124						c.(3157-3159)ttT>ttC		microtubule-associated protein 2	Estramustine(DB01196)						98.0	101.0	100.0					2																	210560053		2203	4300	6503	SO:0001819	synonymous_variant	4133				central nervous system neuron development|dendrite morphogenesis|negative regulation of microtubule depolymerization	cytoplasm|microtubule|microtubule associated complex	beta-dystroglycan binding|calmodulin binding|structural molecule activity	g.chr2:210560053T>C		CCDS2384.1, CCDS2385.1, CCDS33369.1	2q34-q35	2008-05-27			ENSG00000078018	ENSG00000078018		"""A-kinase anchor proteins"""	6839	protein-coding gene	gene with protein product		157130				3103857, 7479905	Standard	XM_005246554		Approved	MAP2A, MAP2B, MAP2C	uc002vde.1	P11137	OTTHUMG00000132962	ENST00000360351.4:c.3159T>C	2.37:g.210560053T>C						MAP2_ENST00000447185.1_Silent_p.F1049F|MAP2_ENST00000361559.4_Intron|MAP2_ENST00000199940.6_Intron|MAP2_ENST00000392194.1_Intron	p.F1053F	NM_002374.3	NP_002365.3	P11137	MAP2_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	7	3665	+		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)	1053					Q17S04|Q8IUX2|Q99975|Q99976	Silent	SNP	ENST00000360351.4	37	c.3159T>C	CCDS2384.1																																																																																				0.468	MAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256521.2	NM_001039538		52	85	0	0	0	1	0	52	85				
SERPINB11	89778	broad.mit.edu	37	18	61377583	61377583	+	RNA	SNP	G	G	A			TCGA-DU-7011-01A-11D-2024-08	TCGA-DU-7011-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a998b8e9-3711-460c-8e4b-6597b6760a15	faf5593b-8173-4404-adef-379c03202b68	g.chr18:61377583G>A	ENST00000382749.5	+	0	401				SERPINB11_ENST00000544088.1_RNA|SERPINB11_ENST00000538847.1_RNA|SERPINB11_ENST00000536691.1_RNA|SERPINB11_ENST00000489748.1_RNA			Q96P15	SPB11_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 11 (gene/pseudogene)						negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|cervix(1)|kidney(1)|lung(3)	6		Esophageal squamous(42;0.129)				AGACTGAAGAGCAATTGGAGA	0.438																																					Ovarian(27;496 784 5942 8975 23930)	ENST00000544088.1																			0				breast(1)|cervix(1)|kidney(1)|lung(3)	6								serpin peptidase inhibitor, clade B (ovalbumin), member 11 (gene/pseudogene)							94.0	87.0	90.0					18																	61377583		1869	4103	5972			89778				regulation of proteolysis	cytoplasm	serine-type endopeptidase inhibitor activity	g.chr18:61377583G>A			18q21.33	2014-02-18	2009-01-22		ENSG00000206072	ENSG00000206072		"""Serine (or cysteine) peptidase inhibitors"""	14221	protein-coding gene	gene with protein product		615682	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 11"", ""serpin peptidase inhibitor, clade B (ovalbumin), member 11"""			17562709, 24172014	Standard	XM_006722569		Approved	EPIPIN	uc002ljk.4	Q96P15	OTTHUMG00000060404		18.37:g.61377583G>A						SERPINB11_ENST00000536691.1_RNA|SERPINB11_ENST00000489748.1_RNA|SERPINB11_ENST00000382749.5_RNA|SERPINB11_ENST00000538847.1_RNA		NM_080475.2	NP_536723.2	Q96P15	SPB11_HUMAN			0	218	+		Esophageal squamous(42;0.129)						A8K9R0|Q5Q120|Q5Q121|Q5Q122|Q5Q123|Q6ISD3|Q96P13|Q96P14	RNA	SNP	ENST00000382749.5	37																																																																																						0.438	SERPINB11-002	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000207392.3	NM_080475		6	36	0	0	0	1	0	6	36				
DCAF4L1	285429	broad.mit.edu	37	4	41984364	41984364	+	Silent	SNP	C	C	A			TCGA-DU-7011-01A-11D-2024-08	TCGA-DU-7011-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a998b8e9-3711-460c-8e4b-6597b6760a15	faf5593b-8173-4404-adef-379c03202b68	g.chr4:41984364C>A	ENST00000333141.5	+	1	652	c.555C>A	c.(553-555)gcC>gcA	p.A185A		NM_001029955.3	NP_001025126.2	Q3SXM0	DC4L1_HUMAN	DDB1 and CUL4 associated factor 4-like 1	185										breast(1)|endometrium(5)|kidney(6)|large_intestine(11)|lung(12)|prostate(1)|skin(1)	37						TCCCAGAGGCCTGGTCCTGTG	0.587																																						ENST00000333141.5																			0				breast(1)|endometrium(5)|kidney(6)|large_intestine(11)|lung(12)|prostate(1)|skin(1)	37						c.(553-555)gcC>gcA		DDB1 and CUL4 associated factor 4-like 1							106.0	102.0	103.0					4																	41984364		2203	4300	6503	SO:0001819	synonymous_variant	285429							g.chr4:41984364C>A	BC035027	CCDS33978.1	4p13	2013-01-09	2009-07-17	2009-07-17		ENSG00000182308		"""WD repeat domain containing"""	27723	protein-coding gene	gene with protein product			"""WD repeat domain 21B"""	WDR21B			Standard	NM_001029955		Approved		uc003gwk.2	Q3SXM0		ENST00000333141.5:c.555C>A	4.37:g.41984364C>A							p.A185A	NM_001029955.3	NP_001025126.2	Q3SXM0	DC4L1_HUMAN			1	652	+			185					B3KVI3|Q3ZCW8|Q499Y5|Q9UFI0	Silent	SNP	ENST00000333141.5	37	c.555C>A	CCDS33978.1																																																																																				0.587	DCAF4L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360958.1	NM_001029955		14	135	1	0	1.52009e-12	1	1.57639e-12	14	135				
WDR78	79819	broad.mit.edu	37	1	67370972	67370972	+	Missense_Mutation	SNP	T	T	C			TCGA-DU-7011-01A-11D-2024-08	TCGA-DU-7011-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a998b8e9-3711-460c-8e4b-6597b6760a15	faf5593b-8173-4404-adef-379c03202b68	g.chr1:67370972T>C	ENST00000371026.3	-	2	312	c.257A>G	c.(256-258)cAa>cGa	p.Q86R	WDR78_ENST00000488333.1_Missense_Mutation_p.Q14R|WDR78_ENST00000371023.3_Missense_Mutation_p.Q86R|WDR78_ENST00000371022.3_Missense_Mutation_p.Q86R|WDR78_ENST00000431318.1_5'UTR	NM_024763.4	NP_079039.4	Q5VTH9	WDR78_HUMAN	WD repeat domain 78	86					hematopoietic progenitor cell differentiation (GO:0002244)					NS(1)|endometrium(3)|kidney(6)|large_intestine(6)|lung(10)|ovary(3)|skin(3)	32						CATTCTGCTTTGATTTGCACC	0.353																																						ENST00000371026.3																			0				NS(1)|endometrium(3)|kidney(6)|large_intestine(6)|lung(10)|ovary(3)|skin(3)	32						c.(256-258)cAa>cGa		WD repeat domain 78							166.0	160.0	162.0					1																	67370972		2203	4300	6503	SO:0001583	missense	79819							g.chr1:67370972T>C	BX648840	CCDS635.1, CCDS44157.1	1p31.2	2014-02-21	2013-02-19	2013-02-19	ENSG00000152763	ENSG00000152763		"""WD repeat domain containing"""	26252	protein-coding gene	gene with protein product						21953912	Standard	NM_207014		Approved	DIC4, FLJ23129	uc001dcx.3	Q5VTH9	OTTHUMG00000009165	ENST00000371026.3:c.257A>G	1.37:g.67370972T>C	ENSP00000360065:p.Gln86Arg					WDR78_ENST00000431318.1_5'UTR|WDR78_ENST00000371022.3_Missense_Mutation_p.Q86R|WDR78_ENST00000371023.3_Missense_Mutation_p.Q86R|WDR78_ENST00000488333.1_Missense_Mutation_p.Q14R	p.Q86R	NM_024763.4	NP_079039.4	Q5VTH9	WDR78_HUMAN			2	312	-			86					A8K9W5|B5MDT3|H7BY80|Q5VTI0|Q8N5G5|Q9H5R9|Q9UF44	Missense_Mutation	SNP	ENST00000371026.3	37	c.257A>G	CCDS635.1	.	.	.	.	.	.	.	.	.	.	T	17.55	3.416968	0.62511	.	.	ENSG00000152763	ENST00000371026;ENST00000371023;ENST00000371022;ENST00000488333	T;T;T	0.57107	0.42;2.17;1.42	3.99	0.0223	0.14133	.	0.591766	0.17050	N	0.188958	T	0.31167	0.0788	L	0.57536	1.79	0.58432	D	0.999999	D;B;B	0.52996	0.957;0.006;0.006	P;B;B	0.51701	0.677;0.002;0.002	T	0.45145	-0.9281	10	0.09590	T	0.72	-5.5853	5.1736	0.15124	0.1746:0.0:0.3612:0.4642	.	86;86;86	Q5TAD8;A0AVI9;Q5VTH9	.;.;WDR78_HUMAN	R	86;86;86;14	ENSP00000360065:Q86R;ENSP00000360062:Q86R;ENSP00000360061:Q86R	ENSP00000360061:Q86R	Q	-	2	0	WDR78	67143560	0.998000	0.40836	0.750000	0.31169	0.620000	0.37586	0.474000	0.22148	-0.016000	0.14127	0.454000	0.30748	CAA		0.353	WDR78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025404.1	NM_024763		6	111	0	0	0	1	0	6	111				
TSSC2	650368	broad.mit.edu	37	11	3427845	3427845	+	RNA	SNP	C	C	T			TCGA-DU-7011-01A-11D-2024-08	TCGA-DU-7011-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a998b8e9-3711-460c-8e4b-6597b6760a15	faf5593b-8173-4404-adef-379c03202b68	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	48	0	0	0	1	0	4	48				
ATRX	546	broad.mit.edu	37	X	76939496	76939496	+	Nonsense_Mutation	SNP	G	G	A			TCGA-DU-7011-01A-11D-2024-08	TCGA-DU-7011-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a998b8e9-3711-460c-8e4b-6597b6760a15	faf5593b-8173-4404-adef-379c03202b68	g.chrX:76939496G>A	ENST00000373344.5	-	9	1466	c.1252C>T	c.(1252-1254)Cga>Tga	p.R418*	ATRX_ENST00000395603.3_Nonsense_Mutation_p.R380*|ATRX_ENST00000480283.1_5'UTR	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	418					ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						TCCATCGCTCGAAACTCGGAA	0.373			"""Mis, F, N"""		"""Pancreatic neuroendocrine tumors, paediatric GBM"""		ATR-X (alpha thalassemia/mental retardation) syndrome																															ENST00000373344.5				Rec	yes		X	Xq21.1	546	"""Mis, F, N"""	alpha thalassemia/mental retardation syndrome X-linked	yes	ATR-X (alpha thalassemia/mental retardation) syndrome	E			"""Pancreatic neuroendocrine tumors, paediatric GBM"""		1	Unknown(1)	p.?(1)	bone(1)	bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						c.(1252-1254)Cga>Tga		alpha thalassemia/mental retardation syndrome X-linked	Phosphatidylserine(DB00144)						163.0	162.0	162.0					X																	76939496		2203	4295	6498	SO:0001587	stop_gained	546				DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent	nuclear heterochromatin	ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding	g.chrX:76939496G>A	U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"""RAD54 homolog (S. cerevisiae)"""	300032	"""alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)"", ""Juberg-Marsidi syndrome"""	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.1252C>T	X.37:g.76939496G>A	ENSP00000362441:p.Arg418*					ATRX_ENST00000395603.3_Nonsense_Mutation_p.R380*|ATRX_ENST00000480283.1_5'UTR	p.R418*	NM_000489.3	NP_000480.2	P46100	ATRX_HUMAN			9	1466	-			418					D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Nonsense_Mutation	SNP	ENST00000373344.5	37	c.1252C>T	CCDS14434.1	.	.	.	.	.	.	.	.	.	.	g	17.75	3.465931	0.63625	.	.	ENSG00000085224	ENST00000373344;ENST00000395603;ENST00000400862	.	.	.	5.06	3.23	0.37069	.	0.919132	0.09194	N	0.835594	.	.	.	.	.	.	0.31534	N	0.660867	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	3.1135	9.6724	0.40019	0.0:0.1335:0.5848:0.2817	.	.	.	.	X	418;380;374	.	ENSP00000362441:R418X	R	-	1	2	ATRX	76826152	0.353000	0.24904	0.102000	0.21198	0.011000	0.07611	1.048000	0.30379	0.334000	0.23590	0.509000	0.49947	CGA		0.373	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489		47	136	0	0	0	1	0	47	136				
UBR2	23304	broad.mit.edu	37	6	42631096	42631096	+	Missense_Mutation	SNP	T	T	C			TCGA-DU-7011-01A-11D-2024-08	TCGA-DU-7011-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a998b8e9-3711-460c-8e4b-6597b6760a15	faf5593b-8173-4404-adef-379c03202b68	g.chr6:42631096T>C	ENST00000372899.1	+	32	3895	c.3637T>C	c.(3637-3639)Tgt>Cgt	p.C1213R	UBR2_ENST00000372883.3_3'UTR|UBR2_ENST00000372901.1_Missense_Mutation_p.C1213R|RNU6-890P_ENST00000384121.1_RNA	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2	1213					cellular response to leucine (GO:0071233)|chromatin silencing (GO:0006342)|histone H2A ubiquitination (GO:0033522)|male meiosis I (GO:0007141)|negative regulation of TOR signaling (GO:0032007)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(10)|kidney(7)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|skin(5)	64	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			TTGCCCCCTTTGTGAATGCTT	0.378																																						ENST00000372899.1																			0				breast(1)|central_nervous_system(1)|endometrium(10)|kidney(7)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|skin(5)	64						c.(3637-3639)Tgt>Cgt		ubiquitin protein ligase E3 component n-recognin 2							200.0	176.0	184.0					6																	42631096		2203	4300	6503	SO:0001583	missense	23304				cellular response to leucine|chromatin silencing|histone H2A ubiquitination|negative regulation of TOR signaling cascade	nucleus|plasma membrane	leucine binding|zinc ion binding	g.chr6:42631096T>C	BC024217	CCDS4870.1, CCDS55001.1	6p21.1	2008-06-23	2005-01-10	2005-01-12	ENSG00000024048	ENSG00000024048		"""Ubiquitin protein ligase E3 component n-recognins"""	21289	protein-coding gene	gene with protein product		609134	"""chromosome 6 open reading frame 133"""	C6orf133			Standard	NM_015255		Approved	bA49A4.1, dJ392M17.3, KIAA0349	uc011dur.2	Q8IWV8	OTTHUMG00000014703	ENST00000372899.1:c.3637T>C	6.37:g.42631096T>C	ENSP00000361990:p.Cys1213Arg					UBR2_ENST00000372901.1_Missense_Mutation_p.C1213R|UBR2_ENST00000372883.3_3'UTR	p.C1213R	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)		32	3895	+	Colorectal(47;0.196)		1213					O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	Missense_Mutation	SNP	ENST00000372899.1	37	c.3637T>C	CCDS4870.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.486284	0.84854	.	.	ENSG00000024048	ENST00000372899;ENST00000372901	T;T	0.66995	-0.24;-0.24	5.3	5.3	0.74995	Zinc finger, RING-type (1);	0.000000	0.85682	D	0.000000	D	0.83403	0.5247	M	0.92268	3.29	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.87929	0.2709	10	0.87932	D	0	-23.4811	15.5395	0.76031	0.0:0.0:0.0:1.0	.	1213;1213	Q8IWV8-4;Q8IWV8	.;UBR2_HUMAN	R	1213	ENSP00000361990:C1213R;ENSP00000361992:C1213R	ENSP00000361990:C1213R	C	+	1	0	UBR2	42739074	1.000000	0.71417	0.999000	0.59377	0.990000	0.78478	7.655000	0.83696	2.129000	0.65627	0.533000	0.62120	TGT		0.378	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040558.2	NM_015255		22	65	0	0	0	1	0	22	65				
PCLO	27445	broad.mit.edu	37	7	82584494	82584494	+	Silent	SNP	T	T	C			TCGA-DU-7011-01A-11D-2024-08	TCGA-DU-7011-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a998b8e9-3711-460c-8e4b-6597b6760a15	faf5593b-8173-4404-adef-379c03202b68	g.chr7:82584494T>C	ENST00000333891.9	-	5	6112	c.5775A>G	c.(5773-5775)acA>acG	p.T1925T	PCLO_ENST00000423517.2_Silent_p.T1925T	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TGTATTTGTGTGTTTTATGCA	0.358																																						ENST00000423517.2																			0				breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						c.(5773-5775)acA>acG		piccolo presynaptic cytomatrix protein							57.0	55.0	56.0					7																	82584494		1867	4092	5959	SO:0001819	synonymous_variant	27445				cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity	g.chr7:82584494T>C	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"""aczonin"""	604918	"""piccolo (presynaptic cytomatrix protein)"""			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.5775A>G	7.37:g.82584494T>C						PCLO_ENST00000333891.8_Silent_p.T1925T	p.T1925T	NM_014510.2	NP_055325.2	Q9Y6V0	PCLO_HUMAN			5	6112	-			1856						Silent	SNP	ENST00000333891.9	37	c.5775A>G	CCDS47630.1																																																																																				0.358	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		18	23	0	0	0	1	0	18	23				
IL27	246778	broad.mit.edu	37	16	28513350	28513350	+	Missense_Mutation	SNP	G	G	C			TCGA-DU-7011-01A-11D-2024-08	TCGA-DU-7011-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a998b8e9-3711-460c-8e4b-6597b6760a15	faf5593b-8173-4404-adef-379c03202b68	g.chr16:28513350G>C	ENST00000356897.1	-	4	431	c.409C>G	c.(409-411)Ctg>Gtg	p.L137V		NM_145659.3	NP_663634.2	Q8TAD2	IL17D_HUMAN	interleukin 27	93					inflammatory response (GO:0006954)	extracellular space (GO:0005615)				endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)	10						ATGGCCCACAGCTGCATCCTC	0.662																																						ENST00000356897.1																			0				endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)	10						c.(409-411)Ctg>Gtg		interleukin 27							81.0	82.0	82.0					16																	28513350		2197	4300	6497	SO:0001583	missense	246778				inflammatory response|innate immune response|positive regulation of interferon-gamma biosynthetic process|regulation of defense response to virus|regulation of T cell proliferation|regulation of T-helper 1 cell differentiation	extracellular space	cytokine activity|interleukin-27 receptor binding	g.chr16:28513350G>C	AY099296	CCDS10633.1	16p11	2011-07-21	2003-12-17	2003-12-19	ENSG00000197272	ENSG00000197272		"""Interleukins and interleukin receptors"""	19157	protein-coding gene	gene with protein product		608273	"""interleukin 30"""	IL30		12121660	Standard	NM_145659		Approved	IL-27, p28, IL27p28, IL-27A, IL27A, MGC71873	uc002dqc.3	Q8NEV9	OTTHUMG00000097023	ENST00000356897.1:c.409C>G	16.37:g.28513350G>C	ENSP00000349365:p.Leu137Val						p.L137V	NM_145659.3	NP_663634.2	Q8NEV9	IL27A_HUMAN			4	431	-			137					B1AM69	Missense_Mutation	SNP	ENST00000356897.1	37	c.409C>G	CCDS10633.1	.	.	.	.	.	.	.	.	.	.	G	15.08	2.726058	0.48833	.	.	ENSG00000197272	ENST00000356897	T	0.55588	0.51	4.04	1.92	0.25849	.	0.000000	0.28659	U	0.014574	T	0.53449	0.1797	L	0.52573	1.65	0.09310	N	1	D	0.64830	0.994	P	0.56088	0.791	T	0.41963	-0.9479	10	0.62326	D	0.03	-2.3226	5.1086	0.14796	0.1146:0.0:0.6842:0.2012	.	137	Q8NEV9	IL27A_HUMAN	V	137	ENSP00000349365:L137V	ENSP00000349365:L137V	L	-	1	2	IL27	28420851	0.006000	0.16342	0.984000	0.44739	0.758000	0.43043	0.629000	0.24538	0.692000	0.31613	0.281000	0.19383	CTG		0.662	IL27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214114.1	NM_145659		6	64	0	0	0	1	0	6	64				
CLIP4	79745	broad.mit.edu	37	2	29355042	29355042	+	Missense_Mutation	SNP	A	A	G			TCGA-DU-7011-01A-11D-2024-08	TCGA-DU-7011-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a998b8e9-3711-460c-8e4b-6597b6760a15	faf5593b-8173-4404-adef-379c03202b68	g.chr2:29355042A>G	ENST00000320081.5	+	4	553	c.298A>G	c.(298-300)Aat>Gat	p.N100D	CLIP4_ENST00000404424.1_Missense_Mutation_p.N100D|CLIP4_ENST00000401617.2_5'UTR|CLIP4_ENST00000401605.1_Missense_Mutation_p.N100D	NM_024692.4	NP_078968.3	Q8N3C7	CLIP4_HUMAN	CAP-GLY domain containing linker protein family, member 4	100										endometrium(4)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|prostate(1)|skin(1)	26	Acute lymphoblastic leukemia(172;0.155)					TTGCAATGTGAATGATAGAGA	0.378																																						ENST00000320081.5																			0				endometrium(4)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|prostate(1)|skin(1)	26						c.(298-300)Aat>Gat		CAP-GLY domain containing linker protein family, member 4							244.0	235.0	238.0					2																	29355042		2203	4300	6503	SO:0001583	missense	79745							g.chr2:29355042A>G	AK024722	CCDS1770.1, CCDS74502.1	2p23	2013-01-10	2007-01-04	2007-01-04	ENSG00000115295	ENSG00000115295		"""Ankyrin repeat domain containing"""	26108	protein-coding gene	gene with protein product			"""restin-like 2"""	RSNL2			Standard	XM_005264562		Approved	FLJ21069	uc002rmv.3	Q8N3C7	OTTHUMG00000097837	ENST00000320081.5:c.298A>G	2.37:g.29355042A>G	ENSP00000327009:p.Asn100Asp					CLIP4_ENST00000401605.1_Missense_Mutation_p.N100D|CLIP4_ENST00000401617.2_5'UTR|CLIP4_ENST00000404424.1_Missense_Mutation_p.N100D	p.N100D	NM_024692.4	NP_078968.3	Q8N3C7	CLIP4_HUMAN			4	553	+	Acute lymphoblastic leukemia(172;0.155)		100					A0AV10|B2RMQ3|B7Z7N8|Q7Z4U3|Q96BR7|Q96MA5|Q9H7C0	Missense_Mutation	SNP	ENST00000320081.5	37	c.298A>G	CCDS1770.1	.	.	.	.	.	.	.	.	.	.	A	19.60	3.857430	0.71834	.	.	ENSG00000115295	ENST00000401605;ENST00000404424;ENST00000402240;ENST00000320081;ENST00000379543;ENST00000449202;ENST00000530644	T;T;T;T	0.57907	0.37;0.37;0.37;0.37	5.44	5.44	0.79542	Ankyrin repeat-containing domain (3);	0.101656	0.64402	D	0.000002	T	0.69115	0.3075	L	0.56396	1.775	0.58432	D	0.999999	D;D	0.89917	0.997;1.0	D;D	0.83275	0.985;0.996	T	0.70883	-0.4751	10	0.54805	T	0.06	.	15.5123	0.75793	1.0:0.0:0.0:0.0	.	100;100	A8K6D0;Q8N3C7	.;CLIP4_HUMAN	D	100;100;100;100;101;100;82	ENSP00000384242:N100D;ENSP00000385594:N100D;ENSP00000327009:N100D;ENSP00000393354:N100D	ENSP00000327009:N100D	N	+	1	0	CLIP4	29208546	1.000000	0.71417	0.997000	0.53966	0.475000	0.33008	9.172000	0.94808	2.056000	0.61249	0.528000	0.53228	AAT		0.378	CLIP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215123.2	NM_024692		8	105	0	0	0	1	0	8	105				
CSPG4	1464	broad.mit.edu	37	15	75975277	75975277	+	Missense_Mutation	SNP	C	C	T			TCGA-DU-7011-01A-11D-2024-08	TCGA-DU-7011-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a998b8e9-3711-460c-8e4b-6597b6760a15	faf5593b-8173-4404-adef-379c03202b68	g.chr15:75975277C>T	ENST00000308508.5	-	6	4647	c.4555G>A	c.(4555-4557)Ggg>Agg	p.G1519R		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	1519	Gly/Ser-rich (glycosaminoglycan attachment domain).				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						ACTACCCGCCCGTTGCTGGGC	0.697																																						ENST00000308508.5																			0				breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						c.(4555-4557)Ggg>Agg		chondroitin sulfate proteoglycan 4							18.0	20.0	19.0					15																	75975277		2189	4291	6480	SO:0001583	missense	1464				angiogenesis|cell differentiation|intracellular signal transduction|positive regulation of peptidyl-tyrosine phosphorylation|tissue remodeling	apical plasma membrane|cell surface|integral to plasma membrane|intracellular|lamellipodium membrane	protein kinase binding|signal transducer activity	g.chr15:75975277C>T	X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"""Proteoglycans / Cell surface : Other"""	2466	protein-coding gene	gene with protein product	"""melanoma-associated chondroitin sulfate proteoglycan"""	601172	"""chondroitin sulfate proteoglycan 4 (melanoma-associated)"""			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.4555G>A	15.37:g.75975277C>T	ENSP00000312506:p.Gly1519Arg						p.G1519R	NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN			6	4647	-			1519			Gly/Ser-rich (glycosaminoglycan attachment domain).		D3DW77|Q92675	Missense_Mutation	SNP	ENST00000308508.5	37	c.4555G>A	CCDS10284.1	.	.	.	.	.	.	.	.	.	.	.	19.20	3.781894	0.70222	.	.	ENSG00000173546	ENST00000308508	T	0.53206	0.63	3.83	3.83	0.44106	.	0.000000	0.53938	D	0.000054	T	0.68668	0.3026	M	0.78049	2.395	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.74893	-0.3509	10	0.87932	D	0	.	15.2397	0.73458	0.0:1.0:0.0:0.0	.	1519	Q6UVK1	CSPG4_HUMAN	R	1519	ENSP00000312506:G1519R	ENSP00000312506:G1519R	G	-	1	0	CSPG4	73762332	1.000000	0.71417	0.282000	0.24776	0.185000	0.23345	7.117000	0.77129	2.151000	0.67156	0.305000	0.20034	GGG		0.697	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897		7	25	0	0	0	1	0	7	25				
CPSF1	29894	broad.mit.edu	37	8	145619157	145619157	+	Missense_Mutation	SNP	G	G	A			TCGA-DU-7011-01A-11D-2024-08	TCGA-DU-7011-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a998b8e9-3711-460c-8e4b-6597b6760a15	faf5593b-8173-4404-adef-379c03202b68	g.chr8:145619157G>A	ENST00000349769.3	-	35	4050	c.3956C>T	c.(3955-3957)gCc>gTc	p.A1319V	MIR939_ENST00000401314.1_RNA|CPSF1_ENST00000531727.1_5'UTR	NM_013291.2	NP_037423.2	Q10570	CPSF1_HUMAN	cleavage and polyadenylation specific factor 1, 160kDa	1319					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)	mRNA 3'-UTR binding (GO:0003730)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.88e-41)|Epithelial(56;1.67e-40)|all cancers(56;1.2e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055)			CCCTTCAGTGGCCCCCCGGCA	0.632																																					NSCLC(133;1088 1848 27708 34777 35269)	ENST00000349769.3																			0				NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						c.(3955-3957)gCc>gTc		cleavage and polyadenylation specific factor 1, 160kDa							68.0	65.0	66.0					8																	145619157		2202	4300	6502	SO:0001583	missense	29894				mRNA cleavage|mRNA export from nucleus|mRNA polyadenylation|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	mRNA cleavage and polyadenylation specificity factor complex	mRNA 3'-UTR binding|protein binding	g.chr8:145619157G>A	U37012	CCDS34966.1	8q24	2014-05-06	2002-08-29		ENSG00000071894	ENSG00000071894			2324	protein-coding gene	gene with protein product		606027	"""cleavage and polyadenylation specific factor 1, 160kD subunit"""			7651824, 7590244	Standard	NM_013291		Approved		uc003zcj.3	Q10570	OTTHUMG00000174612	ENST00000349769.3:c.3956C>T	8.37:g.145619157G>A	ENSP00000339353:p.Ala1319Val					CPSF1_ENST00000531727.1_5'UTR	p.A1319V	NM_013291.2	NP_037423.2	Q10570	CPSF1_HUMAN	OV - Ovarian serous cystadenocarcinoma(54;2.88e-41)|Epithelial(56;1.67e-40)|all cancers(56;1.2e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055)		35	4050	-	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		1319					Q96AF0	Missense_Mutation	SNP	ENST00000349769.3	37	c.3956C>T	CCDS34966.1	.	.	.	.	.	.	.	.	.	.	G	7.143	0.582231	0.13749	.	.	ENSG00000071894	ENST00000349769	T	0.46063	0.88	5.06	5.06	0.68205	Cleavage/polyadenylation specificity factor, A subunit, C-terminal (1);	0.122800	0.56097	D	0.000031	T	0.24314	0.0589	N	0.12746	0.255	0.44635	D	0.997616	B	0.13594	0.008	B	0.19666	0.026	T	0.09574	-1.0668	10	0.15952	T	0.53	-23.452	11.7772	0.51993	0.0:0.1778:0.8222:0.0	.	1319	Q10570	CPSF1_HUMAN	V	1319	ENSP00000339353:A1319V	ENSP00000339353:A1319V	A	-	2	0	CPSF1	145589965	0.944000	0.32072	0.828000	0.32881	0.306000	0.27790	4.868000	0.63021	2.363000	0.80096	0.555000	0.69702	GCC		0.632	CPSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382422.2	NM_013291		3	28	0	0	0	1	0	3	28				
IDH1	3417	broad.mit.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-DU-7011-01A-11D-2024-08	TCGA-DU-7011-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a998b8e9-3711-460c-8e4b-6597b6760a15	faf5593b-8173-4404-adef-379c03202b68	g.chr2:209113112C>T	ENST00000415913.1	-	4	776	c.395G>A	c.(394-396)cGt>cAt	p.R132H	IDH1_ENST00000345146.2_Missense_Mutation_p.R132H|IDH1_ENST00000446179.1_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			18	54	0	0	0	1	0	18	54				
CLTCL1	8218	broad.mit.edu	37	22	19197859	19197859	+	Missense_Mutation	SNP	C	C	A			TCGA-DU-7011-01A-11D-2024-08	TCGA-DU-7011-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a998b8e9-3711-460c-8e4b-6597b6760a15	faf5593b-8173-4404-adef-379c03202b68	g.chr22:19197859C>A	ENST00000263200.10	-	20	3298	c.3226G>T	c.(3226-3228)Gat>Tat	p.D1076Y	CLTCL1_ENST00000353891.5_Missense_Mutation_p.D1076Y|CLTCL1_ENST00000427926.1_Missense_Mutation_p.D1076Y|CLTCL1_ENST00000442042.2_5'Flank	NM_007098.3	NP_009029.3	P53675	CLH2_HUMAN	clathrin, heavy chain-like 1	1076	Heavy chain arm.|Proximal segment.				anatomical structure morphogenesis (GO:0009653)|intracellular protein transport (GO:0006886)|mitotic nuclear division (GO:0007067)|positive regulation of glucose import (GO:0046326)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|coated vesicle (GO:0030135)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|spindle (GO:0005819)|trans-Golgi network (GO:0005802)	signal transducer activity (GO:0004871)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49	Colorectal(54;0.0993)					GCATTCATATCAAACTTGTGG	0.552			T	?	ALCL																																	ENST00000263200.10				Dom	yes		22	22q11.21	8218	T	"""clathrin, heavy polypeptide-like 1"""			L	?		ALCL		0				breast(2)|central_nervous_system(3)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						c.(3226-3228)Gat>Tat		clathrin, heavy chain-like 1							85.0	85.0	85.0					22																	19197859		2103	4243	6346	SO:0001583	missense	8218				anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis	clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network	protein binding|signal transducer activity|structural molecule activity	g.chr22:19197859C>A		CCDS46662.1, CCDS54497.1, CCDS46662.2, CCDS54497.2	22q11.2	2008-06-10	2006-09-29		ENSG00000070371	ENSG00000070371			2093	protein-coding gene	gene with protein product		601273	"""clathrin, heavy polypeptide-like 1"""	CLTCL		8844170, 15133132	Standard	NM_007098		Approved	CLTD, CLH22, CHC22	uc021wle.1	P53675	OTTHUMG00000150109	ENST00000263200.10:c.3226G>T	22.37:g.19197859C>A	ENSP00000445677:p.Asp1076Tyr					CLTCL1_ENST00000353891.5_Missense_Mutation_p.D1076Y|CLTCL1_ENST00000427926.1_Missense_Mutation_p.D1076Y	p.D1076Y	NM_007098.3	NP_009029.3	P53675	CLH2_HUMAN			20	3298	-	Colorectal(54;0.0993)		1076			Heavy chain arm.|Proximal segment.		B7Z7U5|Q14017|Q15808|Q15809	Missense_Mutation	SNP	ENST00000263200.10	37	c.3226G>T	CCDS46662.1	.	.	.	.	.	.	.	.	.	.	C	13.15	2.149935	0.37923	.	.	ENSG00000070371	ENST00000353891;ENST00000263200;ENST00000427926	T;T;T	0.24350	1.86;1.86;1.86	3.81	2.78	0.32641	Tetratricopeptide-like helical (1);Armadillo-type fold (1);	0.204706	0.40064	N	0.001189	T	0.53818	0.1820	M	0.88181	2.935	0.58432	D	0.999999	D;D	0.76494	0.994;0.999	D;D	0.77557	0.968;0.99	T	0.61461	-0.7058	10	0.87932	D	0	-2.5067	11.4185	0.49967	0.0:0.9104:0.0:0.0896	.	1076;1076	P53675-2;P53675	.;CLH2_HUMAN	Y	1076	ENSP00000439662:D1076Y;ENSP00000445677:D1076Y;ENSP00000441158:D1076Y	ENSP00000445677:D1076Y	D	-	1	0	CLTCL1	17577859	1.000000	0.71417	0.453000	0.27007	0.005000	0.04900	6.905000	0.75714	0.811000	0.34303	-0.291000	0.09656	GAT		0.552	CLTCL1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316397.5	NM_007098		7	72	1	0	5.18039e-06	1	5.18039e-06	7	72				
TP53	7157	broad.mit.edu	37	17	7577094	7577094	+	Missense_Mutation	SNP	G	G	A	rs28934574		TCGA-DU-7011-01A-11D-2024-08	TCGA-DU-7011-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a998b8e9-3711-460c-8e4b-6597b6760a15	faf5593b-8173-4404-adef-379c03202b68	g.chr17:7577094G>A	ENST00000269305.4	-	8	1033	c.844C>T	c.(844-846)Cgg>Tgg	p.R282W	TP53_ENST00000413465.2_Intron|TP53_ENST00000359597.4_Missense_Mutation_p.R282W|TP53_ENST00000455263.2_Missense_Mutation_p.R282W|TP53_ENST00000445888.2_Missense_Mutation_p.R282W|TP53_ENST00000420246.2_Missense_Mutation_p.R282W|TP53_ENST00000574684.1_5'Flank	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	282	Interaction with AXIN1. {ECO:0000250}.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		DR -> EW (in sporadic cancers; somatic mutation).|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in a sporadic cancer; somatic mutation).|R -> L (in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|Ref.22}.|R -> W (in LFS; germline mutation and in sporadic cancers; somatic mutation; does not induce SNAI1 degradation; dbSNP:rs28934574). {ECO:0000269|PubMed:8829627}.		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|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)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R282W(401)|p.R282G(29)|p.0?(8)|p.R282fs*24(4)|p.R282R(3)|p.?(2)|p.D281fs*63(2)|p.D281_R282>EW(2)|p.A276_R283delACPGRDRR(1)|p.D281_R282insXX(1)|p.C275fs*20(1)|p.R282_E287delRRTEEE(1)|p.L265_K305del41(1)|p.D281_R282delDR(1)|p.G279fs*59(1)|p.R280fs*62(1)|p.S269fs*21(1)|p.R282fs*63(1)|p.V272_K292del21(1)|p.C275_R283delCACPGRDRR(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TCTGTGCGCCGGTCTCTCCCA	0.557		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	ENST00000420246.2		111	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	"""Mis, N, F"""	tumor protein p53			"""L, E, M, O"""		"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""	"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""		463	Substitution - Missense(430)|Whole gene deletion(8)|Deletion - In frame(6)|Deletion - Frameshift(5)|Insertion - Frameshift(4)|Substitution - coding silent(3)|Unknown(2)|Complex - frameshift(2)|Complex - compound substitution(2)|Insertion - In frame(1)	p.R282W(401)|p.R282G(29)|p.0?(8)|p.R282fs*24(4)|p.R282R(3)|p.?(2)|p.D281fs*63(2)|p.D281_R282>EW(2)|p.A276_R283delACPGRDRR(1)|p.D281_R282insXX(1)|p.C275fs*20(1)|p.R282_E287delRRTEEE(1)|p.L265_K305del41(1)|p.D281_R282delDR(1)|p.G279fs*59(1)|p.R280fs*62(1)|p.S269fs*21(1)|p.R282fs*63(1)|p.V272_K292del21(1)|p.C275_R283delCACPGRDRR(1)	large_intestine(136)|oesophagus(49)|upper_aerodigestive_tract(43)|stomach(33)|central_nervous_system(29)|breast(29)|lung(26)|ovary(21)|skin(20)|urinary_tract(16)|haematopoietic_and_lymphoid_tissue(16)|pancreas(10)|biliary_tract(5)|liver(5)|bone(5)|vulva(4)|prostate(4)|endometrium(3)|peritoneum(2)|thyroid(2)|NS(2)|autonomic_ganglia(1)|soft_tissue(1)|salivary_gland(1)	NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185	GRCh37	CM056413|CM920678	TP53	M	rs28934574	c.(844-846)Cgg>Tgg	Other conserved DNA damage response genes	tumor protein p53		G	TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG	0,4406		0,0,2203	83.0	71.0	75.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	844,844,844,844,448,448,448	1.5	0.3	17	dbSNP_125	75	2,8598	2.2+/-6.3	1,0,4299	no	missense,missense,missense,missense,missense,missense,missense	TP53	NM_000546.4,NM_001126112.1,NM_001126113.1,NM_001126114.1,NM_001126115.1,NM_001126116.1,NM_001126117.1	101,101,101,101,101,101,101	1,0,6502	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	282/394,282/394,282/347,282/342,150/262,150/210,150/215	7577094	2,13004	2203	4300	6503	SO:0001583	missense	7157	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	g.chr17:7577094G>A	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.844C>T	17.37:g.7577094G>A	ENSP00000269305:p.Arg282Trp	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)				TP53_ENST00000413465.2_Intron|TP53_ENST00000445888.2_Missense_Mutation_p.R282W|TP53_ENST00000455263.2_Missense_Mutation_p.R282W|TP53_ENST00000269305.4_Missense_Mutation_p.R282W|TP53_ENST00000359597.4_Missense_Mutation_p.R282W	p.R282W	NM_001126114.2|NM_001276696.1	NP_001119586.1|NP_001263625.1	P04637	P53_HUMAN		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	8	976	-		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)	282		DR -> EW (in sporadic cancers; somatic mutation).|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in a sporadic cancer; somatic mutation).|R -> L (in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> W (in LFS; germline mutation and in sporadic cancers; somatic mutation; dbSNP:rs28934574).	Interaction with AXIN1 (By similarity).|Interaction with E4F1.|Interaction with HIPK1 (By similarity).		Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	c.844C>T	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.057525	0.76074	0.0	2.33E-4	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99869	-7.34;-7.34;-7.34;-7.34;-7.34;-7.34	4.75	1.49	0.22878	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99825	0.9922	M	0.89968	3.075	0.58432	A	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;0.998;1.0;0.999	D	0.97713	1.0192	9	0.87932	D	0	-12.0909	8.7508	0.34613	0.0:0.1376:0.5833:0.2792	rs28934574	282;282;282;282	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	W	282;282;282;282;282;271;150	ENSP00000352610:R282W;ENSP00000269305:R282W;ENSP00000398846:R282W;ENSP00000391127:R282W;ENSP00000391478:R282W;ENSP00000425104:R150W	ENSP00000269305:R282W	R	-	1	2	TP53	7517819	1.000000	0.71417	0.327000	0.25402	0.901000	0.52897	4.477000	0.60223	0.174000	0.19809	0.462000	0.41574	CGG		0.557	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		34	19	0	0	0	1	0	34	19				
EMR1	2015	broad.mit.edu	37	19	6926465	6926465	+	Missense_Mutation	SNP	T	T	C			TCGA-DU-7011-01A-11D-2024-08	TCGA-DU-7011-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a998b8e9-3711-460c-8e4b-6597b6760a15	faf5593b-8173-4404-adef-379c03202b68	g.chr19:6926465T>C	ENST00000312053.4	+	16	2112	c.2075T>C	c.(2074-2076)tTg>tCg	p.L692S	EMR1_ENST00000250572.8_Missense_Mutation_p.L627S|EMR1_ENST00000381404.4_Missense_Mutation_p.L640S|EMR1_ENST00000381407.5_Missense_Mutation_p.L551S|EMR1_ENST00000450315.3_Missense_Mutation_p.L515S	NM_001974.4	NP_001965.3	Q14246	EMR1_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 1	692					cell adhesion (GO:0007155)|G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(31)|ovary(3)|prostate(1)|skin(8)	62	all_hematologic(4;0.166)					ATACTGTTCTTGATGGTCAGA	0.537																																						ENST00000312053.4																			0				NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(31)|ovary(3)|prostate(1)|skin(8)	62						c.(2074-2076)tTg>tCg		egf-like module containing, mucin-like, hormone receptor-like 1							202.0	178.0	186.0					19																	6926465		2203	4300	6503	SO:0001583	missense	2015				cell adhesion|neuropeptide signaling pathway	integral to plasma membrane	calcium ion binding|G-protein coupled receptor activity	g.chr19:6926465T>C	X81479	CCDS12175.1, CCDS58643.1, CCDS58644.1, CCDS58645.1, CCDS58646.1	19p13.3	2014-08-08	2003-11-26					"""-"", ""GPCR / Class B : Orphans"""	3336	protein-coding gene	gene with protein product		600493	"""egf-like module containing, mucin-like, hormone receptor-like sequence 1"""	TM7LN3		7601460, 9500513	Standard	NM_001974		Approved		uc002mfw.4	Q14246		ENST00000312053.4:c.2075T>C	19.37:g.6926465T>C	ENSP00000311545:p.Leu692Ser					EMR1_ENST00000250572.8_Missense_Mutation_p.L627S|EMR1_ENST00000381407.5_Missense_Mutation_p.L551S|EMR1_ENST00000450315.3_Missense_Mutation_p.L515S|EMR1_ENST00000381404.4_Missense_Mutation_p.L640S	p.L692S	NM_001974.4	NP_001965.3	Q14246	EMR1_HUMAN			16	2112	+	all_hematologic(4;0.166)		692					A6NHV2|B7Z486|B7Z489|E7EPX9|E9PD45|H9KV79|Q2I7G5|Q6ZMN0|Q8NGA7	Missense_Mutation	SNP	ENST00000312053.4	37	c.2075T>C	CCDS12175.1	.	.	.	.	.	.	.	.	.	.	t	16.32	3.089199	0.55968	.	.	ENSG00000174837	ENST00000543519;ENST00000312053;ENST00000381404;ENST00000250572;ENST00000381407;ENST00000450315	T;T;T;T;T	0.47528	0.84;0.84;0.84;0.84;0.84	4.18	4.18	0.49190	GPCR, family 2-like (1);	.	.	.	.	T	0.63200	0.2491	L	0.60012	1.86	0.32015	N	0.601604	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.998;1.0;0.999;1.0;0.999	T	0.69614	-0.5098	9	0.87932	D	0	.	11.1938	0.48700	0.0:0.0:0.0:1.0	.	515;551;627;640;692	E7EPX9;B7Z486;Q14246-2;E9PD45;Q14246	.;.;.;.;EMR1_HUMAN	S	627;692;640;627;551;515	ENSP00000311545:L692S;ENSP00000370811:L640S;ENSP00000250572:L627S;ENSP00000370814:L551S;ENSP00000405974:L515S	ENSP00000250572:L627S	L	+	2	0	EMR1	6877465	0.997000	0.39634	0.174000	0.22961	0.743000	0.42351	3.392000	0.52537	1.521000	0.48983	0.477000	0.44152	TTG		0.537	EMR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458485.1			10	80	0	0	0	1	0	10	80				
CLCN4	1183	broad.mit.edu	37	X	10180553	10180553	+	Missense_Mutation	SNP	C	C	T			TCGA-DU-7011-01A-11D-2024-08	TCGA-DU-7011-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a998b8e9-3711-460c-8e4b-6597b6760a15	faf5593b-8173-4404-adef-379c03202b68	g.chrX:10180553C>T	ENST00000380833.4	+	10	1827	c.1436C>T	c.(1435-1437)gCg>gTg	p.A479V	CLCN4_ENST00000380829.1_Missense_Mutation_p.A448V|CLCN4_ENST00000421085.2_Missense_Mutation_p.A385V	NM_001256944.1|NM_001830.3	NP_001243873.1|NP_001821.2	P51793	CLCN4_HUMAN	chloride channel, voltage-sensitive 4	479					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			breast(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(11)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						GGCGCGATAGCGGGCAGGATG	0.577																																					Melanoma(74;1050 1296 1576 30544 38374)	ENST00000380833.4																			0				breast(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(11)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						c.(1435-1437)gCg>gTg		chloride channel, voltage-sensitive 4							88.0	76.0	80.0					X																	10180553		2203	4300	6503	SO:0001583	missense	0					early endosome membrane|integral to membrane|late endosome membrane	antiporter activity|ATP binding|voltage-gated chloride channel activity	g.chrX:10180553C>T	X77197	CCDS14137.1, CCDS59159.1	Xp22.3	2012-09-26	2012-02-23		ENSG00000073464	ENSG00000073464		"""Ion channels / Chloride channels : Voltage-sensitive"""	2022	protein-coding gene	gene with protein product		302910	"""chloride channel 4"""			8069296	Standard	NM_001830		Approved	CLC4, ClC-4	uc004csy.4	P51793	OTTHUMG00000021125	ENST00000380833.4:c.1436C>T	X.37:g.10180553C>T	ENSP00000370213:p.Ala479Val					CLCN4_ENST00000380829.1_Missense_Mutation_p.A448V|CLCN4_ENST00000421085.2_Missense_Mutation_p.A385V	p.A479V	NM_001256944.1|NM_001830.3	NP_001243873.1|NP_001821.2	P51793	CLCN4_HUMAN			10	1827	+			479					A1L3U1|B7Z5Z4|Q9UBU1	Missense_Mutation	SNP	ENST00000380833.4	37	c.1436C>T	CCDS14137.1	.	.	.	.	.	.	.	.	.	.	C	15.95	2.983901	0.53827	.	.	ENSG00000073464	ENST00000380833;ENST00000380829;ENST00000421085	D;D;D	0.93712	-3.27;-3.27;-3.27	5.46	5.46	0.80206	Chloride channel, core (2);	0.046498	0.85682	D	0.000000	D	0.86723	0.6001	N	0.13371	0.34	0.80722	D	1	B	0.27316	0.175	B	0.18561	0.022	D	0.83359	0.0001	10	0.20519	T	0.43	-38.6726	18.4584	0.90729	0.0:1.0:0.0:0.0	.	479	P51793	CLCN4_HUMAN	V	479;448;385	ENSP00000370213:A479V;ENSP00000370209:A448V;ENSP00000405754:A385V	ENSP00000370209:A448V	A	+	2	0	CLCN4	10140553	1.000000	0.71417	0.920000	0.36463	0.944000	0.59088	7.663000	0.83820	2.301000	0.77427	0.513000	0.50165	GCG		0.577	CLCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055730.1			5	43	0	0	0	1	0	5	43				
ATRX	546	broad.mit.edu	37	X	76849194	76849194	+	Nonsense_Mutation	SNP	G	G	A			TCGA-DU-7011-01A-11D-2024-08	TCGA-DU-7011-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a998b8e9-3711-460c-8e4b-6597b6760a15	faf5593b-8173-4404-adef-379c03202b68	g.chrX:76849194G>A	ENST00000373344.5	-	26	6296	c.6082C>T	c.(6082-6084)Cga>Tga	p.R2028*	ATRX_ENST00000395603.3_Nonsense_Mutation_p.R1990*|ATRX_ENST00000480283.1_5'UTR	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	2028	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.|Interaction with MECP2.				ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						TCTGCCATTCGAAGAATTTCA	0.338			"""Mis, F, N"""		"""Pancreatic neuroendocrine tumors, paediatric GBM"""		ATR-X (alpha thalassemia/mental retardation) syndrome																															ENST00000373344.5				Rec	yes		X	Xq21.1	546	"""Mis, F, N"""	alpha thalassemia/mental retardation syndrome X-linked	yes	ATR-X (alpha thalassemia/mental retardation) syndrome	E			"""Pancreatic neuroendocrine tumors, paediatric GBM"""		1	Unknown(1)	p.?(1)	bone(1)	bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						c.(6082-6084)Cga>Tga		alpha thalassemia/mental retardation syndrome X-linked	Phosphatidylserine(DB00144)						71.0	68.0	69.0					X																	76849194		2203	4296	6499	SO:0001587	stop_gained	546				DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent	nuclear heterochromatin	ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding	g.chrX:76849194G>A	U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"""RAD54 homolog (S. cerevisiae)"""	300032	"""alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)"", ""Juberg-Marsidi syndrome"""	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.6082C>T	X.37:g.76849194G>A	ENSP00000362441:p.Arg2028*					ATRX_ENST00000395603.3_Nonsense_Mutation_p.R1990*|ATRX_ENST00000480283.1_5'UTR	p.R2028*	NM_000489.3	NP_000480.2	P46100	ATRX_HUMAN			26	6296	-			2028			Helicase C-terminal.		D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Nonsense_Mutation	SNP	ENST00000373344.5	37	c.6082C>T	CCDS14434.1	.	.	.	.	.	.	.	.	.	.	G	49	15.053386	0.99820	.	.	ENSG00000085224	ENST00000373344;ENST00000395603	.	.	.	5.45	5.45	0.79879	.	0.000000	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.4598	18.3664	0.90392	0.0:0.0:1.0:0.0	.	.	.	.	X	2028;1990	.	ENSP00000362441:R2028X	R	-	1	2	ATRX	76735850	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.457000	0.80775	2.278000	0.76064	0.529000	0.55759	CGA		0.338	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489		14	43	0	0	0	1	0	14	43				
OR5P2	120065	broad.mit.edu	37	11	7817817	7817817	+	Missense_Mutation	SNP	G	G	A	rs374622867		TCGA-DU-7011-01A-11D-2024-08	TCGA-DU-7011-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a998b8e9-3711-460c-8e4b-6597b6760a15	faf5593b-8173-4404-adef-379c03202b68	g.chr11:7817817G>A	ENST00000329434.2	-	1	703	c.673C>T	c.(673-675)Cgc>Tgc	p.R225C	RP11-35J10.5_ENST00000527565.1_lincRNA	NM_153444.1	NP_703145.1	Q8WZ92	OR5P2_HUMAN	olfactory receptor, family 5, subfamily P, member 2	225						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R225C(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)	22				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		TCAGTGGAGCGCATCTTCAGG	0.493																																						ENST00000329434.2																			1	Substitution - Missense(1)	p.R225C(1)	endometrium(1)	central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)	22						c.(673-675)Cgc>Tgc		olfactory receptor, family 5, subfamily P, member 2		G	CYS/ARG	0,4214		0,0,2107	108.0	111.0	110.0		673	-0.2	1.0	11		110	1,8583		0,1,4291	no	missense	OR5P2	NM_153444.1	180	0,1,6398	AA,AG,GG		0.0116,0.0,0.0078	benign	225/323	7817817	1,12797	2107	4292	6399	SO:0001583	missense	120065				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr11:7817817G>A	AF173006	CCDS7782.1	11p15.4	2012-08-09			ENSG00000183303	ENSG00000183303		"""GPCR / Class A : Olfactory receptors"""	14783	protein-coding gene	gene with protein product							Standard	NM_153444		Approved	JCG3	uc001mfp.1	Q8WZ92	OTTHUMG00000165668	ENST00000329434.2:c.673C>T	11.37:g.7817817G>A	ENSP00000331823:p.Arg225Cys					RP11-35J10.5_ENST00000527565.1_lincRNA	p.R225C	NM_153444.1	NP_703145.1	Q8WZ92	OR5P2_HUMAN		Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)	1	703	-			225					Q3MIS8	Missense_Mutation	SNP	ENST00000329434.2	37	c.673C>T	CCDS7782.1	.	.	.	.	.	.	.	.	.	.	G	12.71	2.019959	0.35606	0.0	1.16E-4	ENSG00000183303	ENST00000329434	T	0.40225	1.04	5.5	-0.15	0.13416	GPCR, rhodopsin-like superfamily (1);	1.249150	0.05210	N	0.506500	T	0.42200	0.1192	L	0.55990	1.75	0.31868	N	0.620146	B	0.24920	0.114	B	0.30572	0.117	T	0.51371	-0.8714	10	0.66056	D	0.02	3.4885	8.7296	0.34491	0.0744:0.0:0.4262:0.4993	.	225	Q8WZ92	OR5P2_HUMAN	C	225	ENSP00000331823:R225C	ENSP00000331823:R225C	R	-	1	0	OR5P2	7774393	0.000000	0.05858	0.994000	0.49952	0.888000	0.51559	-0.444000	0.06854	0.120000	0.18254	0.555000	0.69702	CGC		0.493	OR5P2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385696.1	NM_153444		17	57	0	0	0	1	0	17	57				
LAMP1	3916	broad.mit.edu	37	13	113960856	113960856	+	Missense_Mutation	SNP	G	G	A			TCGA-DU-7011-01A-11D-2024-08	TCGA-DU-7011-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a998b8e9-3711-460c-8e4b-6597b6760a15	faf5593b-8173-4404-adef-379c03202b68	g.chr13:113960856G>A	ENST00000332556.4	+	2	312	c.118G>A	c.(118-120)Gcg>Acg	p.A40T	LAMP1_ENST00000397181.3_Missense_Mutation_p.A40T	NM_005561.3	NP_005552.3	P11279	LAMP1_HUMAN	lysosomal-associated membrane protein 1	40	First lumenal domain.			VKNGNGTA -> MARGGRVR (in Ref. 7; AAA59524). {ECO:0000305}.	autophagic cell death (GO:0048102)|autophagy (GO:0006914)|establishment of protein localization to organelle (GO:0072594)|Golgi to lysosome transport (GO:0090160)|granzyme-mediated apoptotic signaling pathway (GO:0008626)|positive regulation of natural killer cell degranulation (GO:0043323)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|protein stabilization (GO:0050821)|regulation of organelle transport along microtubule (GO:1902513)	alveolar lamellar body (GO:0097208)|cytolytic granule (GO:0044194)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|melanosome (GO:0042470)|membrane (GO:0016020)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|phagolysosome membrane (GO:0061474)|sarcolemma (GO:0042383)	enzyme binding (GO:0019899)			NS(1)|central_nervous_system(2)|endometrium(3)|large_intestine(4)|lung(2)|prostate(1)|skin(1)|stomach(2)	16	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0482)|all_epithelial(44;0.0148)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.025)|GBM - Glioblastoma multiforme(44;0.206)|Epithelial(84;0.246)			CAACGGGACCGCGTGCATAAT	0.507																																						ENST00000332556.4																			0				NS(1)|central_nervous_system(2)|endometrium(3)|large_intestine(4)|lung(2)|prostate(1)|skin(1)|stomach(2)	16						c.(118-120)Gcg>Acg		lysosomal-associated membrane protein 1							157.0	153.0	155.0					13																	113960856		2046	4205	6251	SO:0001583	missense	3916					endosome membrane|integral to plasma membrane|lysosomal membrane|membrane fraction		g.chr13:113960856G>A	J03263	CCDS41909.1	13q34	2011-11-24			ENSG00000185896	ENSG00000185896		"""CD molecules"""	6499	protein-coding gene	gene with protein product		153330					Standard	NM_005561		Approved	CD107a	uc001vtm.1	P11279	OTTHUMG00000017380	ENST00000332556.4:c.118G>A	13.37:g.113960856G>A	ENSP00000333298:p.Ala40Thr					LAMP1_ENST00000397181.3_Missense_Mutation_p.A40T	p.A40T	NM_005561.3	NP_005552.3	P11279	LAMP1_HUMAN	all cancers(43;0.025)|GBM - Glioblastoma multiforme(44;0.206)|Epithelial(84;0.246)		2	312	+	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0482)|all_epithelial(44;0.0148)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	40	VKNGNGTA -> MARGGRVR (in Ref. 6; AAA59524).		First lumenal domain.		B4DWL3|Q8WU33|Q96I40|Q9BRD2|Q9NP13	Missense_Mutation	SNP	ENST00000332556.4	37	c.118G>A	CCDS41909.1	.	.	.	.	.	.	.	.	.	.	G	1.992	-0.431466	0.04669	.	.	ENSG00000185896	ENST00000332556;ENST00000397181	T;T	0.26957	1.7;1.88	5.17	2.41	0.29592	Lysosome-associated membrane glycoprotein, conserved site (1);	0.263285	0.38492	N	0.001667	T	0.09730	0.0239	N	0.16016	0.355	0.09310	N	1	B;B	0.30361	0.214;0.277	B;B	0.22601	0.04;0.016	T	0.33752	-0.9856	10	0.05436	T	0.98	-8.2894	7.2397	0.26090	0.2728:0.0:0.7272:0.0	.	40;40	B4DWL3;P11279	.;LAMP1_HUMAN	T	40	ENSP00000333298:A40T;ENSP00000415354:A40T	ENSP00000333298:A40T	A	+	1	0	LAMP1	113008857	0.001000	0.12720	0.156000	0.22583	0.018000	0.09664	-0.176000	0.09811	0.657000	0.30906	0.609000	0.83330	GCG		0.507	LAMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045876.2			38	81	0	0	0	1	0	38	81				
MLLT3	4300	broad.mit.edu	37	9	20414340	20414340	+	Silent	SNP	G	G	A			TCGA-DU-7011-01A-11D-2024-08	TCGA-DU-7011-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a998b8e9-3711-460c-8e4b-6597b6760a15	faf5593b-8173-4404-adef-379c03202b68	g.chr9:20414340G>A	ENST00000380338.4	-	5	790	c.504C>T	c.(502-504)agC>agT	p.S168S	MLLT3_ENST00000355930.6_5'UTR|MLLT3_ENST00000429426.2_Silent_p.S165S|MLLT3_ENST00000475957.1_5'UTR	NM_004529.2	NP_004520.2	P42568	AF9_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3	168	Poly-Ser.				anterior/posterior pattern specification (GO:0009952)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|regulation of transcription, DNA-templated (GO:0006355)|segment specification (GO:0007379)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)		p.S168S(5)		central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(6)|lung(24)|ovary(1)|prostate(4)|skin(1)|urinary_tract(7)	66				GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)		tgctgctgctgctactgctgc	0.537			T	MLL	ALL																																	ENST00000380338.4				Dom	yes		9	9p22	4300	T	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3 (AF9)"""			L	MLL		ALL		5	Substitution - coding silent(5)	p.S168S(5)	lung(2)|urinary_tract(1)|endometrium(1)|kidney(1)	central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(6)|lung(24)|ovary(1)|prostate(4)|skin(1)|urinary_tract(7)	66						c.(502-504)agC>agT		myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3							9.0	16.0	13.0					9																	20414340		1646	3412	5058	SO:0001819	synonymous_variant	4300				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding	g.chr9:20414340G>A	L13744	CCDS6494.1	9p22	2008-02-05	2001-11-28		ENSG00000171843	ENSG00000171843			7136	protein-coding gene	gene with protein product		159558	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 3"""			8506309, 8414510	Standard	NM_001286691		Approved	AF-9, AF9, YEATS3	uc003zoe.2	P42568	OTTHUMG00000019650	ENST00000380338.4:c.504C>T	9.37:g.20414340G>A						MLLT3_ENST00000429426.2_Silent_p.S165S|MLLT3_ENST00000355930.6_5'UTR|MLLT3_ENST00000475957.1_5'UTR	p.S168S	NM_004529.2	NP_004520.2	P42568	AF9_HUMAN		GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)	5	790	-			168			Poly-Ser.		B1AMQ2|B2R7B3|B7Z755|D3DRJ8|Q8IVB0	Silent	SNP	ENST00000380338.4	37	c.504C>T	CCDS6494.1																																																																																				0.537	MLLT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051872.1	NM_004529		6	53	0	0	0	1	0	6	53				
PCSK9	255738	broad.mit.edu	37	1	55505552	55505553	+	In_Frame_Ins	INS	-	-	CTG	rs35574083|rs371488778|rs113330492|rs45454392|rs67610340	byFrequency	TCGA-DU-7011-01A-11D-2024-08	TCGA-DU-7011-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a998b8e9-3711-460c-8e4b-6597b6760a15	faf5593b-8173-4404-adef-379c03202b68	g.chr1:55505552_55505553insCTG	ENST00000302118.5	+	1	332_333	c.42_43insCTG	c.(43-45)ctg>CTGctg	p.15_15L>LL	PCSK9_ENST00000543384.1_5'Flank|PCSK9_ENST00000452118.2_In_Frame_Ins_p.15_15L>LL	NM_174936.3	NP_777596.2	Q8NBP7	PCSK9_HUMAN	proprotein convertase subtilisin/kexin type 9	15					apoptotic process (GO:0006915)|cellular response to insulin stimulus (GO:0032869)|cellular response to starvation (GO:0009267)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|kidney development (GO:0001822)|lipoprotein metabolic process (GO:0042157)|liver development (GO:0001889)|low-density lipoprotein particle receptor catabolic process (GO:0032802)|lysosomal transport (GO:0007041)|negative regulation of low-density lipoprotein particle clearance (GO:0010989)|negative regulation of receptor recycling (GO:0001920)|neurogenesis (GO:0022008)|neuron differentiation (GO:0030182)|phospholipid metabolic process (GO:0006644)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of receptor internalization (GO:0002092)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)|regulation of low-density lipoprotein particle receptor catabolic process (GO:0032803)|regulation of neuron apoptotic process (GO:0043523)|regulation of receptor activity (GO:0010469)|triglyceride metabolic process (GO:0006641)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|extracellular space (GO:0005615)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|lysosome (GO:0005764)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	apolipoprotein binding (GO:0034185)|apolipoprotein receptor binding (GO:0034190)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein particle receptor binding (GO:0050750)|poly(A) RNA binding (GO:0044822)|protein self-association (GO:0043621)|serine-type endopeptidase activity (GO:0004252)|sodium channel inhibitor activity (GO:0019871)|very-low-density lipoprotein particle binding (GO:0034189)|very-low-density lipoprotein particle receptor binding (GO:0070326)	p.P14_L15insL(2)		NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(1)|liver(2)|lung(4)|ovary(3)|prostate(3)|skin(1)|urinary_tract(1)	32						Ggccgctgccactgctgctgct	0.703																																					Pancreas(137;1454 1827 5886 22361 42375)	ENST00000302118.5																			2	Insertion - In frame(2)	p.P14_L15insL(2)	breast(1)|central_nervous_system(1)	NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(1)|liver(2)|lung(4)|ovary(3)|prostate(3)|skin(1)|urinary_tract(1)	32						c.(40-45)cctgct>ccCTGtgct		proprotein convertase subtilisin/kexin type 9																																				SO:0001652	inframe_insertion	255738				cellular response to insulin stimulus|cellular response to starvation|cholesterol homeostasis|cholesterol metabolic process|kidney development|liver development|low-density lipoprotein particle receptor catabolic process|lysosomal transport|negative regulation of catalytic activity|negative regulation of low-density lipoprotein particle clearance|negative regulation of receptor recycling|neuron differentiation|positive regulation of neuron apoptosis|positive regulation of receptor internalization|protein autoprocessing|regulation of receptor activity	extracellular space|late endosome|lysosome|perinuclear region of cytoplasm	apolipoprotein receptor binding|identical protein binding|low-density lipoprotein particle receptor binding|serine-type endopeptidase activity|very-low-density lipoprotein particle receptor binding	g.chr1:55505552_55505553insCTG	AX207686	CCDS603.1	1p34.1-p32	2014-09-17	2003-05-13		ENSG00000169174	ENSG00000169174			20001	protein-coding gene	gene with protein product		607786	"""hypercholesterolemia, autosomal dominant 3"""	HCHOLA3		12552133, 12730697	Standard	NM_174936		Approved	NARC-1, FH3	uc001cyf.2	Q8NBP7	OTTHUMG00000008136	ENST00000302118.5:c.61_63dupCTG	1.37:g.55505559_55505561dupCTG	ENSP00000303208:p.Leu23dup					PCSK9_ENST00000452118.2_In_Frame_Ins_p.14_15PA>PCA	p.14_15PA>PCA	NM_174936.3	NP_777596.2	Q8NBP7	PCSK9_HUMAN			1	332_333	+			14					A8T640|C0JYY9|Q5PSM5|Q5SZQ2	In_Frame_Ins	INS	ENST00000302118.5	37	c.42_43insCTG	CCDS603.1																																																																																				0.703	PCSK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022280.1	NM_174936		3	4						3	4	---	---	---	---
OR2T35	403244	broad.mit.edu	37	1	248801602	248801603	+	Frame_Shift_Ins	INS	-	-	CA	rs370874670|rs375058001		TCGA-DU-7011-01A-11D-2024-08	TCGA-DU-7011-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a998b8e9-3711-460c-8e4b-6597b6760a15	faf5593b-8173-4404-adef-379c03202b68	g.chr1:248801602_248801603insCA	ENST00000317450.3	-	1	956_957	c.957_958insTG	c.(955-960)gtgatcfs	p.I320fs		NM_001001827.1	NP_001001827.1	Q8NGX2	O2T35_HUMAN	olfactory receptor, family 2, subfamily T, member 35	320						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I320fs*1(1)		endometrium(1)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)|skin(1)	6	all_cancers(71;2.04e-05)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.237)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CCCTTCCTGATCACAGTCGCCA	0.545																																						ENST00000317450.3																			1	Insertion - Frameshift(1)	p.I320fs*1(1)	prostate(1)	endometrium(1)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)|skin(1)	6						c.(955-960)gttcagfs		olfactory receptor, family 2, subfamily T, member 35																																				SO:0001589	frameshift_variant	403244				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr1:248801602_248801603insCA	BK004475	CCDS31123.1	1q44	2012-08-09			ENSG00000177151	ENSG00000177151		"""GPCR / Class A : Olfactory receptors"""	31257	protein-coding gene	gene with protein product							Standard	NM_001001827		Approved		uc001ies.1	Q8NGX2	OTTHUMG00000040380	ENST00000317450.3:c.956_957dupTG	1.37:g.248801605_248801606dupCA	ENSP00000324369:p.Ile320fs						p.Q320fs	NM_001001827.1	NP_001001827.1	Q8NGX2	O2T35_HUMAN	OV - Ovarian serous cystadenocarcinoma(106;0.0265)		1	956_957	-	all_cancers(71;2.04e-05)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.237)	320					Q6IEY7	Frame_Shift_Ins	INS	ENST00000317450.3	37	c.957_958insTG	CCDS31123.1																																																																																				0.545	OR2T35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097130.1	NM_001001827		2	4						2	4	---	---	---	---
AC016995.3	0	broad.mit.edu	37	2	38710017	38710019	+	lincRNA	DEL	AAT	AAT	-	rs2005502|rs57303101|rs538061888|rs200292719	byFrequency	TCGA-DU-7011-01A-11D-2024-08	TCGA-DU-7011-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a998b8e9-3711-460c-8e4b-6597b6760a15	faf5593b-8173-4404-adef-379c03202b68	g.chr2:38710017_38710019delAAT	ENST00000417039.1	-	0	696																											TTCTTtaaaaaataaataaataa	0.246																																						ENST00000417039.1																			0																																																			0							g.chr2:38710017_38710019delAAT																													2.37:g.38710017_38710019delAAT														0	696	-									RNA	DEL	ENST00000417039.1	37																																																																																						0.246	AC016995.3-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000331173.1			3	6						3	6	---	---	---	---
PRSS3P2	154754	broad.mit.edu	37	7	142481743	142481745	+	RNA	DEL	CTA	CTA	-	rs587750077|rs376315825	byFrequency	TCGA-DU-7011-01A-11D-2024-08	TCGA-DU-7011-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a998b8e9-3711-460c-8e4b-6597b6760a15	faf5593b-8173-4404-adef-379c03202b68	g.chr7:142481743_142481745delCTA	ENST00000603901.1	+	0	454					NR_001296.3		Q8NHM4	TRY6_HUMAN	protease, serine, 3 pseudogene 2						endothelial cell migration (GO:0043542)	extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)										ACCCACATTTCTACTTTCTTTAT	0.517																																						ENST00000603901.1																			0																																																			0							g.chr7:142481743_142481745delCTA			7q34	2012-03-06			ENSG00000250606	ENSG00000275896			43788	pseudogene	pseudogene	"""trypsinogen C"""						Standard	NR_001296		Approved	TRY6	uc011ksq.2	Q8NHM4	OTTHUMG00000158904		7.37:g.142481743_142481745delCTA								NR_001296.3						0	454	+									RNA	DEL	ENST00000603901.1	37																																																																																						0.517	PRSS3P2-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000470000.1	NR_001296		8	165						8	165	---	---	---	---
PRSS3P2	154754	broad.mit.edu	37	7	142482280	142482280	+	RNA	DEL	T	T	-	rs554627905		TCGA-DU-7011-01A-11D-2024-08	TCGA-DU-7011-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a998b8e9-3711-460c-8e4b-6597b6760a15	faf5593b-8173-4404-adef-379c03202b68	g.chr7:142482280delT	ENST00000603901.1	+	0	660					NR_001296.3		Q8NHM4	TRY6_HUMAN	protease, serine, 3 pseudogene 2						endothelial cell migration (GO:0043542)	extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)										GCTATGGCTGTGCCCAGAAGA	0.517																																						ENST00000603901.1																			0																																																			0							g.chr7:142482280delT			7q34	2012-03-06			ENSG00000250606	ENSG00000275896			43788	pseudogene	pseudogene	"""trypsinogen C"""						Standard	NR_001296		Approved	TRY6	uc011ksq.2	Q8NHM4	OTTHUMG00000158904		7.37:g.142482280delT								NR_001296.3						0	660	+									RNA	DEL	ENST00000603901.1	37																																																																																						0.517	PRSS3P2-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000470000.1	NR_001296		8	82						8	82	---	---	---	---
AL132989.1	0	broad.mit.edu	37	14	58752042	58752053	+	5'Flank	DEL	GAAGAGGATGAG	GAAGAGGATGAG	-	rs112158888		TCGA-DU-7011-01A-11D-2024-08	TCGA-DU-7011-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a998b8e9-3711-460c-8e4b-6597b6760a15	faf5593b-8173-4404-adef-379c03202b68	g.chr14:58752042_58752053delGAAGAGGATGAG	ENST00000598233.1	+	0	0				RP11-349A22.5_ENST00000555707.1_RNA|RP11-349A22.5_ENST00000554378.1_RNA|RP11-349A22.5_ENST00000556400.1_RNA|RP11-349A22.5_ENST00000554360.1_RNA|RP11-349A22.5_ENST00000553657.1_RNA|RP11-349A22.5_ENST00000556002.1_RNA|RP11-349A22.5_ENST00000551597.2_RNA|RP11-349A22.5_ENST00000557412.1_RNA|RP11-349A22.5_ENST00000555275.1_RNA|RP11-349A22.5_ENST00000557660.1_RNA|RP11-349A22.5_ENST00000555037.1_RNA																							Tgagaaagatgaagaggatgaggaagaggatg	0.392																																						ENST00000554360.1																			0																																																	SO:0001631	upstream_gene_variant	0							g.chr14:58752042_58752053delGAAGAGGATGAG																													14.37:g.58752042_58752053delGAAGAGGATGAG	Exception_encountered					RP11-349A22.5_ENST00000556002.1_RNA|RP11-349A22.5_ENST00000555707.1_RNA|RP11-349A22.5_ENST00000553657.1_RNA|RP11-349A22.5_ENST00000557660.1_RNA|RP11-349A22.5_ENST00000556400.1_RNA|RP11-349A22.5_ENST00000555275.1_RNA|RP11-349A22.5_ENST00000554378.1_RNA		NR_029434.1						0	414	-									RNA	DEL	ENST00000598233.1	37																																																																																						0.392	AL132989.1-201	NOVEL	basic|appris_principal	protein_coding	protein_coding				7	5						7	5	---	---	---	---
TPTE	7179	broad.mit.edu	37	21	10944697	10944697	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DU-7011-01A-11D-2024-08	TCGA-DU-7011-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a998b8e9-3711-460c-8e4b-6597b6760a15	faf5593b-8173-4404-adef-379c03202b68	g.chr21:10944697delA	ENST00000361285.4	-	11	866	c.537delT	c.(535-537)tttfs	p.F179fs	TPTE_ENST00000415664.2_5'UTR|TPTE_ENST00000298232.7_Frame_Shift_Del_p.F161fs|TPTE_ENST00000342420.5_Frame_Shift_Del_p.F141fs	NM_199261.2	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	179					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		ACTTAATGTCAAAAAAAATGT	0.299																																						ENST00000298232.7																			0				NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130						c.(481-483)ttfs		transmembrane phosphatase with tensin homology							157.0	168.0	164.0					21																	10944697		2203	4300	6503	SO:0001589	frameshift_variant	7179				signal transduction	integral to membrane	ion channel activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	g.chr21:10944697delA	AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	12023	protein-coding gene	gene with protein product	"""PTEN-related tyrosine phosphatase"", ""cancer/testis antigen 44"""	604336				10830953, 14659893	Standard	NM_001290224		Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000361285.4:c.537delT	21.37:g.10944697delA	ENSP00000355208:p.Phe179fs					TPTE_ENST00000415664.2_5'UTR|TPTE_ENST00000361285.4_Frame_Shift_Del_p.F179fs|TPTE_ENST00000342420.5_Frame_Shift_Del_p.F141fs	p.F161fs	NM_199259.2	NP_954868.1	P56180	TPTE_HUMAN	Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)	10	850	-			179					B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	Frame_Shift_Del	DEL	ENST00000361285.4	37	c.483delT	CCDS13560.2																																																																																				0.299	TPTE-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000157413.1			7	229						7	229	---	---	---	---
CRYBB2P1	1416	broad.mit.edu	37	22	25855682	25855683	+	RNA	INS	-	-	GT	rs61433517|rs71322752		TCGA-DU-7011-01A-11D-2024-08	TCGA-DU-7011-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a998b8e9-3711-460c-8e4b-6597b6760a15	faf5593b-8173-4404-adef-379c03202b68	g.chr22:25855682_25855683insGT	ENST00000609084.1	+	0	0									crystallin, beta B2 pseudogene 1																		CCTGGCAGCTGgtgtgtgtgtg	0.53																																						ENST00000354451.2																			0																																																			0							g.chr22:25855682_25855683insGT	M18441		22q11.2-q12.1	2012-02-29			ENSG00000100058	ENSG00000100058			2399	pseudogene	pseudogene				CRYB2B			Standard	NR_033733		Approved		uc003abu.4		OTTHUMG00000150874		22.37:g.25855691_25855692dupGT														0	366	+									RNA	INS	ENST00000609084.1	37																																																																																						0.530	CRYBB2P1-006	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000472347.1			2	4						2	4	---	---	---	---
TRIOBP	11078	broad.mit.edu	37	22	38119882	38119884	+	In_Frame_Del	DEL	CCT	CCT	-			TCGA-DU-7011-01A-11D-2024-08	TCGA-DU-7011-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a998b8e9-3711-460c-8e4b-6597b6760a15	faf5593b-8173-4404-adef-379c03202b68	g.chr22:38119882_38119884delCCT	ENST00000406386.3	+	7	1574_1576	c.1319_1321delCCT	c.(1318-1323)gcctcc>gcc	p.S442del		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	442					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					AATCCCAGAGCCTCCTCTCCCAG	0.601																																						ENST00000406386.3																			0				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12						c.(1318-1323)gcc>g		TRIO and F-actin binding protein				8,3622		3,2,1810						-5.6	0.0			78	10,7846		3,4,3921	no	coding	TRIOBP	NM_001039141.2		6,6,5731	A1A1,A1R,RR		0.1273,0.2204,0.1567				18,11468				SO:0001651	inframe_deletion	11078				actin modification|barbed-end actin filament capping	actin cytoskeleton|cytoplasm|nucleus	actin binding|GTP-Rho binding|myosin II binding|protein binding|ubiquitin protein ligase binding	g.chr22:38119882_38119884delCCT	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"""Pleckstrin homology (PH) domain containing"""	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.1319_1321delCCT	22.37:g.38119885_38119887delCCT	ENSP00000384312:p.Ser442del					RP1-37E16.12_ENST00000455236.1_RNA	p.AS440del	NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN			7	1574_1576	+	Melanoma(58;0.0574)		440					B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	In_Frame_Del	DEL	ENST00000406386.3	37	c.1319_1321delCCT	CCDS43015.1																																																																																				0.601	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2			7	126						7	126	---	---	---	---
ATRX	546	broad.mit.edu	37	X	76855019	76855019	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DU-7011-01A-11D-2024-08	TCGA-DU-7011-10A-01D-2024-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a998b8e9-3711-460c-8e4b-6597b6760a15	faf5593b-8173-4404-adef-379c03202b68	g.chrX:76855019delT	ENST00000373344.5	-	25	6031	c.5817delA	c.(5815-5817)aaafs	p.K1939fs	ATRX_ENST00000395603.3_Frame_Shift_Del_p.K1901fs|ATRX_ENST00000480283.1_5'UTR	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	1939	Poly-Lys.				ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						AGCTACTATCTTTTTTCCCCT	0.353			"""Mis, F, N"""		"""Pancreatic neuroendocrine tumors, paediatric GBM"""		ATR-X (alpha thalassemia/mental retardation) syndrome																															ENST00000373344.5				Rec	yes		X	Xq21.1	546	"""Mis, F, N"""	alpha thalassemia/mental retardation syndrome X-linked	yes	ATR-X (alpha thalassemia/mental retardation) syndrome	E			"""Pancreatic neuroendocrine tumors, paediatric GBM"""		1	Unknown(1)	p.?(1)	bone(1)	bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						c.(5815-5817)aafs		alpha thalassemia/mental retardation syndrome X-linked	Phosphatidylserine(DB00144)						380.0	352.0	362.0					X																	76855019		2203	4295	6498	SO:0001589	frameshift_variant	546				DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent	nuclear heterochromatin	ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding	g.chrX:76855019delT	U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"""RAD54 homolog (S. cerevisiae)"""	300032	"""alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)"", ""Juberg-Marsidi syndrome"""	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.5817delA	X.37:g.76855019delT	ENSP00000362441:p.Lys1939fs					ATRX_ENST00000395603.3_Frame_Shift_Del_p.K1901fs|ATRX_ENST00000480283.1_5'UTR	p.K1939fs	NM_000489.3	NP_000480.2	P46100	ATRX_HUMAN			25	6031	-			1939			Poly-Lys.		D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Frame_Shift_Del	DEL	ENST00000373344.5	37	c.5817delA	CCDS14434.1																																																																																				0.353	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489		61	242						61	242	---	---	---	---
