tx annotations missing for mt variants #534
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bug
Something isn't working
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Multiple reasons for that: since cdot 0.2.26, it contains fake-rna-* transcripts for MT transcripts that refseq does not have. However, not all of the refseq cdot data release files actually contain that information. |
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@tedil this should not be forgotten |
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Should be fixed with varfish-org/mehari-data-tx#50 |
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@tedil what's the status? |
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Should now really be fixed with varfish-org/mehari-data-tx#54 and the upcoming 0.7.6 txdb release |
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Describe the bug
Currently, mehari does not annotate tx on the MT chromosome.
{ "version": { "tx_db": "0.26.1", "mehari": "0.28.1" }, "query": { "genome_release": "grch37", "chromosome": "MT", "position": 73, "reference": "A", "alternative": "G", "hgnc_id": "HGNC:7481" }, "result": [] }Interestingly the information for the gene is available via annonars:
{ "genes": { "HGNC:7481": { "dbnsfp": { "geneName": "MT-TF", "ensemblGene": "ENSG00000210049", "chr": "M", "geneOldNames": [ "MTTF" ], "geneOtherNames": [ "trnF" ], "uniprotAcc": ".", "uniprotId": ".", "entrezGeneId": "4558", "ucscId": "uc064xos.1", "mimId": [ "590070" ], "omimId": [ "590070" ], "geneFullName": "mitochondrially encoded tRNA phenylalanine", "pathwayUniprot": ".", "pathwayConsensusPathDb": [ "Aminoacyl-tRNA biosynthesis - Homo sapiens (human)" ], "orphanetDisorderId": [ "550", "551" ], "orphanetDisorder": [ "MELAS", "MERRF" ], "orphanetAssociationType": [ "Disease-causing germline mutation(s) in", "Disease-causing germline mutation(s) in" ], "hipred": ".", "knownRecInfo": ".", "exacCnvFlag": ".", "gdpAllDiseaseCausing": ".", "gdpAllMendelian": ".", "gdpAllMendelianAd": ".", "gdpMendelianAr": ".", "gdpPid": ".", "gdpPidAd": ".", "gdpPidAr": ".", "gdpCancer": ".", "gdbCancerRec": ".", "gdpCancerDom": ".", "sorvaLofMaf5HetOrHom": 0, "sorvaLofMaf5HomOrComphet": 0, "sorvaLofMaf1HetOrHom": 0, "sorvaLofMaf1HomOrComphet": 0, "sorvaLofOrMisMaf5HetOrHom": 0, "sorvaLofOrMisMaf5HomOrComphet": 0, "sorvaLofOrMisMaf1HetOrHom": 0, "sorvaLofOrMisMaf1HomOrComphet": 0, "essentialGene": ".", "essentialGeneCrispr": ".", "essentialGeneCrispr2": ".", "essentialGeneGeneTrap": ".", "geneIndispensabilityPred": ".", "mgiMouseGene": "mt-Tf", "mgiMousePhenotype": ".", "zfinZebrafishGene": ".", "zfinZebrafishStructure": ".", "zfinZebrafishPhenotypeQuality": ".", "zfinZebrafishPhenotypeTag": "." }, "hgnc": { "hgncId": "HGNC:7481", "symbol": "MT-TF", "name": "mitochondrially encoded tRNA-Phe (UUU/C)", "locusGroup": "non-coding RNA", "locusType": "RNA, transfer", "status": "HGNC_STATUS_APPROVED", "location": "mitochondria", "locationSortable": "mitochondria", "aliasSymbol": [ "trnF" ], "prevSymbol": [ "MTTF" ], "prevName": [ "tRNA phenylalanine", "mitochondrially encoded tRNA phenylalanine" ], "geneGroup": [ "Mitochondrially encoded transfer RNAs" ], "geneGroupId": [843], "dateApprovedReserved": "1989-10-11", "dateSymbolChanged": "2005-02-16", "dateNameChanged": "2018-11-16", "dateModified": "2021-12-02", "entrezId": "4558", "ensemblGeneId": "ENSG00000210049", "ucscId": "uc064xos.1", "pubmedId": [7219534], "mgdId": [ "MGI:102487" ], "omimId": [ "590070" ], "orphanet": 167909, "mamitTrnadb": 20, "agr": "HGNC:7481" }, "ncbi": { "geneId": "4558", "summary": "", "rifEntries": [ { "text": "This is the 18th MT-TF point mutation associated with a mitochondrial disorder. The onset and the severity of the disease, however, is unique in this case and broadens the clinical picture related to mutations of mitochondrial tRNA-Phe.", "pmids": [31009750] }, { "text": "Optic neuropathy, cardiomyopathy, and cognitive disability was found in patients with a homozygous mutation in the nuclear MTO1 and a mitochondrial MT-TF variant.", "pmids": [26061759] }, { "text": "role of the point mutation at position 616 in the MT-TF gene (T\u003EC or T\u003EG)in severe epilepsy", "pmids": [20142618] }, { "text": "Observational study of gene-disease association. (HuGE Navigator)", "pmids": [19758471] }, { "text": "We report a novel heteroplasmic T--\u003EC mutation at nt position 582 within the mitochondrial tRNA(Phe) gene of a 70-year-old woman with mitochondrial myopathy; This adds to the previously described four pathogenic mutations in the tRNA(Phe) gene", "pmids": [14659412] } ] }, "omim": { "hgncId": "HGNC:7481", "omimDiseases": [ { "omimId": "OMIM:540000", "label": "Mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes" }, { "omimId": "OMIM:545000", "label": "Myoclonic epilepsy associated with ragged-red fibers" } ] }, "gtex": { "hgncId": "HGNC:7481", "ensemblGeneId": "ENSG00000210049", "ensemblGeneVersion": "1", "records": [ { "tissue": "GTEX_TISSUE_ADIPOSE_TISSUE", "tissueDetailed": "GTEX_TISSUE_DETAILED_ADIPOSE_SUBCUTANEOUS", "tpms": [0, 0, 0.7093, 1.421, 68.42] }, { "tissue": "GTEX_TISSUE_ADIPOSE_TISSUE", "tissueDetailed": "GTEX_TISSUE_DETAILED_ADIPOSE_VISCERAL_OMENTUM", "tpms": [0, 0, 0.6078, 1.295, 88.18] }, { "tissue": "GTEX_TISSUE_ADRENAL_GLAND", "tissueDetailed": "GTEX_TISSUE_DETAILED_ADRENAL_GLAND", "tpms": [0, 0.436525, 0.9288, 1.94025, 71.6] }, { "tissue": "GTEX_TISSUE_BLADDER", "tissueDetailed": "GTEX_TISSUE_DETAILED_BLADDER", "tpms": [0, 0, 0, 0.5159, 1.601] }, { "tissue": "GTEX_TISSUE_BLOOD", "tissueDetailed": "GTEX_TISSUE_DETAILED_CELLS_EBV_TRANSFORMED_LYMPHOCYTES", "tpms": [0, 0.58265, 1.3655, 2.3605, 13.01] }, { "tissue": "GTEX_TISSUE_BLOOD", "tissueDetailed": "GTEX_TISSUE_DETAILED_WHOLE_BLOOD", "tpms": [0, 0, 0.3929, 0.8903, 11.17] }, { "tissue": "GTEX_TISSUE_BLOOD_VESSEL", "tissueDetailed": "GTEX_TISSUE_DETAILED_ARTERY_AORTA", "tpms": [0, 0, 0, 0.8349, 23.69] }, { "tissue": "GTEX_TISSUE_BLOOD_VESSEL", "tissueDetailed": "GTEX_TISSUE_DETAILED_ARTERY_CORONARY", "tpms": [0, 0, 0.50785, 1.11, 50.93] }, { "tissue": "GTEX_TISSUE_BLOOD_VESSEL", "tissueDetailed": "GTEX_TISSUE_DETAILED_ARTERY_TIBIAL", "tpms": [0, 0, 0.675, 1.528, 47.23] }, { "tissue": "GTEX_TISSUE_BRAIN", "tissueDetailed": "GTEX_TISSUE_DETAILED_BRAIN_AMYGDALA", "tpms": [3.942, 11.3675, 16.275, 22.27, 141.9] }, { "tissue": "GTEX_TISSUE_BRAIN", "tissueDetailed": "GTEX_TISSUE_DETAILED_BRAIN_ANTERIOR_CINGULATE_CORTEX", "tpms": [2.637, 9.812, 14.355, 19.6475, 202.5] }, { "tissue": "GTEX_TISSUE_BRAIN", "tissueDetailed": "GTEX_TISSUE_DETAILED_BRAIN_CAUDATE_BASAL_GANGLIA", "tpms": [1.601, 8.695, 13.165, 18.6975, 193.3] }, { "tissue": "GTEX_TISSUE_BRAIN", "tissueDetailed": "GTEX_TISSUE_DETAILED_BRAIN_CEREBELLAR_HEMISPHERE", "tpms": [0, 2.8235, 4.783, 8.2705, 141.6] }, { "tissue": "GTEX_TISSUE_BRAIN", "tissueDetailed": "GTEX_TISSUE_DETAILED_BRAIN_CEREBELLUM", "tpms": [0, 2.716, 4.11, 7.01, 44.99] }, { "tissue": "GTEX_TISSUE_BRAIN", "tissueDetailed": "GTEX_TISSUE_DETAILED_BRAIN_CORTEX", "tpms": [0.8125, 9.12, 12.7, 19.325, 389.3] }, { "tissue": "GTEX_TISSUE_BRAIN", "tissueDetailed": "GTEX_TISSUE_DETAILED_BRAIN_FRONTAL_CORTEX", "tpms": [3.464, 8.407, 12.79, 19.8, 161.6] }, { "tissue": "GTEX_TISSUE_BRAIN", "tissueDetailed": "GTEX_TISSUE_DETAILED_BRAIN_HIPPOCAMPUS", "tpms": [1.935, 9.329, 12.94, 18.2, 263.3] }, { "tissue": "GTEX_TISSUE_BRAIN", "tissueDetailed": "GTEX_TISSUE_DETAILED_BRAIN_HYPOTHALAMUS", "tpms": [1.104, 7.65, 11.955, 17.5075, 233.6] }, { "tissue": "GTEX_TISSUE_BRAIN", "tissueDetailed": "GTEX_TISSUE_DETAILED_BRAIN_NUCLEUS_ACCUMBENS", "tpms": [2.058, 8.77825, 13.26, 19.575, 359.1] }, { "tissue": "GTEX_TISSUE_BRAIN", "tissueDetailed": "GTEX_TISSUE_DETAILED_BRAIN_PUTAMEN_BASAL_GANGLIA", "tpms": [2.809, 9.49, 13.81, 20.31, 162.5] }, { "tissue": "GTEX_TISSUE_BRAIN", "tissueDetailed": "GTEX_TISSUE_DETAILED_BRAIN_SPINAL_CORD", "tpms": [0.8108, 4.3485, 7.187, 11.265, 38.09] }, { "tissue": "GTEX_TISSUE_BRAIN", "tissueDetailed": "GTEX_TISSUE_DETAILED_BRAIN_SUBSTANTIA_NIGRA", "tpms": [1.844, 10.5, 14.64, 21.935, 84.67] }, { "tissue": "GTEX_TISSUE_BREAST", "tissueDetailed": "GTEX_TISSUE_DETAILED_BREAST_MAMMARY_TISSUE", "tpms": [0, 0, 0.6253, 1.319, 76.41] }, { "tissue": "GTEX_TISSUE_CERVIX_UTERI", "tissueDetailed": "GTEX_TISSUE_DETAILED_CERVIX_ECTOCERVIX", "tpms": [0, 0, 0, 0.6911, 2.324] }, { "tissue": "GTEX_TISSUE_CERVIX_UTERI", "tissueDetailed": "GTEX_TISSUE_DETAILED_CERVIX_ENDOCERVIX", "tpms": [0, 0, 0, 0, 0.8622] }, { "tissue": "GTEX_TISSUE_COLON", "tissueDetailed": "GTEX_TISSUE_DETAILED_COLON_SIGMOID", "tpms": [0, 0, 0.6293, 1.4, 26.87] }, { "tissue": "GTEX_TISSUE_COLON", "tissueDetailed": "GTEX_TISSUE_DETAILED_COLON_TRANSVERSE", "tpms": [0, 0, 0.6406, 1.42325, 97.36] }, { "tissue": "GTEX_TISSUE_ESOPHAGUS", "tissueDetailed": "GTEX_TISSUE_DETAILED_ESOPHAGUS_GASTROESOPHAGEAL_JUNCTION", "tpms": [0, 0, 0.7114, 1.527, 31.79] }, { "tissue": "GTEX_TISSUE_ESOPHAGUS", "tissueDetailed": "GTEX_TISSUE_DETAILED_ESOPHAGUS_MUCOSA", "tpms": [0, 0, 0, 0.76515, 12.67] }, { "tissue": "GTEX_TISSUE_ESOPHAGUS", "tissueDetailed": "GTEX_TISSUE_DETAILED_ESOPHAGUS_MUSCULARIS", "tpms": [0, 0, 0.6698, 1.503, 70.48] }, { "tissue": "GTEX_TISSUE_FALLOPIAN_TUBE", "tissueDetailed": "GTEX_TISSUE_DETAILED_FALLOPIAN_TUBE", "tpms": [0, 0, 0, 0.8533, 2.425] }, { "tissue": "GTEX_TISSUE_HEART", "tissueDetailed": "GTEX_TISSUE_DETAILED_HEART_ATRIAL_APPENDAGE", "tpms": [0, 0.4647, 1.062, 2.134, 144.8] }, { "tissue": "GTEX_TISSUE_HEART", "tissueDetailed": "GTEX_TISSUE_DETAILED_HEART_LEFT_VENTRICLE", "tpms": [0, 0.981225, 1.7375, 3.32425, 107.2] }, { "tissue": "GTEX_TISSUE_KIDNEY", "tissueDetailed": "GTEX_TISSUE_DETAILED_KIDNEY_CORTEX", "tpms": [0, 1.367, 3.137, 6.952, 50.48] }, { "tissue": "GTEX_TISSUE_KIDNEY", "tissueDetailed": "GTEX_TISSUE_DETAILED_KIDNEY_MEDULLA", "tpms": [0.3035, 1.989875, 3.852, 5.29875, 5.739] }, { "tissue": "GTEX_TISSUE_LIVER", "tissueDetailed": "GTEX_TISSUE_DETAILED_LIVER", "tpms": [0, 0, 0.4147, 0.8382, 13.73] }, { "tissue": "GTEX_TISSUE_LUNG", "tissueDetailed": "GTEX_TISSUE_DETAILED_LUNG", "tpms": [0, 0, 0.5483, 1.14, 43.75] }, { "tissue": "GTEX_TISSUE_MUSCLE", "tissueDetailed": "GTEX_TISSUE_DETAILED_MUSCLE_SKELETAL", "tpms": [0, 0.30855, 0.6814, 1.541, 2348] }, { "tissue": "GTEX_TISSUE_NERVE", "tissueDetailed": "GTEX_TISSUE_DETAILED_NERVE_TIBIAL", "tpms": [0, 0, 0.8314, 1.752, 80.65] }, { "tissue": "GTEX_TISSUE_OVARY", "tissueDetailed": "GTEX_TISSUE_DETAILED_OVARY", "tpms": [0, 0, 0, 0.549025, 5.582] }, { "tissue": "GTEX_TISSUE_PANCREAS", "tissueDetailed": "GTEX_TISSUE_DETAILED_PANCREAS", "tpms": [0, 0, 0.2328, 0.555275, 16.19] }, { "tissue": "GTEX_TISSUE_PITUITARY", "tissueDetailed": "GTEX_TISSUE_DETAILED_PITUITARY", "tpms": [0, 0, 0.37, 0.9071, 29.02] }, { "tissue": "GTEX_TISSUE_PROSTATE", "tissueDetailed": "GTEX_TISSUE_DETAILED_PROSTATE", "tpms": [0, 0, 0.5792, 1.215, 79.53] }, { "tissue": "GTEX_TISSUE_SALIVARY_GLAND", "tissueDetailed": "GTEX_TISSUE_DETAILED_MINOR_SALIVARY_GLAND", "tpms": [0, 0, 0, 0.879325, 8.49] }, { "tissue": "GTEX_TISSUE_SKIN", "tissueDetailed": "GTEX_TISSUE_DETAILED_CELLS_CULTURED_FIBROBLASTS", "tpms": [0, 0, 0.4233, 1.05075, 85.73] }, { "tissue": "GTEX_TISSUE_SKIN", "tissueDetailed": "GTEX_TISSUE_DETAILED_SKIN_NOT_SUN_EXPOSED_SUPRAPUBIC", "tpms": [0, 0, 0.6594, 1.597, 103.3] }, { "tissue": "GTEX_TISSUE_SKIN", "tissueDetailed": "GTEX_TISSUE_DETAILED_SKIN_SUN_EXPOSED_LOWER_LEG", "tpms": [0, 0, 0.6767, 1.583, 57.55] }, { "tissue": "GTEX_TISSUE_SMALL_INTESTINE", "tissueDetailed": "GTEX_TISSUE_DETAILED_SMALL_INTESTINE_TERMINAL_ILEUM", "tpms": [0, 0, 0.4972, 1.0155, 62.76] }, { "tissue": "GTEX_TISSUE_SPLEEN", "tissueDetailed": "GTEX_TISSUE_DETAILED_SPLEEN", "tpms": [0, 0, 0.5443, 1.12, 31.4] }, { "tissue": "GTEX_TISSUE_STOMACH", "tissueDetailed": "GTEX_TISSUE_DETAILED_STOMACH", "tpms": [0, 0, 0.8154, 1.8775, 99.46] }, { "tissue": "GTEX_TISSUE_TESTIS", "tissueDetailed": "GTEX_TISSUE_DETAILED_TESTIS", "tpms": [0, 0, 0.7311, 1.507, 55.01] }, { "tissue": "GTEX_TISSUE_THYROID", "tissueDetailed": "GTEX_TISSUE_DETAILED_THYROID", "tpms": [0, 0, 0.5193, 1.168, 77.33] }, { "tissue": "GTEX_TISSUE_UTERUS", "tissueDetailed": "GTEX_TISSUE_DETAILED_UTERUS", "tpms": [0, 0, 0, 0.692075, 5.236] }, { "tissue": "GTEX_TISSUE_VAGINA", "tissueDetailed": "GTEX_TISSUE_DETAILED_VAGINA", "tpms": [0, 0, 0, 0.76875, 5.604] } ] }, "panelapp": [ { "geneData": { "hgncId": "HGNC:7481", "hgncSymbol": "MT-TF", "geneSymbol": "MT-TF" }, "entityType": "ENTITY_TYPE_GENE", "entityName": "MT-TF", "confidenceLevel": "CONFIDENCE_LEVEL_GREEN", "penetrance": "PENETRANCE_COMPLETE", "publications": [ "28267784", "11231339", "20142618", "23135609" ], "evidence": [ "Expert Review Green", "Literature" ], "phenotypes": [ "Tubulointerstitial kidney disease", "tubulointerstitial nephritis", "renal insufficiency", "renal failure" ], "modeOfInheritance": "MITOCHONDRIAL", "panel": { "id": 548, "name": "Tubulointerstitial kidney disease", "version": "3.3", "versionCreated": "2023-10-26T01:25:09.269688Z", "relevantDisorders": [ "R202" ], "stats": { "numberOfGenes": 25 }, "types": [ { "name": "GMS Rare Disease", "slug": "gms-rare-disease", "description": "This panel type is used for GMS panels that are not virtual (i.e. could be a wet lab test)" }, { "name": "GMS signed-off", "slug": "gms-signed-off", "description": "This panel has undergone review by a NHSE GMS disease specialist group and processes to be signed-off for use within the GMS." } ] } }, { "geneData": { "hgncId": "HGNC:7481", "hgncSymbol": "MT-TF", "geneSymbol": "MT-TF" }, "entityType": "ENTITY_TYPE_GENE", "entityName": "MT-TF", "confidenceLevel": "CONFIDENCE_LEVEL_GREEN", "penetrance": "PENETRANCE_COMPLETE", "evidence": [ "Expert Review Green", "UKGTN" ], "modeOfInheritance": "MITOCHONDRIAL", "panel": { "id": 112, "hashId": "55928cf522c1fc4f7d26e960", "name": "Mitochondrial disorders", "diseaseGroup": "Metabolic disorders", "diseaseSubGroup": "Mitochondrial", "version": "6.9", "versionCreated": "2024-06-18T16:46:16.654654Z", "relevantDisorders": [ "Lactic acidosis", "All recognised syndromes and those with suggestive features" ], "stats": { "numberOfGenes": 487, "numberOfStrs": 2, "numberOfRegions": 1 }, "types": [ { "name": "Rare Disease 100K", "slug": "rare-disease-100k", "description": "Rare Disease 100K" }, { "name": "GMS Rare Disease Virtual", "slug": "gms-rare-disease-virtual", "description": "This is a panel for the Genomic Medicine Service for an exome/genome/panel based test that requires a virtual gene panel for rare disease in the Test Directory." }, { "name": "Component Of Super Panel", "slug": "component-of-super-panel", "description": "This panel is a component of a Super Panel" }, { "name": "GMS signed-off", "slug": "gms-signed-off", "description": "This panel has undergone review by a NHSE GMS disease specialist group and processes to be signed-off for use within the GMS." } ] } }, { "geneData": { "hgncId": "HGNC:7481", "hgncSymbol": "MT-TF", "geneSymbol": "MT-TF" }, "entityType": "ENTITY_TYPE_GENE", "entityName": "MT-TF", "confidenceLevel": "CONFIDENCE_LEVEL_GREEN", "publications": [ "20142618", "11231339", "28267784", "23135609" ], "evidence": [ "Expert Review Green", "NHS GMS" ], "phenotypes": [ "renal insufficiency", "Tubulointerstitial kidney disease", "tubulointerstitial nephritis", "renal failur" ], "modeOfInheritance": "MITOCHONDRIAL", "panel": { "id": 678, "name": "Unexplained young onset end-stage renal disease", "version": "4.7", "versionCreated": "2024-06-20T14:24:59.533108Z", "relevantDisorders": [ "Unexplained paediatric onset end-stage renal disease", "R257" ], "stats": { "numberOfGenes": 306, "numberOfRegions": 3 }, "types": [ { "name": "GMS Rare Disease", "slug": "gms-rare-disease", "description": "This panel type is used for GMS panels that are not virtual (i.e. could be a wet lab test)" }, { "name": "GMS signed-off", "slug": "gms-signed-off", "description": "This panel has undergone review by a NHSE GMS disease specialist group and processes to be signed-off for use within the GMS." }, { "name": "GMS Rare Disease Virtual", "slug": "gms-rare-disease-virtual", "description": "This is a panel for the Genomic Medicine Service for an exome/genome/panel based test that requires a virtual gene panel for rare disease in the Test Directory." } ] } }, { "geneData": { "hgncId": "HGNC:7481", "hgncSymbol": "MT-TF", "geneSymbol": "MT-TF" }, "entityType": "ENTITY_TYPE_GENE", "entityName": "MT-TF", "confidenceLevel": "CONFIDENCE_LEVEL_GREEN", "penetrance": "PENETRANCE_COMPLETE", "evidence": [ "Expert Review Green" ], "modeOfInheritance": "MITOCHONDRIAL", "panel": { "id": 302, "hashId": "5763f1518f620350a22bccdb", "name": "Undiagnosed metabolic disorders", "diseaseGroup": "Metabolic disorders", "diseaseSubGroup": "Specific metabolic abnormalities", "version": "1.620", "versionCreated": "2024-06-11T17:15:32.196373Z", "relevantDisorders": [ "Undiagnosed Metabolic Panel" ], "stats": { "numberOfGenes": 752, "numberOfStrs": 1, "numberOfRegions": 1 }, "types": [ { "name": "Rare Disease 100K", "slug": "rare-disease-100k", "description": "Rare Disease 100K" } ] } }, { "geneData": { "hgncId": "HGNC:7481", "hgncSymbol": "MT-TF", "geneSymbol": "MT-TF" }, "entityType": "ENTITY_TYPE_GENE", "entityName": "MT-TF", "confidenceLevel": "CONFIDENCE_LEVEL_GREEN", "evidence": [ "Expert Review Green" ], "modeOfInheritance": "MITOCHONDRIAL", "panel": { "id": 467, "name": "Likely inborn error of metabolism - targeted testing not possible", "version": "5.22", "versionCreated": "2024-06-20T15:25:37.896887Z", "relevantDisorders": [ "Likely inborn error of metabolism - targeted testing not possible", "Likely inborn error of metabolism", "Inborn errors of metabolism", "R98" ], "stats": { "numberOfGenes": 935, "numberOfStrs": 3, "numberOfRegions": 1 }, "types": [ { "name": "GMS Rare Disease Virtual", "slug": "gms-rare-disease-virtual", "description": "This is a panel for the Genomic Medicine Service for an exome/genome/panel based test that requires a virtual gene panel for rare disease in the Test Directory." }, { "name": "Component Of Super Panel", "slug": "component-of-super-panel", "description": "This panel is a component of a Super Panel" }, { "name": "GMS signed-off", "slug": "gms-signed-off", "description": "This panel has undergone review by a NHSE GMS disease specialist group and processes to be signed-off for use within the GMS." } ] } }, { "geneData": { "hgncId": "HGNC:7481", "hgncSymbol": "MT-TF", "geneSymbol": "MT-TF" }, "entityType": "ENTITY_TYPE_GENE", "entityName": "MT-TF", "confidenceLevel": "CONFIDENCE_LEVEL_GREEN", "publications": [ "30847515" ], "evidence": [ "Next Generation Children Project", "Expert Review Green", "Expert list" ], "phenotypes": [ "MYOPATHY, MITOCHONDRIAL, LATE-ONSET", "EPILEPSY, MITOCHONDRIAL", "NEPHROPATHY, TUBULOINTERSTITIAL", "ENCEPHALOPATHY, MITOCHONDRIAL", "MELAS SYNDROME", "MERRF SYNDROME" ], "modeOfInheritance": "MITOCHONDRIAL", "panel": { "id": 921, "name": "Severe Paediatric Disorders", "version": "1.184", "versionCreated": "2024-04-09T15:06:23.215649Z", "stats": { "numberOfGenes": 2691, "numberOfStrs": 1 }, "types": [ { "name": "Research", "slug": "research", "description": "This is a gene panel used for research." } ] } }, { "geneData": { "hgncId": "HGNC:7481", "hgncSymbol": "MT-TF", "geneSymbol": "MT-TF" }, "entityType": "ENTITY_TYPE_GENE", "entityName": "MT-TF", "confidenceLevel": "CONFIDENCE_LEVEL_NONE", "evidence": [ "Expert Review Removed", "London North GLH" ], "modeOfInheritance": "MITOCHONDRIAL", "panel": { "id": 847, "name": "Childhood onset dystonia, chorea or related movement disorder", "version": "4.6", "versionCreated": "2024-06-24T12:38:52.339071Z", "relevantDisorders": [ "Childhood onset dystonia or chorea or related movement disorder", "R57" ], "stats": { "numberOfGenes": 976, "numberOfStrs": 5 }, "types": [ { "name": "GMS Rare Disease", "slug": "gms-rare-disease", "description": "This panel type is used for GMS panels that are not virtual (i.e. could be a wet lab test)" }, { "name": "GMS signed-off", "slug": "gms-signed-off", "description": "This panel has undergone review by a NHSE GMS disease specialist group and processes to be signed-off for use within the GMS." }, { "name": "GMS Rare Disease Virtual", "slug": "gms-rare-disease-virtual", "description": "This is a panel for the Genomic Medicine Service for an exome/genome/panel based test that requires a virtual gene panel for rare disease in the Test Directory." } ] } } ], "conditions": { "hgncId": "HGNC:7481", "diseaseAssociations": [ { "hgncId": "HGNC:7481", "labeledDisorders": [ { "termId": "ORPHA:620371", "title": "Gitelman-like kidney tubulopathy due to mitochondrial DNA mutation" } ], "diseaseName": "Gitelman-like kidney tubulopathy due to mitochondrial DNA mutation", "sources": [ "GENE_DISEASE_ASSOCIATION_SOURCE_ORPHANET" ], "confidence": "CONFIDENCE_LEVEL_HIGH" }, { "hgncId": "HGNC:7481", "labeledDisorders": [ { "termId": "OMIM:545000", "title": "Myoclonic epilepsy associated with ragged-red fibers" }, { "termId": "ORPHA:551", "title": "MERRF" } ], "diseaseName": "MERRF", "diseaseDefinition": "A rare mitochondrial oxidative phosphorylation disorder characterized by myoclonic seizures, ataxia, generalized epilepsy, muscle weakness and ragged red fibers in the muscle biopsy.", "sources": [ "GENE_DISEASE_ASSOCIATION_SOURCE_OMIM", "GENE_DISEASE_ASSOCIATION_SOURCE_ORPHANET" ], "confidence": "CONFIDENCE_LEVEL_HIGH" }, { "hgncId": "HGNC:7481", "labeledDisorders": [ { "termId": "OMIM:540000", "title": "Mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes" }, { "termId": "ORPHA:550", "title": "MELAS" } ], "diseaseName": "MELAS", "diseaseDefinition": "A rare neurometabolic genetic disorder which is progressive and multisystemic due to mitochondrial dysfunction and that is characterized by encephalomyopathy, lactic acidosis, and stroke-like episodes.", "sources": [ "GENE_DISEASE_ASSOCIATION_SOURCE_OMIM", "GENE_DISEASE_ASSOCIATION_SOURCE_ORPHANET" ], "confidence": "CONFIDENCE_LEVEL_HIGH" } ], "panelappAssociations": [ { "hgncId": "HGNC:7481", "confidenceLevel": "PANELAPP_CONFIDENCE_GREEN", "entityType": "PANELAPP_ENTITY_TYPE_GENE", "modeOfInheritance": "MITOCHONDRIAL", "phenotypes": [ "Tubulointerstitial kidney disease", "tubulointerstitial nephritis", "renal insufficiency", "renal failure" ], "panel": { "id": 548, "name": "Tubulointerstitial kidney disease", "version": "3.3" } }, { "hgncId": "HGNC:7481", "confidenceLevel": "PANELAPP_CONFIDENCE_GREEN", "entityType": "PANELAPP_ENTITY_TYPE_GENE", "modeOfInheritance": "MITOCHONDRIAL", "panel": { "id": 112, "name": "Mitochondrial disorders", "version": "6.9" } }, { "hgncId": "HGNC:7481", "confidenceLevel": "PANELAPP_CONFIDENCE_GREEN", "entityType": "PANELAPP_ENTITY_TYPE_GENE", "modeOfInheritance": "MITOCHONDRIAL", "phenotypes": [ "renal insufficiency", "Tubulointerstitial kidney disease", "tubulointerstitial nephritis", "renal failur" ], "panel": { "id": 678, "name": "Unexplained young onset end-stage renal disease", "version": "4.7" } }, { "hgncId": "HGNC:7481", "confidenceLevel": "PANELAPP_CONFIDENCE_GREEN", "entityType": "PANELAPP_ENTITY_TYPE_GENE", "modeOfInheritance": "MITOCHONDRIAL", "panel": { "id": 302, "name": "Undiagnosed metabolic disorders", "version": "1.620" } }, { "hgncId": "HGNC:7481", "confidenceLevel": "PANELAPP_CONFIDENCE_GREEN", "entityType": "PANELAPP_ENTITY_TYPE_GENE", "modeOfInheritance": "MITOCHONDRIAL", "panel": { "id": 467, "name": "Likely inborn error of metabolism - targeted testing not possible", "version": "5.22" } }, { "hgncId": "HGNC:7481", "confidenceLevel": "PANELAPP_CONFIDENCE_GREEN", "entityType": "PANELAPP_ENTITY_TYPE_GENE", "modeOfInheritance": "MITOCHONDRIAL", "phenotypes": [ "MYOPATHY, MITOCHONDRIAL, LATE-ONSET", "EPILEPSY, MITOCHONDRIAL", "NEPHROPATHY, TUBULOINTERSTITIAL", "ENCEPHALOPATHY, MITOCHONDRIAL", "MELAS SYNDROME", "MERRF SYNDROME" ], "panel": { "id": 921, "name": "Severe Paediatric Disorders", "version": "1.184" } }, { "hgncId": "HGNC:7481", "confidenceLevel": "PANELAPP_CONFIDENCE_NONE", "entityType": "PANELAPP_ENTITY_TYPE_GENE", "modeOfInheritance": "MITOCHONDRIAL", "panel": { "id": 847, "name": "Childhood onset dystonia, chorea or related movement disorder", "version": "4.6" } } ] } } } }The text was updated successfully, but these errors were encountered: