tx annotations missing for mt variants

[stolpeo]

Describe the bug

Currently, mehari does not annotate tx on the MT chromosome.

curl 'http://mehari:8080/seqvars/csq?genome_release=grch37&chromosome=MT&position=73&reference=A&alternative=G&hgnc_id=HGNC:7481'

{
  "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:

curl 'http://annonars:8080/genes/info?hgnc_id=HGNC:7481'

{
  "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"
            }
          }
        ]
      }
    }
  }
}

[tedil]

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. Also, because these are synthetic entries, the corresponding sequence may be missing from the seqrepo we use during building of the txdb -- which is why I re-enabled grafting the MT txs from ensembl onto refseq again (not yet pushed).

[holtgrewe]

@tedil this should not be forgotten

[tedil]

Should be fixed with https://github.com/varfish-org/mehari-data-tx/pull/50 -- but I will verify with the examples given by Oliver first.

[holtgrewe]

@tedil what's the status?

[tedil]

Should now really be fixed with https://github.com/varfish-org/mehari-data-tx/pull/54 and the upcoming 0.7.6 txdb release