{
  "name": "open-cmt-gene-table",
  "title": "Open CMT Gene Table",
  "description": "Genes linked to Charcot-Marie-Tooth disease and related inherited neuropathies, one row per ClinGen gene-disease curation, with subtype names, sources and plain-language notes.",
  "version": "v2026.10 + later edits",
  "created": "2026-10-14T15:30:23Z",
  "homepage": "https://dknauss.github.io/cmt-gene-table/",
  "licenses": [
    {
      "name": "CC-BY-4.0",
      "title": "Creative Commons Attribution 4.0",
      "path": "https://creativecommons.org/licenses/by/4.0/"
    }
  ],
  "contributors": [
    {
      "title": "Dan Knauss",
      "role": "author",
      "path": "https://cmt.blog/"
    }
  ],
  "sources": [
    {
      "title": "ClinGen Gene-Disease Validity",
      "path": "https://search.clinicalgenome.org/kb/gene-validity"
    },
    {
      "title": "Mondo Disease Ontology via the Monarch Initiative",
      "path": "https://monarchinitiative.org/"
    },
    {
      "title": "GeneReviews",
      "path": "https://www.ncbi.nlm.nih.gov/books/NBK1116/"
    },
    {
      "title": "Genomics England PanelApp and PanelApp Australia",
      "path": "https://panelapp.genomicsengland.co.uk/"
    },
    {
      "title": "ClinicalTrials.gov",
      "path": "https://clinicaltrials.gov/"
    }
  ],
  "resources": [
    {
      "name": "cmt-genes",
      "path": "cmt-genes.csv",
      "format": "csv",
      "mediatype": "text/csv",
      "encoding": "utf-8",
      "schema": {
        "fields": [
          {
            "name": "gene",
            "type": "string",
            "description": "HGNC symbol and ID (Source: ClinGen.)"
          },
          {
            "name": "hgnc_id",
            "type": "string",
            "description": "HGNC symbol and ID (Source: ClinGen.)"
          },
          {
            "name": "clingen_disease_label",
            "type": "string",
            "description": "The disease the gene was curated for (Source: ClinGen.)"
          },
          {
            "name": "mondo_id",
            "type": "string",
            "description": "The disease the gene was curated for (Source: ClinGen.)"
          },
          {
            "name": "inheritance",
            "type": "string",
            "description": "AD, AR, XL or SD (semidominant) (Source: ClinGen.)"
          },
          {
            "name": "clingen_classification",
            "type": "string",
            "description": "Definitive, Strong, Moderate, Limited, Disputed… (Source: ClinGen.)"
          },
          {
            "name": "classification_date",
            "type": "date",
            "description": "Definitive, Strong, Moderate, Limited, Disputed… (Source: ClinGen.)"
          },
          {
            "name": "clingen_report",
            "type": "string",
            "description": "Link to the full curation (Source: ClinGen.)"
          },
          {
            "name": "type_named_in_label",
            "type": "string",
            "description": "The CMT type named in ClinGen's own label, if any (Source: Derived.)"
          },
          {
            "name": "curation_subtype_names",
            "type": "string",
            "description": "Subtype names for the disease rated in this row, separated by semicolons. See \"Names Matched to Curations\" in the README (Source: ClinGen + Mondo.)"
          },
          {
            "name": "curation_names_basis",
            "type": "string",
            "description": "How those names were matched to the curation (Source: Build notes.)"
          },
          {
            "name": "other_gene_names",
            "type": "string",
            "description": "Other subtype names with a causal link to the gene that this curation does not cover. The rating in this row does not apply to them (Source: Mondo via Monarch.)"
          },
          {
            "name": "unverified_names",
            "type": "string",
            "description": "Names that come only from Monarch correlated (not causal) associations. Kept for review, not presented as subtypes (Source: Mondo via Monarch.)"
          },
          {
            "name": "rejected_names",
            "type": "string",
            "description": "Names checked and found not to belong to the gene, from data/name-reviews.csv (each with a source URL). Left off the page (Source: Hand-checked.)"
          },
          {
            "name": "clingen_included_omim",
            "type": "string",
            "description": "The OMIM phenotypes ClinGen's panel included in, or excluded from, this curation (Source: ClinGen curation page.)"
          },
          {
            "name": "clingen_excluded_omim",
            "type": "string",
            "description": "The OMIM phenotypes ClinGen's panel included in, or excluded from, this curation (Source: ClinGen curation page.)"
          },
          {
            "name": "historical_subtype_names",
            "type": "string",
            "description": "Every subtype name linked to the gene, causal or correlated, separated by semicolons. Gene-wide, so it is the same for every curation of a gene; use curation_subtype_names for the names that go with a rating (Source: Mondo via Monarch.)"
          },
          {
            "name": "subtype_mondo_ids",
            "type": "string",
            "description": "The Mondo terms those names come from (Source: Mondo via Monarch.)"
          },
          {
            "name": "omim_phenotype_ids",
            "type": "string",
            "description": "IDs only; no OMIM text is reproduced (Source: Mondo cross-references.)"
          },
          {
            "name": "subtype_review_note",
            "type": "string",
            "description": "Provenance and anything flagged for human review (Source: Build notes.)"
          },
          {
            "name": "phenotype",
            "type": "string",
            "description": "One or more of axonal, demyelinating, intermediate, motor-predominant, sensory-predominant (Source: Hand-checked.)"
          },
          {
            "name": "genereviews",
            "type": "string",
            "description": "Chapter title and link for every GeneReviews chapter NCBI maps to the gene, separated by semicolons. Starts [overview only] when every chapter is an overview (Source: NCBI GeneReviews report files.)"
          },
          {
            "name": "panelapp",
            "type": "string",
            "description": "Rating (Green/Amber/Red), panel, version and gene-page link on Genomics England panel 846 and PanelApp Australia panel 3070 (Source: PanelApp APIs.)"
          },
          {
            "name": "therapy_programs",
            "type": "string",
            "description": "Trials of drugs, biologics or gene therapies for the disease in this row, found by the ClinicalTrials.gov searches in the source URL, with phase, status and link. \"None found\" means none found by that search, not that no research exists. A registered trial is not a promising or available treatment (Source: Hand-checked.)"
          },
          {
            "name": "other_condition_trials",
            "type": "string",
            "description": "Trials that target the gene but in a different condition, such as LTX-002 for SPTLC1 in ALS (Source: Hand-checked.)"
          },
          {
            "name": "plain_note",
            "type": "string",
            "description": "One sentence in plain language, written for this table (Source: Hand-checked.)"
          }
        ],
        "primaryKey": [
          "gene",
          "mondo_id"
        ]
      }
    }
  ]
}