Forge Tools clingen_dosage

clingen_dosage read

scidex.forge.clingen_dosage

Query ClinGen Dosage Sensitivity Map for haploinsufficiency (HI) and triplosensitivity (TS) scores for human genes. ClinGen has curated 3,000+ genes for dosage sensitivity — critical for CNV interpretation, gene essentiality scoring, and pathogenicity assessment. Scores range 0–3 (0=No evidence, 1=Little, 2=Moderate, 3=Sufficient). Complements scidex.forge.clingen_gene_validity (gene-disease validity) and scidex.forge.gnomad_constraint (population constraint) with ClinGen's curated dosage sensitivity track. REST API: https://search.clinicalgenome.org/kb/gene-dosage — free, no auth.

HTTP: POST /api/scidex/forge/clingen_dosage

Invoke

Calls scidex.tool.invoke on the substrate with this tool name. Edit the JSON below — it must match the input schema. The substrate runs the tool, records the call in substrate_tool_calls, and returns a structured envelope.

Sign in to invoke this tool. Schema and curl snippet are visible to anyone.

Schemas

Input schema 
{
  "additionalProperties": false,
  "description": "Input schema for ``scidex.forge.clingen_dosage``.",
  "properties": {
    "gene": {
      "description": "Gene symbol or identifier to query (e.g. ``'BRCA1'``, ``'TP53'``). ClinGen returns dosage sensitivity records matching this search term.",
      "maxLength": 64,
      "title": "Gene",
      "type": "string"
    },
    "query_type": {
      "default": "gene_symbol",
      "description": "Type of identifier provided. Currently ``'gene_symbol'`` is the supported type (used as the search parameter against ClinGen).",
      "title": "Query Type",
      "type": "string"
    }
  },
  "required": [
    "gene"
  ],
  "title": "ForgeClingenDosageIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "ClinGenDosageScore": {
      "description": "Dosage sensitivity record for one gene from the ClinGen Dosage Map.",
      "properties": {
        "gene_symbol": {
          "description": "HGNC gene symbol.",
          "title": "Gene Symbol",
          "type": "string"
        },
        "gene_id": {
          "description": "ClinGen or HGNC gene identifier (curie).",
          "title": "Gene Id",
          "type": "string"
        },
        "haploinsufficiency_score": {
          "description": "Haploinsufficiency (HI) assertion score 0–3 (0=No evidence, 1=Little, 2=Moderate, 3=Sufficient). Score 30 = autosomal recessive; 40 = dosage sensitivity unlikely.",
          "title": "Haploinsufficiency Score",
          "type": "integer"
        },
        "triplosensitivity_score": {
          "description": "Triplosensitivity (TS) assertion score 0–3 (0=No evidence, 1=Little, 2=Moderate, 3=Sufficient). Score 30 = autosomal recessive; 40 = dosage sensitivity unlikely.",
          "title": "Triplosensitivity Score",
          "type": "integer"
        },
        "haploinsufficiency_description": {
          "description": "Human-readable description of the haploinsufficiency score.",
          "title": "Haploinsufficiency Description",
          "type": "string"
        },
        "triplosensitivity_description": {
          "description": "Human-readable description of the triplosensitivity score.",
          "title": "Triplosensitivity Description",
          "type": "string"
        },
        "genomic_location": {
          "default": "",
          "description": "Genomic coordinates of the gene (GRCh38, e.g. 'chr17:43044295-43125364').",
          "title": "Genomic Location",
          "type": "string"
        },
        "online_report_url": {
          "default": "",
          "description": "URL to the ClinGen online dosage sensitivity report for this gene.",
          "title": "Online Report Url",
          "type": "string"
        }
      },
      "required": [
        "gene_symbol",
        "gene_id",
        "haploinsufficiency_score",
        "triplosensitivity_score",
        "haploinsufficiency_description",
        "triplosensitivity_description"
      ],
      "title": "ClinGenDosageScore",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.clingen_dosage``.",
  "properties": {
    "query": {
      "description": "The gene identifier that was queried.",
      "title": "Query",
      "type": "string"
    },
    "query_type": {
      "description": "The query type used (e.g. 'gene_symbol').",
      "title": "Query Type",
      "type": "string"
    },
    "dosage_data": {
      "description": "ClinGen dosage sensitivity records for the queried gene. Each record includes haploinsufficiency and triplosensitivity scores (0–3).",
      "items": {
        "$ref": "#/$defs/ClinGenDosageScore"
      },
      "title": "Dosage Data",
      "type": "array"
    },
    "not_found": {
      "description": "True when ClinGen has no dosage sensitivity curation for this gene. False when at least one record was returned.",
      "title": "Not Found",
      "type": "boolean"
    }
  },
  "required": [
    "query",
    "query_type",
    "not_found"
  ],
  "title": "ForgeClingenDosageOut",
  "type": "object"
}

curl snippet

Replace $SCIDEX_JWT with a valid bearer token. Read verbs are usually accessible without auth in dev; production requires a JWT.

curl -sS -X POST '/api/scidex/forge/clingen_dosage' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "gene": ""
}'

Discussion

Posting anonymously. Sign in for attribution.

No comments yet — be the first.