ClinGen through GeneFoundry
Review ClinGen gene–disease validity, dosage, actionability and expert-panel evidence as distinct curation domains.
- Research area
- Gene–disease
- Namespace
clingen- Listed tools
- 17
- Upstream source
- ClinGen
Research tasks
- Find gene–disease validity curations
- Compare the scope of dosage and validity evidence
Start with tool discovery
The catalog lists clingen_get_gene_validity as a representative tool. After connecting your client, inspect the tools and input requirements returned by the service before submitting a query.
Identifiers to prepare
- Gene symbol or alias
- HGNC identifier
- MONDO disease identifier
All available tools (17)
The router surfaces these tools namespaced under clingen_*:
get_server_capabilitiesUse this when a client needs the supported tools, ClinGen datasets + per-domain snapshot freshness, recommended workflows, token-cost hints, error taxonomy, parameter conventions, or the capabilities_version content hash. Returns ~4kB.
Use this when a client needs the supported tools, ClinGen datasets + per-domain snapshot freshness, recommended workflows, token-cost hints, error taxonomy, parameter conventions, or the capabilities_version content hash. Returns ~4kB.
search_genesUse this FIRST to resolve a free-text gene (symbol / HGNC id / alias) into a canonical ClinGen gene plus its per-domain availability and counts. Follow the _meta.next_commands into get_gene_summary. Unknown input returns a not_found envelope with a fallback. Returns ~1-3kB.
Use this FIRST to resolve a free-text gene (symbol / HGNC id / alias) into a canonical ClinGen gene plus its per-domain availability and counts. Follow the _meta.next_commands into get_gene_summary. Unknown input returns a not_found envelope with a fallback. Returns ~1-3kB.
Input parameters
query(string) [required] — Gene symbol, HGNC id, or alias to resolve (e.g. BRCA1, HGNC:1100).response_mode(string) — compact (default) trims null fields; full keeps everything.
get_gene_summaryUse this for a one-call cross-domain overview of a gene: validity classifications by disease, dosage haplo/triplo scores, actionability adult/pediatric, and ERepo variant counts. Resolve free text with search_genes first. The _meta.next_commands drill into each domain tool. Returns compact ~3-8kB (minimal ~0.5kB).
Use this for a one-call cross-domain overview of a gene: validity classifications by disease, dosage haplo/triplo scores, actionability adult/pediatric, and ERepo variant counts. Resolve free text with search_genes first. The _meta.next_commands drill into each domain tool. Returns compact ~3-8kB (minimal ~0.5kB).
Input parameters
gene_symbol(string) [required] — Canonical gene symbol or HGNC id (resolve with search_genes first).response_mode(string) — minimal = headline + counts only; compact (default) trims verbose fields; standard keeps nulls; full returns every field.
get_gene_validityUse this to list ClinGen gene-disease validity assertions (Definitive…Refuted) for one gene, optionally filtered by classification or mode of inheritance. Each record carries a CGGV permalink + recommended_citation. Returns ~1-6kB.
Use this to list ClinGen gene-disease validity assertions (Definitive…Refuted) for one gene, optionally filtered by classification or mode of inheritance. Each record carries a CGGV permalink + recommended_citation. Returns ~1-6kB.
Input parameters
classification(any) — Filter to one ClinGen validity classification.gene_symbol(string) [required] — Gene symbol or HGNC id (resolve with search_genes first).moi(any) — Filter to one mode of inheritance.response_mode(string) — compact (default) trims verbose fields; full keeps everything.
search_validityUse this to search ClinGen gene-disease validity by disease text/MONDO, expert panel, classification, MOI, or gene. Paginated; a `truncated` block appears when more matches exist. Each record carries a recommended_citation. Returns ~2-10kB.
Use this to search ClinGen gene-disease validity by disease text/MONDO, expert panel, classification, MOI, or gene. Paginated; a `truncated` block appears when more matches exist. Each record carries a recommended_citation. Returns ~2-10kB.
Input parameters
classification(any) — Filter to one classification.disease(any) — Free-text disease name (FTS).expert_panel(any) — Substring of the curating expert panel name.gene_symbol(any) — Restrict to one gene symbol.moi(any) — Filter to one mode of inheritance.mondo(any) — MONDO disease id.page(integer) — 1-based page number.response_mode(string) — compact (default) trims verbose fields; full keeps everything.size(integer) — Page size (max 100).
get_gene_dosageUse this for ClinGen dosage sensitivity of a gene: haploinsufficiency + triplosensitivity score with plain-English interpretation, GRCh37/GRCh38 coordinates, disease/MONDO, and PMIDs. Resolve free text with search_genes first. Returns ~1-3kB.
Use this for ClinGen dosage sensitivity of a gene: haploinsufficiency + triplosensitivity score with plain-English interpretation, GRCh37/GRCh38 coordinates, disease/MONDO, and PMIDs. Resolve free text with search_genes first. Returns ~1-3kB.
Input parameters
gene_symbol(string) [required] — Gene symbol or HGNC id (resolve with search_genes first).response_mode(string) — compact (default) trims verbose fields; full keeps the PMID lists.
search_dosageUse this to search ClinGen dosage (genes + regions) by text, ISCA region, cytoband, or haplo/triplo score, optionally restricted to gene or region records. Paginated; a `truncated` block appears when more matches exist. Returns ~2-10kB.
Use this to search ClinGen dosage (genes + regions) by text, ISCA region, cytoband, or haplo/triplo score, optionally restricted to gene or region records. Paginated; a `truncated` block appears when more matches exist. Returns ~2-10kB.
Input parameters
cytoband(any) — Cytoband prefix (e.g. 17q21).haplo_score(any) — Exact ClinGen haploinsufficiency score CODE (not its description): 0 no evidence, 1 little, 2 some, 3 sufficient evidence; 30 gene associated with an autosomal-recessive phenotype; 40 dosage sensitivity unlikely. 30 and 40 are flags, not 'more than 3'.page(integer) — 1-based page number.query(any) — Free-text gene / disease / ISCA text (FTS).record_type(any) — Restrict to gene or region records.region(any) — ISCA region id.response_mode(string) — compact (default) trims verbose fields; full keeps the PMID lists.size(integer) — Page size (max 100).triplo_score(any) — Exact ClinGen triplosensitivity score CODE (same scale as haplo_score). Genes upstream has not evaluated carry no code and are not matched by any.
get_gene_actionabilityUse this for ClinGen clinical actionability of a gene: adult/pediatric assertion status, release, disease, and SEPIO links. Set include_detail=true to fetch the live SEPIO assertion document for the chosen context. Resolve free text with search_genes first. Returns snapshot ~1-4kB; include_detail adds the live SEPIO payload.
Use this for ClinGen clinical actionability of a gene: adult/pediatric assertion status, release, disease, and SEPIO links. Set include_detail=true to fetch the live SEPIO assertion document for the chosen context. Resolve free text with search_genes first. Returns snapshot ~1-4kB; include_detail adds the live SEPIO payload.
Input parameters
context(string) — Adult (default) or Pediatric assertion context.gene_symbol(string) [required] — Gene symbol or HGNC id (resolve with search_genes first).include_detail(boolean) — Fetch the live SEPIO assertion document for each curation in the requested context (extra upstream calls). False (default) returns snapshot rows.response_mode(string) — compact (default) trims SEPIO IRIs; full keeps everything.
search_actionabilityUse this to search ClinGen clinical actionability by disease text or gene. Paginated; a `truncated` block appears when more matches exist. Each record carries the actionability permalink + recommended_citation. Returns ~2-8kB.
Use this to search ClinGen clinical actionability by disease text or gene. Paginated; a `truncated` block appears when more matches exist. Each record carries the actionability permalink + recommended_citation. Returns ~2-8kB.
Input parameters
assertion(any) — Curation status of the adult OR pediatric assertion to filter by (e.g. 'Released'). A value outside the enum is rejected by validation.context(any) — Seed the citation with this assertion context.disease(any) — Free-text disease name (FTS).gene_symbol(any) — Gene symbol that the curation lists.page(integer) — 1-based page number.response_mode(string) — compact (default) trims SEPIO IRIs; full keeps everything.size(integer) — Page size (max 100).
get_variant_interpretationsUse this to list ClinGen ERepo expert-panel variant interpretations by gene, disease (disease text/MONDO), expert panel, or classification. Returns each variant's CAID, canonical HGVS, MONDO, ACMG classification, VCEP, dates, and permalink. Drill into one with get_variant_interpretation. Paginated. Returns ~2-12kB.
Use this to list ClinGen ERepo expert-panel variant interpretations by gene, disease (disease text/MONDO), expert panel, or classification. Returns each variant's CAID, canonical HGVS, MONDO, ACMG classification, VCEP, dates, and permalink. Drill into one with get_variant_interpretation. Paginated. Returns ~2-12kB.
Input parameters
classification(any) — Filter to one ACMG classification.disease(any) — Disease text (FTS) or MONDO id.expert_panel(any) — Substring of the curating VCEP name.gene_symbol(any) — Gene symbol (resolve with search_genes first).page(integer) — 1-based page number.response_mode(string) — compact (default) trims evidence-code/PubMed lists; full keeps them.size(integer) — Page size (max 100).
get_variant_interpretationUse this for the full ACMG interpretation of one expert-panel variant: evidence codes Met / Not Met, the classification outcome, guideline/CSpec, PubMed evidence, and the permalink. variant_id takes a CAID, a ClinVar VariationID, or an HGVS expression. refresh=true bypasses the snapshot for the live SEPIO JSON. Returns ~2-8kB.
Use this for the full ACMG interpretation of one expert-panel variant: evidence codes Met / Not Met, the classification outcome, guideline/CSpec, PubMed evidence, and the permalink. variant_id takes a CAID, a ClinVar VariationID, or an HGVS expression. refresh=true bypasses the snapshot for the live SEPIO JSON. Returns ~2-8kB.
Input parameters
refresh(boolean) — Bypass the snapshot and fetch the live SEPIO interpretation.response_mode(string) — compact (default) trims verbose blocks; full keeps every field.variant_id(string) [required] — The variant to look up, in any ONE of the three identifier shapes ERepo keys on: a ClinGen Allele Registry id (CA003783), a ClinVar VariationID (17662), or an HGVS expression (NM_007294.4:c.68_69del). The shape is detected from the value.
list_cspecsUse this to browse ClinGen criteria-specification (CSpec) headers, filtered by gene, curating affiliation (VCEP), or lifecycle status. Each row carries the GN id, affiliation, label, version, and status. Drill into one with get_cspec. Paginated; returns ~1-8kB.
Use this to browse ClinGen criteria-specification (CSpec) headers, filtered by gene, curating affiliation (VCEP), or lifecycle status. Each row carries the GN id, affiliation, label, version, and status. Drill into one with get_cspec. Paginated; returns ~1-8kB.
Input parameters
affiliation(any) — ClinGen affiliation id of the curating VCEP.gene_symbol(any) — Gene symbol covered by the spec (resolve with search_genes first).page(integer) — 1-based page number.response_mode(string) — compact (default) drops nulls + verbose header fields.size(integer) — Page size (max 100).status(any) — CSpec lifecycle status filter (cspecStatus). A value outside the enum is rejected by validation.
get_cspecUse this for one criteria specification in full: its genes/diseases, every ACMG/AMP criterion with strength rules, and the attached guidance files. Resolve a gn_id first with list_cspecs (by gene, affiliation, or status). Returns ~3-30kB depending on the spec.
Use this for one criteria specification in full: its genes/diseases, every ACMG/AMP criterion with strength rules, and the attached guidance files. Resolve a gn_id first with list_cspecs (by gene, affiliation, or status). Returns ~3-30kB depending on the spec.
Input parameters
gn_id(string) [required] — CSpec GN identifier. Resolve one from a gene, an affiliation (VCEP) or a status with list_cspecs, whose rows carry the gn_id.response_mode(string) — compact (default) trims verbose header fields; full keeps them.
get_cspec_criterionUse this for a single CSpec criterion's specification: its ACMG/AMP code, description, the VCEP's strength rules, and any attached evidence files. Addressed by its natural key — the specification (gn_id) plus the ACMG/AMP code — with rule_set_id only for a code a spec defines twice. Returns ~1-4kB.
Use this for a single CSpec criterion's specification: its ACMG/AMP code, description, the VCEP's strength rules, and any attached evidence files. Addressed by its natural key — the specification (gn_id) plus the ACMG/AMP code — with rule_set_id only for a code a spec defines twice. Returns ~1-4kB.
Input parameters
code(string) [required] — ACMG/AMP code within that specification.gn_id(string) [required] — CSpec GN id (from list_cspecs / get_cspec / search_cspec).response_mode(string) — compact (default) trims nulls; full keeps every field.rule_set_id(any) — Only needed for the few codes a spec defines in more than one rule set; the ambiguous_query error names it and lists the rule sets.
search_cspecUse this to full-text search the CSpec catalog (spec labels, criteria descriptions, attachment filenames). Each hit names its entity_type + ids so you can chain into get_cspec or get_cspec_criterion. Paginated; returns ~1-6kB.
Use this to full-text search the CSpec catalog (spec labels, criteria descriptions, attachment filenames). Each hit names its entity_type + ids so you can chain into get_cspec or get_cspec_criterion. Paginated; returns ~1-6kB.
Input parameters
page(integer) — 1-based page number.query(string) [required] — Full-text query across spec labels, criteria, and filenames.size(integer) — Page size (max 100).
list_expert_panelsUse this to list ClinGen GCEP/VCEP expert panels (affiliates) with their curation counts, optionally filtered by label text. Useful to resolve an expert-panel name before filtering validity or variant interpretations. Returns ~1-5kB.
Use this to list ClinGen GCEP/VCEP expert panels (affiliates) with their curation counts, optionally filtered by label text. Useful to resolve an expert-panel name before filtering validity or variant interpretations. Returns ~1-5kB.
Input parameters
query(any) — Filter by expert-panel label text (FTS).response_mode(string) — compact (default) is the same compact list; full is identical.
get_diagnosticsUse this when an LLM hits repeated errors or needs server health information; returns recent error history, server version, snapshot freshness, and recent_schema_drift entries so an LLM that hit output_validation_failed can self-diagnose. Returns <1kB.
Use this when an LLM hits repeated errors or needs server health information; returns recent error history, server version, snapshot freshness, and recent_schema_drift entries so an LLM that hit output_validation_failed can self-diagnose. Returns <1kB.
Database & release provenance
- Data mode
external-reference- Attestation
- attested-reference
- Data release tag
data-clingen-de5f403028d2e1e1- Release version
v4.0.9
sha256:74dc6e1a82f773b17303d33ff82b63c96e9aed0b16fa5f3020b13fd69ffdf789ghcr.io/berntpopp/clingen-link@sha256:c1c1466f89b4b222dd151c315a4847e88e97ed700409e69fbedf6bdb17bb7998Review the response
Keep the source record link and submitted identifiers with your notes. Record the dataset version and retrieval date when available. This page does not contain a captured ClinGen response.