Clinvar Tools#

Configuration File: clinvar_tools.json Tool Type: Local Tools Count: 3

This page contains all tools defined in the clinvar_tools.json configuration file.

Available Tools#

ClinVar_get_clinical_significance (Type: ClinVarGetClinicalSignificance)#

Get clinical significance information for a variant from ClinVar. Returns pathogenicity classific…

ClinVar_get_clinical_significance tool specification

Tool Information:

  • Name: ClinVar_get_clinical_significance

  • Type: ClinVarGetClinicalSignificance

  • Description: Get clinical significance information for a variant from ClinVar. Returns pathogenicity classification and clinical interpretations.

Parameters:

  • variant_id (string) (required) ClinVar variant ID (e.g., ‘12345’, ‘123456’)

Example Usage:

query = {
    "name": "ClinVar_get_clinical_significance",
    "arguments": {
        "variant_id": "example_value"
    }
}
result = tu.run(query)

ClinVar_get_variant_details (Type: ClinVarGetVariantDetails)#

Get variant summary information from ClinVar by variant ID. Returns accession, title, genes, clin…

ClinVar_get_variant_details tool specification

Tool Information:

  • Name: ClinVar_get_variant_details

  • Type: ClinVarGetVariantDetails

  • Description: Get variant summary information from ClinVar by variant ID. Returns accession, title, genes, clinical significance, review status, chromosome location, and variation name. For the same variant, this provides a different field view than ClinVar_get_clinical_significance.

Parameters:

  • variant_id (string) (required) ClinVar variant ID (e.g., ‘12345’, ‘123456’)

Example Usage:

query = {
    "name": "ClinVar_get_variant_details",
    "arguments": {
        "variant_id": "example_value"
    }
}
result = tu.run(query)

ClinVar_search_variants (Type: ClinVarSearchVariants)#

Search for variants in ClinVar database by gene name, condition, variant ID, or variant name (pro…

ClinVar_search_variants tool specification

Tool Information:

  • Name: ClinVar_search_variants

  • Type: ClinVarSearchVariants

  • Description: Search for variants in ClinVar database by gene name, condition, variant ID, or variant name (protein change / HGVS notation). Returns variant identifiers and basic information. At least one of gene, condition, variant_id, or variant_name must be provided. Combine gene + variant_name for an exact-match lookup of one specific known variant instead of browsing all of a gene’s ClinVar entries.

Parameters:

  • gene (string) (optional) Gene name or symbol (e.g., ‘BRCA1’, ‘BRCA2’) At least one of gene, condition, or variant_id must be provided.

  • condition (string) (optional) Disease or condition name (e.g., ‘breast cancer’, ‘diabetes’) At least one of gene, condition, or variant_id must be provided. Matched against ClinVar’s disease index, which carries MedGen’s own condition names exactly – a synonym, a locus name or a misspelling (‘Lebers congenital amaurosis’ for the indexed ‘Leber congenital amaurosis’) matches nothing there, so the search falls back to an unrestricted free-text match. When that happens the response says so: ‘condition_filter_applied’: false plus a ‘condition_filter_warning’, meaning total_count is NOT a disease-filtered count. Use MedGen_search_conditions to get the indexed name.

  • variant_id (string) (optional) ClinVar variant ID (e.g., ‘12345’) At least one of gene, condition, or variant_id must be provided.

  • variant_name ([‘string’, ‘array’, ‘null’]) (optional) Protein change or HGVS notation to search for (e.g., ‘Glu6Val’, ‘V600E’, ‘c.20A>T’), matched against ClinVar’s own [Variant name] index – combine with ‘gene’ for an exact-match lookup of a specific known variant instead of browsing all of a gene’s ClinVar entries. A gene-level browse can silently miss well-known but old/low-ID records once a gene has more entries than max_results (e.g. HBB’s canonical sickle-cell record, NM_000518.5(HBB):c.20A>T (p.Glu7Val), isn’t within the first 100-425 gene-level rows). Accepts a list to try multiple candidate names in one call (e.g. every allele at a multi-allelic site) – combined with OR.

  • max_results (integer) (optional) Maximum number of results to return (default: 20). Alias: limit.

  • limit (integer) (optional) Alias for max_results: maximum number of results to return.

  • clinical_significance (string) (optional) Filter by clinical significance. Must be one of the classes ClinVar’s index actually recognizes: ‘Pathogenic’, ‘Likely pathogenic’, ‘Uncertain significance’, ‘VUS’, ‘Likely benign’, ‘Benign’, ‘Established risk allele’, ‘Likely risk allele’, ‘Uncertain risk allele’, ‘drug response’, ‘risk factor’, ‘not provided’, ‘other’. Case-insensitive; underscores/hyphens are treated as spaces. Combine two classes with ‘/’ to search their union (e.g. ‘Pathogenic/Likely pathogenic’). Any other value is rejected with an error rather than silently filtering the results to nothing.

  • gene_symbol ([‘string’, ‘null’]) (optional) Alias for gene. HGNC gene symbol (e.g., “DPYD”, “CYP2C19”).

  • significance ([‘string’, ‘null’]) (optional) Alias for clinical_significance (e.g., “pathogenic”, “benign”, “uncertain_significance”). Same accepted value set and same validation as clinical_significance.

  • query ([‘string’, ‘null’]) (optional) Alias for condition. Free-text search mapped to condition/disease field.

Example Usage:

query = {
    "name": "ClinVar_search_variants",
    "arguments": {
    }
}
result = tu.run(query)