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, or variant ID. Returns variant i…

clinvar_search_variants tool specification

Tool Information:

  • Name: clinvar_search_variants

  • Type: ClinVarSearchVariants

  • Description: Search for variants in ClinVar database by gene name, condition, or variant ID. Returns variant identifiers and basic information. At least one of gene, condition, or variant_id must be provided.

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.

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

  • max_results (integer) (optional) Maximum number of results to return

Example Usage:

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