Clingen Tools

Configuration File: clingen_tools.json Tool Type: Local Tools Count: 8

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

Available Tools

ClinGen_get_actionability_adult (Type: ClinGenTool)

Get ClinGen clinical actionability curations for adult context. Returns genes with actionable fin…

ClinGen_get_actionability_adult tool specification

Tool Information:

  • Name: ClinGen_get_actionability_adult

  • Type: ClinGenTool

  • Description: Get ClinGen clinical actionability curations for adult context. Returns genes with actionable findings, intervention scores, and outcome scores. Actionability scores help prioritize which incidental findings to return. Example: BRCA1/2 have high actionability for cancer screening.

Parameters:

  • gene (string) (optional) Optional: Filter by gene symbol

Example Usage:

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

ClinGen_get_actionability_pediatric (Type: ClinGenTool)

Get ClinGen clinical actionability curations for pediatric context. Returns genes with actionable…

ClinGen_get_actionability_pediatric tool specification

Tool Information:

  • Name: ClinGen_get_actionability_pediatric

  • Type: ClinGenTool

  • Description: Get ClinGen clinical actionability curations for pediatric context. Returns genes with actionable findings in children, intervention recommendations, and evidence scores. Pediatric curations may differ from adult context due to age-specific interventions.

Parameters:

  • gene (string) (optional) Optional: Filter by gene symbol

Example Usage:

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

ClinGen_get_dosage_sensitivity (Type: ClinGenTool)

Get all ClinGen dosage sensitivity curations. Returns haploinsufficiency and triplosensitivity sc…

ClinGen_get_dosage_sensitivity tool specification

Tool Information:

  • Name: ClinGen_get_dosage_sensitivity

  • Type: ClinGenTool

  • Description: Get all ClinGen dosage sensitivity curations. Returns haploinsufficiency and triplosensitivity scores for curated genes. Set include_regions=true to also get recurrent CNV regions. Scores: 0=No evidence, 1=Little, 2=Emerging, 3=Sufficient evidence.

Parameters:

  • gene (string) (optional) Optional: Filter by gene symbol

  • include_regions (boolean) (optional) Include recurrent CNV regions (default: false)

Example Usage:

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

ClinGen_get_gene_validity (Type: ClinGenTool)

Get all ClinGen gene-disease validity curations. Returns comprehensive list of gene-disease relat…

ClinGen_get_gene_validity tool specification

Tool Information:

  • Name: ClinGen_get_gene_validity

  • Type: ClinGenTool

  • Description: Get all ClinGen gene-disease validity curations. Returns comprehensive list of gene-disease relationships with classifications (Definitive, Strong, Moderate, Limited). Useful for batch analysis or exploring curated genes. Optional gene filter available.

Parameters:

  • gene (string) (optional) Optional: Filter by gene symbol

Example Usage:

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

ClinGen_get_variant_classifications (Type: ClinGenTool)

Get variant pathogenicity classifications from ClinGen Evidence Repository. Returns expert-curate…

ClinGen_get_variant_classifications tool specification

Tool Information:

  • Name: ClinGen_get_variant_classifications

  • Type: ClinGenTool

  • Description: Get variant pathogenicity classifications from ClinGen Evidence Repository. Returns expert-curated variant classifications with supporting evidence. Optional filters by gene or variant. Classifications follow ACMG/AMP guidelines with expert review.

Parameters:

  • gene (string) (optional) Optional: Filter by gene symbol

  • variant (string) (optional) Optional: Filter by variant (HGVS notation or protein change)

Example Usage:

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

ClinGen_search_actionability (Type: ClinGenTool)

Search ClinGen clinical actionability across both adult and pediatric contexts by gene. Returns a…

ClinGen_search_actionability tool specification

Tool Information:

  • Name: ClinGen_search_actionability

  • Type: ClinGenTool

  • Description: Search ClinGen clinical actionability across both adult and pediatric contexts by gene. Returns actionability data from both contexts for comparison. Useful for comprehensive actionability assessment of a gene across age groups.

Parameters:

  • gene (string) (required) Gene symbol to search (e.g., BRCA1, MLH1, LDLR)

Example Usage:

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

ClinGen_search_dosage_sensitivity (Type: ClinGenTool)

Search ClinGen dosage sensitivity curations by gene symbol. Returns haploinsufficiency (HI) and t…

ClinGen_search_dosage_sensitivity tool specification

Tool Information:

  • Name: ClinGen_search_dosage_sensitivity

  • Type: ClinGenTool

  • Description: Search ClinGen dosage sensitivity curations by gene symbol. Returns haploinsufficiency (HI) and triplosensitivity (TS) scores (0-3 scale). Score 3 = Sufficient evidence for dosage pathogenicity. Critical for CNV interpretation. Example: MECP2 has HI score of 3.

Parameters:

  • gene (string) (required) Gene symbol to search (e.g., MECP2, PMP22, RAI1)

Example Usage:

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

ClinGen_search_gene_validity (Type: ClinGenTool)

Search ClinGen gene-disease validity curations by gene symbol. Returns classification (Definitive…

ClinGen_search_gene_validity tool specification

Tool Information:

  • Name: ClinGen_search_gene_validity

  • Type: ClinGenTool

  • Description: Search ClinGen gene-disease validity curations by gene symbol. Returns classification (Definitive, Strong, Moderate, Limited, Disputed, Refuted), disease associations, and inheritance patterns. Essential for ACMG variant classification. Example: BRCA1 returns validity scores for hereditary breast/ovarian cancer.

Parameters:

  • gene (string) (required) Gene symbol to search (e.g., BRCA1, TP53, CFTR)

Example Usage:

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