Gencc Tools

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

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

Available Tools

GenCC_get_classifications (Type: GenCCTool)

Get summary statistics of gene-disease validity classifications from GenCC. Returns counts per cl…

GenCC_get_classifications tool specification

Tool Information:

  • Name: GenCC_get_classifications

  • Type: GenCCTool

  • Description: Get summary statistics of gene-disease validity classifications from GenCC. Returns counts per classification level (Definitive, Strong, Moderate, Limited, etc.). Optionally filter by gene_symbol (e.g., ‘GBA’), disease name substring, or submitter organization. Without filters, returns global stats across all 40,000+ curated submissions.

Parameters:

  • operation (string) (optional) Operation type (fixed: get_classifications)

  • gene_symbol (string) (optional) Optional HGNC gene symbol to filter classification stats (e.g., ‘GBA’, ‘BRCA2’)

  • disease (string) (optional) Optional disease name substring to filter classification stats (e.g., ‘Gaucher’, ‘breast cancer’)

  • submitter (string) (optional) Optional filter by submitting organization name (e.g., ‘ClinGen’, ‘Ambry’, ‘Genomics England’)

Example Usage:

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

GenCC_search_disease (Type: GenCCTool)

Find genes with validity evidence for a disease from GenCC (Gene Curation Coalition). Search by d…

GenCC_search_disease tool specification

Tool Information:

  • Name: GenCC_search_disease

  • Type: GenCCTool

  • Description: Find genes with validity evidence for a disease from GenCC (Gene Curation Coalition). Search by disease name or MONDO/OMIM identifier. Returns gene-disease validity classifications from multiple expert curators. Useful for identifying established gene-disease relationships for clinical interpretation.

Parameters:

  • operation (string) (optional) Operation type (fixed: search_disease)

  • disease (string) (optional) Disease name or ID to search (e.g., ‘Marfan syndrome’, ‘MONDO:0007947’, ‘breast cancer’)

  • disease_name (string) (optional) Alias for disease. Disease name or ID to search.

  • classification (string) (optional) Optional filter by classification level (e.g., Definitive, Strong)

Example Usage:

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

GenCC_search_gene (Type: GenCCTool)

Get gene-disease validity classifications for a gene from GenCC (Gene Curation Coalition). Return…

GenCC_search_gene tool specification

Tool Information:

  • Name: GenCC_search_gene

  • Type: GenCCTool

  • Description: Get gene-disease validity classifications for a gene from GenCC (Gene Curation Coalition). Returns curated evidence levels (Definitive, Strong, Moderate, Limited, Disputed, Refuted) from multiple expert panels including ClinGen, Ambry Genetics, Genomics England PanelApp, and Orphanet. Essential for assessing clinical validity of gene-disease associations in genetic testing.

Parameters:

  • operation (string) (optional) Operation type (fixed: search_gene)

  • gene_symbol (string) (required) HGNC gene symbol (e.g., BRCA2, TP53, FBN1, CFTR)

  • classification (string) (optional) Optional filter by classification level (e.g., Definitive, Strong, Moderate, Limited)

Example Usage:

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