Panelapp Tools

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

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

Available Tools

PanelApp_get_panel (Type: BaseRESTTool)

Get the full gene list and details for a specific Genomics England PanelApp gene panel by panel I…

PanelApp_get_panel tool specification

Tool Information:

  • Name: PanelApp_get_panel

  • Type: BaseRESTTool

  • Description: Get the full gene list and details for a specific Genomics England PanelApp gene panel by panel ID. Returns all genes in the panel with their confidence levels (3=green/diagnostic, 2=amber/borderline, 1=red/limited), mode of inheritance, mode of pathogenicity, penetrance, phenotypes, publications, and evidence sources. This is the definitive resource for which genes are included in clinical genetic testing panels used by the NHS. Use PanelApp_search_panels to find panel IDs.

Parameters:

  • panel_id (integer) (required) PanelApp panel ID (e.g., 504 for ‘Inherited polyposis and early onset colorectal cancer’). Find IDs using PanelApp_search_panels.

Example Usage:

query = {
    "name": "PanelApp_get_panel",
    "arguments": {
        "panel_id": 10
    }
}
result = tu.run(query)

PanelApp_search_genes (Type: BaseRESTTool)

Search for a gene across all Genomics England PanelApp panels to find which clinical testing pane…

PanelApp_search_genes tool specification

Tool Information:

  • Name: PanelApp_search_genes

  • Type: BaseRESTTool

  • Description: Search for a gene across all Genomics England PanelApp panels to find which clinical testing panels include it. Returns all panels containing the gene, along with the confidence level, mode of inheritance, and associated phenotypes for each panel. This is invaluable for understanding the clinical significance of a gene - if it appears in multiple high-confidence panels, it has strong clinical evidence. Use gene symbols (e.g., ‘TP53’, ‘BRCA1’).

Parameters:

  • gene_symbol (string) (required) Gene symbol to search across all panels (e.g., ‘TP53’, ‘BRCA1’, ‘EGFR’, ‘MLH1’)

Example Usage:

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

PanelApp_search_panels (Type: BaseRESTTool)

Search Genomics England PanelApp for gene panels used in clinical genetic testing. PanelApp is th…

PanelApp_search_panels tool specification

Tool Information:

  • Name: PanelApp_search_panels

  • Type: BaseRESTTool

  • Description: Search Genomics England PanelApp for gene panels used in clinical genetic testing. PanelApp is the authoritative source for curated gene panels used by the NHS and global genomic medicine services. Returns panel IDs, names, disease groups, status, version, and gene count statistics. Use this to find relevant gene panels for a disease area, then use PanelApp_get_panel to get the full gene list. Panels contain genes with confidence levels (green=3 for diagnostic grade, amber=2 for borderline, red=1 for limited evidence).

Parameters:

  • search (string) (required) Search query for panel name or disease (e.g., ‘breast cancer’, ‘epilepsy’, ‘hearing loss’, ‘intellectual disability’)

Example Usage:

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