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 a gene across Genomics England PanelApp panels with case-normalized symbols and page metad…

PanelApp_search_genes tool specification

Tool Information:

  • Name: PanelApp_search_genes

  • Type: BaseRESTTool

  • Description: Search a gene across Genomics England PanelApp panels with case-normalized symbols and page metadata. Lowercase symbols are converted to uppercase because PanelApp otherwise returns a silent empty success. Continue with metadata.next_page if metadata.has_more becomes true.

Parameters:

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

  • page (integer) (optional) One-based PanelApp response page. Continue with metadata.next_page when available.

Example Usage:

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

PanelApp_search_panels (Type: PanelAppSearchTool)#

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: PanelAppSearchTool

  • 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). Matches only against panel-level metadata (name/disease group), not gene-level phenotype text, so some disease names (e.g. ‘haemophilia’) won’t match any panel directly even though a relevant panel exists – if a disease-name search returns nothing, try PanelApp_search_genes with the causal gene symbol instead (e.g. F8, F9 for haemophilia).

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)