gnomAD MCP Server

Instructions

Implementation Reference

• server.py:8-39 (handler)

  The get_gene_info tool implementation in server.py, which acts as an MCP tool to fetch gene information from gnomAD.

  @mcp.tool()
  def get_gene_info(
      gene_id: Optional[str] = None,
      gene_symbol: Optional[str] = None,
      dataset: str = 'gnomad_r4',
      reference_genome: str = 'GRCh38'
  ) -> dict:
      """
      [gnomAD API] Retrieve gene information (v4 only)
      Args:
          gene_id (str, optional): Ensembl gene ID (e.g. ENSG00000139618)
          gene_symbol (str, optional): Gene symbol (e.g. PCSK9)
      Returns:
          dict: gene info
      Note:
          Not supported in v2/v3. Use search_for_genes instead.
      """
  
      if dataset != 'gnomad_r4':
          raise ValueError("Only v4 is supported for gene info.")
      if reference_genome != 'GRCh38':
          raise ValueError("Only GRCh38 is supported for gene info.")
  
      if not gene_id and not gene_symbol:
          raise ValueError("Either gene_id or gene_symbol must be provided.")
      variables = {
          'dataset': dataset,
          'reference_genome': reference_genome,
          'gene_id': gene_id,
          'gene_symbol': gene_symbol,
      }
      return run_query_with_metadata('gene', variables)