GWAS-MCP

A single MCP server that bundles gene, variant, protein-interaction, structure, pathway, and drug-target lookups across 14 public biological databases, so Claude can run a variant-to-target research workflow without wiring up each source separately.

   
Type MCP server
Supplier ZaEyAsa
Availability GA — PyPI gwas-mcp v1.0.2 (2026-02-09)
Pricing Free / OSS (MIT) — wraps public database APIs; no key documented
Capabilities Read-only — queries public REST APIs (UniProt, Ensembl, NCBI, ClinVar, GWAS Catalog, GTEx, STRING, InterPro, AlphaFold, PDB, KEGG, Open Targets, PharmGKB, OMIM)
Verified works · 2026-07-20
Security caution · 2026-07-20 — PyPI gwas-mcp 1.0.2 MIT resolves but canonical owner is muslus/gwas-mcp, single-maintainer/stale

How to install

Requires Python 3.10+. Install the package first, then register the stdio server.

  • Install the package (both clients need this): 
    pip install gwas-mcp
  • Claude Code — direct MCP add (stdio; Claude Code launches python -m gwas_mcp.server itself — do not run it separately): 
    claude mcp add --transport stdio gwas-bioinformatics -- python -m gwas_mcp.server
  • Claude Desktop — add to claude_desktop_config.json (locations: macOS ~/Library/Application Support/Claude/claude_desktop_config.json, Linux ~/.config/Claude/claude_desktop_config.json, Windows %APPDATA%\Claude\claude_desktop_config.json), then restart Claude Desktop: 
    {
  "mcpServers": {
    "gwas-bioinformatics": {
      "command": "python",
      "args": ["-m", "gwas_mcp.server"]
    }
  }
}

No API key is documented for any of the wrapped databases. Responses are cached for one hour.

What it does

30+ tools grouped into six areas:

  • Protein & gene — search_uniprot, get_protein_details, search_ncbi_gene, search_ensembl_gene, get_variant_info, get_interpro_domains
  • Clinical & variants — search_clinvar, get_clinvar_variant, annotate_snps, query_gwas_catalog, get_eqtl_data
  • Protein interactions — get_protein_interactions, get_interaction_network, get_functional_enrichment
  • Structure & pathways — get_alphafold_structure, search_alphafold, search_pdb_structures, get_pdb_structure, search_kegg_pathway, get_kegg_pathway, get_gene_pathways
  • Drug discovery — get_drug_targets, get_disease_associations, search_open_targets, search_pharmgkb, get_drug_gene_interactions
  • Genetic diseases — search_omim, get_gene_diseases

Primary use cases: GWAS variant annotation, variant-to-gene-to-target prioritization, gene/disease association lookup, cross-database evidence gathering.

Notes

A convenience aggregator: each underlying database is also catalogued here as its own dedicated entry (Ensembl, ClinVar, GWAS Catalog, STRING, AlphaFold, KEGG, Open Targets, GtoPdb, UniProt). Use GWAS-MCP when you want one install covering the whole variant-to-target chain; use the individual entries when you need a single source’s full feature surface. Read-only; smart caching (1-hour TTL) reduces repeated API calls. OMIM coverage is via public search endpoints, not the licensed OMIM API.

Sources

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