pgx-mcp

An open-source MCP server that gives Claude real-time access to pharmacogenomics databases — turning genetic variant lookups and drug interaction checks from a 45-minute manual workflow into a single conversation.

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Features

• ClinVar: Variant clinical significance and pathogenicity
• PharmGKB: Drug-gene interactions, clinical annotations, CPIC/DPWG dosing guidelines
• gnomAD: Population allele frequencies across ancestries
• Open Targets: Drug-target-disease associations, pharmacogenomics evidence
• ClinicalTrials.gov: Clinical trial search (US and international)

Installation

pip install pgx-mcp

Or with uvx:

uvx pgx-mcp

Claude Desktop Configuration

Add to your Claude Desktop config (~/Library/Application Support/Claude/claude_desktop_config.json):

{
  "mcpServers": {
    "pgx-mcp": {
      "command": "uvx",
      "args": ["pgx-mcp"]
    }
  }
}

For local development:

{
  "mcpServers": {
    "pgx-mcp": {
      "command": "uv",
      "args": ["--directory", "/path/to/mcp-pharmacogenomics", "run", "pgx-mcp"]
    }
  }
}

Available Tools

Tool	Source	Description
lookup_variant_clinvar	ClinVar	Variant clinical significance
search_gene_variants_clinvar	ClinVar	List variants in a gene
get_drug_gene_interactions	PharmGKB	Clinical annotations for drug-gene pairs
get_drug_info	PharmGKB	Drug details and cross-references
get_dosing_guideline	PharmGKB	CPIC/DPWG dosing recommendations
search_drug_targets	Open Targets	Drug mechanisms, indications, PGx evidence
get_variant_frequency	gnomAD	Population allele frequencies
search_clinical_trials	ClinicalTrials.gov	Trial search with filters
get_trial_details	ClinicalTrials.gov	Full trial details
pgx_consultation	All	Comprehensive PGx consultation report

Example Usage

Ask Claude:

"My patient is a CYP2D6 poor metabolizer (*4/*4) and needs pain management. What should I prescribe?"

"What are the CPIC guidelines for clopidogrel and CYP2C19?"

"Are there any recruiting pharmacogenomics clinical trials in Germany?"

Configuration

All settings are optional and configured via environment variables (or a .env file):

Variable	Default	Description
PGX_MCP_NCBI_API_KEY	None	NCBI API key for higher ClinVar rate limits (3/s → 9/s)
PGX_MCP_CACHE_TTL_SECONDS	3600	Cache duration in seconds

Development

git clone https://github.com/Julius-Schmidt/mcp-pharmacogenomics.git
cd mcp-pharmacogenomics
pip install -e ".[dev]"
pytest

Roadmap

• [ ] Demo video/GIF in README
• [ ] EU Clinical Trials Register integration (currently no public API — European trials are covered through ClinicalTrials.gov registrations)
• [ ] PharmVar star-allele nomenclature lookups
• [ ] FDA Pharmacogenomic Biomarkers table integration

License

MIT