About Pharmacogenomics
Pharmacogenomics is an MCP server published by Julius-Schmidt in the Developer Tools category: mCP server for pharmacogenomics — ClinVar, PharmGKB, gnomAD, OpenTargets, and clinical trials from Claude.
Six months or more without a commit doesn't mean the server is broken, but check the open issues before depending on it in production.
Install
git clone https://github.com/Julius-Schmidt/mcp-pharmacogenomicsThis server has no ConduID identity, so agent calls to it are not receipted. Pin the version you install and review the source before granting it credentials.
Tools (10)
get_dosing_guidelinePharmGKB
Parameters not published.
get_drug_gene_interactionsPharmGKB
Parameters not published.
get_drug_infoPharmGKB
Parameters not published.
get_trial_detailsClinicalTrials.gov
Parameters not published.
get_variant_frequencygnomAD
Parameters not published.
lookup_variant_clinvarClinVar
Parameters not published.
pgx_consultationAll
Parameters not published.
search_clinical_trialsClinicalTrials.gov
Parameters not published.
search_drug_targetsOpen Targets
Parameters not published.
search_gene_variants_clinvarClinVar
Parameters not published.
Ask AI
Ask AI about Pharmacogenomics
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README
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.
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
README copy captured when this server was indexed; it may lag the repository. The original is authoritative.