ClinPGx (Clinical Pharmacogenomics Database) is a comprehensive resource for\nclinical pharmacogenomics, the successor to PharmGKB. It consolidates data from\nPharmGKB, CPIC, and PharmCAT, providing curated information on how genetic\nvariation affects medication response. Access gene-drug pairs, clinical\nguidelines, allele functions, and drug labels for precision medicine.
\nUse this skill for:
\n| Scenario | \nUse Instead | \n
|---|---|
| Germline/somatic variant pathogenicity or ClinVar review status | \nalterlab-clinvar | \n
| Population allele frequencies for a variant (gnomAD v4) | \nalterlab-gnomad | \n
| Drug–drug interactions or general pharmacology with no genetic component | \nalterlab-drugbank | \n
| FDA adverse-event reports, recalls, or full-text label search | \nalterlab-fda | \n
Only requests is needed. Run the helper script (or any snippet) with an\nephemeral dependency — no venv to manage:
uv run --with requests python scripts/query_clinpgx.py\n# or, inside an existing project venv: uv pip install requests\nBase URL: https://api.clinpgx.org/v1/data/ — the legacy api.pharmgkb.org host was\nturned off on 2026-07-20, so older PharmGKB scripts must switch hostnames (paths are\nunchanged).
PA128, CYP2C9 = PA126), not by gene\nsymbols or rsIDs. To resolve a symbol or rsID, query the collection endpoint\nwith parameters (e.g. GET /v1/data/gene?symbol=CYP2D6,\nGET /v1/data/variant?symbol=rs4244285) and read the accession ID from the\nresponse.{\"status\": \"success\"|\"fail\", \"data\": [...]} — the payload is never a bare\nlist. Read results from response.json()[\"data\"]; on status == \"fail\",\ndata is {\"errors\": [...]} (e.g. \"No results matching criteria\").relatedGenes.symbol\n(the .name form fails), while chemicals/drugs filter on\nrelatedChemicals.name — relatedChemicals.symbol silently returns\nstatus: \"fail\" with zero results. The gene collection takes ?symbol=, the\nchemical collection takes ?name=, and variant accepts ?symbol=/?name=.symbol= parameters.gene, chemical, guidelineAnnotation,\nsummaryAnnotation, variantAnnotation, variant, label, or pathway.\nThere is no /allele resource — use PharmVar (https://www.pharmvar.org/)\nfor star-allele definitions and population frequencies.relatedGenes.symbol for genes, relatedChemicals.name for drugs), or the\n/report/pair/{firstObjId}/{secondObjId}/{resultType} endpoint.For ready-made functions with rate limiting and error handling, see\nscripts/query_clinpgx.py.
references/endpoints-and-capabilities.md.references/query-workflows.md.references/rate-limiting-and-error-handling.md.references/api_reference.md.references/api_reference.md — Complete endpoint listing, request/response\nformats, filter operators, data schemas, rate-limit details, and\ntroubleshooting.references/endpoints-and-capabilities.md — Worked code for all nine\ncapability areas (gene, drug/chemical, gene-drug pair, CPIC guidelines,\nallele/PharmVar, variant, clinical annotations, drug labels, pathways),\nincluding key pharmacogenes and evidence-level definitions.references/query-workflows.md — Five end-to-end workflows (decision support,\ngene panel, drug safety, population pharmacogenomics, literature review) plus\ncommon use cases (pre-emptive testing, medication therapy management, trial\neligibility).references/rate-limiting-and-error-handling.md — Reusable helpers for rate\nlimiting, retries with exponential backoff, and result caching.PharmDOG (formerly DDRx) is ClinPGx's clinical decision support tool for\ninterpreting pharmacogenomic test results. Features: phenoconversion calculator\n(adjusts phenotype for drug-drug interactions affecting CYP2D6), custom genotype\ninput, QR-code report sharing, selectable guidance sources (CPIC, DPWG, FDA), and\nmulti-drug analysis. Access:\nhttps://www.clinpgx.org/pharmacogenomic-decision-support
\nData sources — ClinPGx consolidates PharmGKB (now part of ClinPGx), CPIC,\nPharmCAT, DPWG, and FDA/EMA labels. As of July 2025, all PharmGKB URLs redirect\nto corresponding ClinPGx pages.
\nClinical considerations — Always check evidence strength before clinical\napplication; allele frequencies vary significantly across populations; account\nfor phenoconversion (drug-drug interactions) and multi-gene effects; non-genetic\nfactors (age, organ function) also affect response; not all clinically relevant\nalleles are detected by all assays.
\nData updates / API stability — ClinPGx updates continuously; check\npublication dates and the ClinPGx Blog (https://blog.clinpgx.org/). API endpoints\nare relatively stable but may change during development — pin versions and test\nin development before production.
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