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allele-registry-mcp-server

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allele-registry-mcp-server

MCP server wrapping the ClinGen Allele Registry (https://reg.clinicalgenome.org) — canonical allele identity for genetic variants. Resolves any HGVS / dbSNP / ClinVar / gnomAD reference to a stable ClinGen Allele Registry ID (CA#) and its cross-references, so a variant keeps one identity across genome builds and transcript versions.

Cloudflare Worker built on McpAgent (agents/mcp), REST + Code Mode via @bio-mcp/shared. Read endpoints only; no auth. Dev port 8905.

Why it exists

tmVar3's ~550 GB of chromosome-sharded SQLite exists to turn an HGVS string into a canonical allele. The Allele Registry does the same thing over a free public REST API — so we wrap the API instead of re-hosting the index. Every allele_registry_execute result carries a verifiable _meta.citation, and a CA# is a content-addressed allele identifier that drops straight into the fleet's attestation story.

Related MCP server: clingen-link

Tools (Code Mode)

  • allele_registry_search — discover endpoints in the curated catalog

  • allele_registry_execute — run JS against the API in a V8 isolate (api.get/api.post, searchSpec, no network/keys); results carry _meta.citation

  • allele_registry_get_schema / allele_registry_query_data — inspect + SQL-query staged results

Develop

./scripts/dev-servers.sh allele-registry   # wrangler dev on :8905
pnpm --filter allele-registry-mcp-server run test

Upstream

  • Base: https://reg.clinicalgenome.org — GET /allele?hgvs=…, GET /allele/{CAid}, resolution by dbSNP / ClinVar / gnomAD / MyVariantInfo.

  • Source descriptor: ClinGen Allele Registry (ClinGen / NIH, freely available).

This server cannot be deployed

One endpoint for every MCP toolRayrun runs every MCP server behind one URL and holds the credentials. Each call is decided per client, tool, and argument, then recorded.ray.runAd

Maintenance

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Resources

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