Koskamo

GeneFoundry MCP

GeneFoundry is a hosted MCP gateway that federates 22 biomedical data sources, including gnomAD, ClinVar, and HPO, into a single endpoint. It provides namespaced tools for variant interpretation, gene lookup, and phenotype association, allowing AI agents to query biomedical databases without managing multiple connections.

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Endpoint and access

OAuth sign-in: the first time you connect, your client opens the vendor's own authorization prompt in a browser.

GeneFoundry MCP logo, by Bernt PoppCommunity listingStreamable HTTPOAuth sign-inEndpoint checked 2026-11-06Published by Bernt Popp
MCP endpoint (Streamable HTTP)
https://genefoundry.org/mcp
Vendor documentation

Checks and signals

Each line is separate evidence, not a trust score.

  • Passed Endpoint answered the live check ·
  • Availability 1 of 1 checks passed in 30 days

What you can do with it

  • Look up gene constraint metrics and population frequencies in gnomAD
  • Retrieve variant classifications and review status from ClinVar
  • Find genes associated with specific phenotypes using HPO terms
  • Search biomedical literature for entity annotations via PubTator3

Source and maintenance

Community listingRegistry 0.10.10
mcp-registry: io.github.berntpopp/genefoundry@0.10.10Source repositoryProject website
Maintenance checked

Tools

Reported by the attributed source; not independently observed by Koskamo.

No tool definitions available.

90-day uptime

A lightweight connection check about every six hours, sampled on hosts with many listings. It shows the server answered, not that its tools work.

Too few checks for a percentage yet (1 of 1 answered).

  1. 2026-11-06: 1 of 1 checks answered

30-day availability

Aggregated from read-only remote checks; this is not a tool-execution or security guarantee.

Successful checks
1 of 1 (100%)
Average latency
314 ms
95th percentile latency
314 ms

Maintenance history

Public check and source-refresh events. Editorial and ownership records remain private.

  • · probe · passed · 314 ms · metadata changed · refuses unauthenticated initialize (HTTP 401)

Connect from your client

Each snippet registers the same endpoint; pick the client you use.

This server is operated by the named third party. Listing and endpoint checks are not an endorsement or a security audit. Review the operator's permissions, terms, and data handling before connecting. How listings are checked and corrected.

Claude Code

Run this once in a terminal. It registers the remote server. Use --scope project to write .mcp.json for the repo.
Claude Code configuration
claude mcp add --transport http genefoundry-mcp https://genefoundry.org/mcp

Codex

Run this once. Codex stores MCP servers in ~/.codex/config.toml (or .codex/config.toml in a trusted project).
Codex configuration
codex mcp add genefoundry-mcp --url https://genefoundry.org/mcp

Cursor

Merge this server into .cursor/mcp.json in your project, then enable genefoundry-mcp in your MCP settings.
Cursor configuration
{
  "mcpServers": {
    "genefoundry-mcp": {
      "url": "https://genefoundry.org/mcp"
    }
  }
}

Cline

Merge this into cline_mcp_settings.json (Cline → MCP Servers → Configure).
Cline configuration
{
  "mcpServers": {
    "genefoundry-mcp": {
      "type": "streamableHttp",
      "url": "https://genefoundry.org/mcp",
      "disabled": false
    }
  }
}

VS Code

Merge this server into .vscode/mcp.json. Use MCP: List Servers to start genefoundry-mcp and inspect its tools.
VS Code configuration
{
  "servers": {
    "genefoundry-mcp": {
      "type": "http",
      "url": "https://genefoundry.org/mcp"
    }
  }
}

Gemini CLI

Run this once. It writes .gemini/settings.json in the current project; pass --scope user for ~/.gemini/settings.json.
Gemini CLI configuration
gemini mcp add --transport http genefoundry-mcp https://genefoundry.org/mcp

Claude Desktop

Open Claude Settings > Connectors > Add custom connector, enter this server URL and enable it for the conversation. This is a manual remote-connector handoff, not a desktop JSON configuration.
Claude Desktop configuration
https://genefoundry.org/mcp

Windsurf

Merge this into ~/.codeium/windsurf/mcp_config.json, then refresh MCP in Cascade. Windsurf remote servers use serverUrl, not url.
Windsurf configuration
{
  "mcpServers": {
    "genefoundry-mcp": {
      "serverUrl": "https://genefoundry.org/mcp"
    }
  }
}

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