gnomAD MCP Server

@koido

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其他

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stdio

作者

koido

提交者

Masaru Koido

关于 gnomAD MCP Server

This MCP server provides a programmatic interface to the Genome Aggregation Database (gnomAD) API, supporting multiple API versions (v2.1.1, v3.1.2, v4.1.0).

#bioinformatics#gnomad#mcp-server

gnomAD MCP Server 配置

使用下面的配置,将此服务器添加到你的 MCP 客户端。

{
  "mcpServers": {
    "gnomad": {
      "command": "uv",
      "args": [
        "--directory",
        "where you cloned the repo",
        "run",
        "server.py"
      ],
      "env": {}
    }
  }
}

gnomAD MCP Server 工具

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工具是从 README 中自动提取的。维护者可以在 ## Tools 标题下列出工具,即可填充这部分内容。

概览

What is gnomAD MCP Server?

The gnomAD MCP Server provides a programmatic interface to the Genome Aggregation Database (gnomAD) API, supporting multiple API versions (v2.1.1, v3.1.2, v4.1.0). It abstracts version-specific field and schema differences, exposing a unified API for downstream tools and users.

How to use gnomAD MCP Server?

Install dependencies with uv sync, activate the virtual environment with . .venv/bin/activate, test the server with uv --directory ./ run mcp dev server.py, and add it to your MCP client configuration (Claude, Cursor, etc.) using the JSON format shown in the README.

Key features of gnomAD MCP Server

Supports three gnomAD API versions (v2, v3, v4)
Queries include variant, gene, region, ClinVar, STR, and more
Uses QueryTemplateEngine for version-specific GraphQL queries
Unified API abstracts version-specific field differences
Python >= 3.13 required; uses FastMCP, aiohttp, httpx

Use cases of gnomAD MCP Server

Retrieve variant metadata and population frequency data by variantId
Search for genes by symbol or name across gnomAD versions
Retrieve ClinVar variant data and clinical significance
Obtain gene metadata and constraint metrics (v4 only)
Retrieve structural variant, copy number variant, and repeat data

常见问题

What gnomAD API versions are supported?

v2.1.1 (gnomad_r2), v3.1.2 (gnomad_r3), and v4.1.0 (gnomad_r4) are supported, with varying query availability per version.

What queries are available for gnomAD MCP Server?

Queries include get_variant_info, get_clinvar_variant_info, search_for_variants, search_for_genes, and more; v4 supports additional queries like get_gene_info, get_region_info, and get_str_info.

What are the runtime requirements?

Python >= 3.13 with dependencies aiohttp >= 3.11.18, fastmcp >= 2.2.1, gql >= 3.5.2, httpx >= 0.28.1, mcp[cli] >= 1.6.0, nest-asyncio >= 1.6.0, and testing packages.

How is gnomAD MCP Server configured for use with clients?

Add to MCP client config (Claude, Cursor, etc.) with command `"uv"`, args `["--directory", "repo_path", "run", "server.py"]`, and an empty `env` object.

What is the current status of gnomAD MCP Server?

Under active development; APIs and features may change without notice.

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