Gnomad MCP Server

🚀 gnomAD MCP Server

A Model Context Protocol (MCP) server that provides access to the gnomAD (Genome Aggregation Database) GraphQL API. This server allows AI assistants to query genetic variant data, gene constraints, and population genetics information from gnomAD.

🚀 Quick Start

The gnomAD MCP Server is a powerful tool for querying genetic data from the gnomAD database. It offers a wide range of features to help you access and analyze genetic information.

✨ Features

• 🧬 Gene Information: Search for and retrieve detailed gene data, including constraint scores.
• 🔬 Variant Analysis: Query specific variants and their population frequencies.
• 📊 Population Genetics: Access allele frequencies across different populations.
• 🧮 Constraint Scores: Obtain pLI, LOEUF, and other constraint metrics.
• 🔍 Region Queries: Find variants within specific genomic regions.
• 🧪 Transcript Data: Access transcript - specific information and constraints.
• 📈 Coverage Data: Retrieve sequencing coverage statistics.
• 🔄 Structural Variants: Query structural variant data.
• 🧲 Mitochondrial Variants: Access mitochondrial genome variants.

📦 Installation

Prerequisites

• Node.js 18 or higher
• npm or yarn

Install from source

git clone https://github.com/yourusername/gnomad-mcp-server.git
cd gnomad-mcp-server
npm install
npm run build

📚 Documentation

Configuration

Claude Desktop

Add the following to your Claude Desktop configuration file:

macOS: ~/Library/Application Support/Claude/claude_desktop_config.json Windows: %APPDATA%\Claude\claude_desktop_config.json

{
  "mcpServers": {
    "gnomad": {
      "command": "node",
      "args": ["/path/to/gnomad-mcp-server/dist/index.js"]
    }
  }
}

With MCP CLI

npx @modelcontextprotocol/cli gnomad-mcp-server

Available Tools

1. search

Search for genes, variants, or regions in gnomAD.

Parameters:

• query (required): Search query (gene symbol, gene ID, variant ID, rsID)
• reference_genome: Reference genome (GRCh37 or GRCh38, default: GRCh38)
• dataset: Dataset ID (gnomad_r4, gnomad_r3, gnomad_r2_1, etc., default: gnomad_r4)

Example:

{
  "query": "TP53",
  "reference_genome": "GRCh38"
}

2. get_gene

Get detailed information about a gene including constraint scores.

Parameters:

• gene_id: Ensembl gene ID (e.g., ENSG00000141510)
• gene_symbol: Gene symbol (e.g., TP53)
• reference_genome: Reference genome (default: GRCh38)

Example:

{
  "gene_symbol": "BRCA1",
  "reference_genome": "GRCh38"
}

3. get_variant

Get detailed information about a specific variant.

Parameters:

• variant_id (required): Variant ID in format: chr - pos - ref - alt