Provides access to the gnomAD (Genome Aggregation Database) GraphQL API for querying genetic variant data, gene constraints, population genetics information, and genomic coverage statistics.
Click on "Deploy Server".
Wait a few minutes for the server to deploy. Once ready, it will show a "Started" state.
In the chat, type @ followed by the MCP server name and your instructions, e.g., "@gnomAD MCP Server get gene constraint scores for BRCA1"
That's it! The server will respond to your query, and you can continue using it as needed.
Here is a step-by-step guide with screenshots.
A Model Context Protocol (MCP) server that provides access to the gnomAD (Genome Aggregation Database) GraphQL API. This server enables AI assistants to query genetic variant data, gene constraints, and population genetics information from gnomAD.
🧬 Gene Information: Search 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: Get 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
Related MCP server: Open Targets Platform MCP
Node.js 18 or higher
npm or yarn
git clone https://github.com/yourusername/gnomad-mcp-server.git
cd gnomad-mcp-server
npm install
npm run buildAdd 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"]
}
}
}npx @modelcontextprotocol/cli gnomad-mcp-serversearchSearch 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"
}get_geneGet 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"
}get_variantGet detailed information about a specific variant.
Parameters:
variant_id (required): Variant ID in format: chr-pos-ref-alt (e
Get coverage information for a gene
Inputs: gene_id, gene_symbol, dataset, reference_genome.
Get detailed information about a gene including constraint scores
Inputs: gene_id, gene_symbol, reference_genome.
Get mitochondrial variants
Inputs: dataset.
Get variants in a specific genomic region
Inputs: chrom (required), start (required), stop (required), dataset, +1 more.
Get structural variants in a genomic region
Inputs: chrom (required), start (required), stop (required), dataset, +1 more.
Get information about a specific transcript
Inputs: transcript_id (required), reference_genome.
Get detailed information about a specific variant
Inputs: variant_id (required), dataset.
Get all variants in a specific gene
Inputs: gene_id, gene_symbol, dataset, reference_genome.
Search for genes, variants, or regions in gnomAD
Inputs: query (required), reference_genome, dataset.
Recent tool additions, removals, and schema changes observed during successful MCP inspections.
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Scored across 9 tools
Most tools have distinct purposes targeting specific genomic entities (e.g., genes, variants, regions), but some overlap exists between 'get_variants_in_gene' and 'get_region_variants' which could cause confusion when querying gene regions. The descriptions help clarify, but the boundaries aren't perfectly clear.
All tool names follow a consistent 'verb_noun' pattern with 'get_' or 'search' prefixes, using snake_case uniformly. This predictability makes it easy for agents to understand and select tools without naming confusion.
With 9 tools, this server is well-scoped for querying genomic data from gnomAD. Each tool serves a specific purpose (e.g., coverage, genes, variants), and the count aligns with the domain's complexity without being overwhelming or insufficient.
The toolset covers core query operations for genes, variants, transcripts, and regions, with a general search function. Minor gaps exist, such as no explicit tools for filtering or aggregating results, but agents can work around this using the provided tools for most workflows.
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