io.github.cyanheads/gnomad-genetics-mcp-server

up checked 2026-11-11T12:37:47.189Z

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Publisher-provided description

Ancestry allele frequencies, LoF constraint, variant lists, and coverage from gnomAD, with ClinVar.

Summary by lookupd

Queries gnomAD population allele frequencies, gene constraint, variant lists, coverage, and ClinVar classifications for genetics analysis.

Install

Claude Code, remote (streamable-http)

claude mcp add --transport http gnomad-genetics-mcp-server https://gnomad-genetics.caseyjhand.com/mcp

Claude Code, npm package (stdio)

claude mcp add gnomad-genetics-mcp-server -- npx -y @cyanheads/gnomad-genetics-mcp-server

Claude Code, npm package (stdio)

claude mcp add gnomad-genetics-mcp-server -- npx -y @cyanheads/gnomad-genetics-mcp-server

Codex, remote (streamable-http)

codex mcp add gnomad-genetics-mcp-server --url https://gnomad-genetics.caseyjhand.com/mcp

Codex, npm package (stdio)

codex mcp add gnomad-genetics-mcp-server -- npx -y @cyanheads/gnomad-genetics-mcp-server

Codex, npm package (stdio)

codex mcp add gnomad-genetics-mcp-server -- npx -y @cyanheads/gnomad-genetics-mcp-server

Cursor, remote (streamable-http) → .cursor/mcp.json

{
  "mcpServers": {
    "gnomad-genetics-mcp-server": {
      "url": "https://gnomad-genetics.caseyjhand.com/mcp"
    }
  }
}

Cursor, npm package (stdio) → .cursor/mcp.json

{
  "mcpServers": {
    "gnomad-genetics-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/gnomad-genetics-mcp-server"
      ]
    }
  }
}

Cursor, npm package (stdio) → .cursor/mcp.json

{
  "mcpServers": {
    "gnomad-genetics-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/gnomad-genetics-mcp-server"
      ]
    }
  }
}

Other clients: docs. Or tell your agent: Set up lookupd for me: read https://lookupd.com/agent.md and follow it.

Tools (8 tools)

Publisher-provided text

• gnomad_get_variant Fetch the full gnomAD population record for one or more variants — allele count/number/frequency overall and broken down per genetic-ancestry group, the filteri
• gnomad_get_gene_constraint Fetch gnomAD loss-of-function constraint for a gene — pLI (probability of LoF intolerance; >0.9 intolerant), LOEUF (oe_lof_upper, the headline metric) plus its
• gnomad_list_gene_variants List every gnomAD variant in a gene, transcript, or region with allele frequencies, filtering allele frequencies, zygosity counts, predicted consequences with L
• gnomad_get_coverage Fetch gnomAD sequencing-coverage summary across a gene, transcript, or region — mean and median read depth, plus the mean fraction of samples covered at each de
• gnomad_get_variant_cooccurrence Estimate whether two variants in the same gene sit on different haplotypes (in trans — compound heterozygous) or on the same one (in cis), from gnomAD v2.1 exom
• gnomad_search_clinvar Search ClinVar (NCBI E-utilities) for a gene and return its classified variants — the germline clinical significance with its review status, 0–4 star rating, an
• gnomad_dataframe_query Run a read-only SQL SELECT against a canvas table staged by gnomad_list_gene_variants (table gene_variants) or gnomad_search_clinvar (table clinvar_variants) an
• gnomad_dataframe_describe List the tables staged on a canvas and their columns (name and type) so you can write correct SQL for gnomad_dataframe_query. Use the canvas_id returned by gnom

Details

• Version: 0.6.0
• Transports: streamable-http, stdio
• Uptime (7 days): 100%
• Median latency: 714 ms
• First indexed: 2026-11-01T09:26:05.489Z
• Last seen in registry: 2026-11-04T07:17:28.607Z
• Repository: https://github.com/cyanheads/gnomad-genetics-mcp-server

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