gnomad-genetics-mcp-server

Human population genetics over gnomAD — variant allele frequencies by ancestry, gene loss-of-function constraint, and per-gene variant lists with ClinVar…

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What it can do

  • 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, homozygote and hemizygote count
  • 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; <0.6 intolerant in v4
  • Gnomad List Gene Variants: List every gnomAD variant in a gene, transcript, or region with allele frequencies and predicted consequences, optionally filtered to one consequence class (lof, missense, s

What data it sees

Do you need an account

No: the server works without sign-in

Human population genetics over gnomAD — variant allele frequencies by ancestry, gene loss-of-function constraint, and per-gene variant lists with ClinVar significance.

How to connect

How to connect gnomad-genetics-mcp-server to Claude

The server address to paste into Claude settings:

https://gnomad-genetics-mcp-server--cyanheads.run.tools

  1. Open Claude (claude.ai or the desktop app).
  2. Go to Settings → Connectors.
  3. Click Add custom connector.
  4. Paste the server address copied below into Remote MCP server URL and click Add.
  5. In a chat, click + → Connectors and switch the new connector on.

Custom connectors are available on Free, Pro, Max, Team and Enterprise plans (Free is limited to one). On Team and Enterprise an organization Owner adds the connector first under Organization settings → Connectors.

Authorization

After you click Add, a sign-in window for the service opens. Sign in with your own account and approve access. Claude never sees your password.

How to connect gnomad-genetics-mcp-server to ChatGPT

The server address to paste into ChatGPT settings:

https://gnomad-genetics-mcp-server--cyanheads.run.tools

  1. Open ChatGPT in a browser (chatgpt.com). A Plus, Pro, Business, Enterprise or Edu plan is required.
  2. Turn on developer mode once: Settings → Apps → Advanced settings → Developer mode.
  3. Open Settings → Connectors and click Create.
  4. Fill in the form: Name (anything), Description (one line about what the service does), MCP server URL (copy it below).
  5. Under Authentication choose OAuth if the service requires sign-in, otherwise None. Click Create.
  6. In a new chat open + → Apps/Connectors and enable the connector.

OpenAI has renamed this section before (Connectors → Apps/Plugins). If the label differs, search settings for "developer mode". On Business/Enterprise workspaces an admin must allow custom connectors first.

Authorization

On first use ChatGPT opens the service's sign-in window. Sign in and approve access.

How to connect gnomad-genetics-mcp-server to Cursor

The server address to paste into Cursor settings:

https://gnomad-genetics-mcp-server--cyanheads.run.tools

Fastest: click Open in Cursor below and confirm the prompt.

Manually:

  1. In Cursor open Settings → Cursor Settings → MCP and click Add new global MCP server.
  2. Paste the JSON copied below into ~/.cursor/mcp.json (per project: .cursor/mcp.json in the repo root).
  3. Save the file. The server appears in the MCP list; authorize it there if asked.

Authorization

If the service needs sign-in, an authorize button appears next to the server in the MCP list.

Server tool list (7)

Raw names from tools/list. Only developers need these.

gnomad_get_variantFetch the full gnomAD population record for one or more variants — allele count/number/frequency overall and broken down per genetic-ancestry group, homozygote and hemizygote counts, quality flags, transcript consequence, in-silico predictor scores, and joined ClinVar clinical significance. The "how common, is it benign" answer in one call. Accepts a batch of up to 25 IDs (chrom-pos-ref-alt or rsID) with per-item partial success: a malformed or absent ID lands in failed[] without failing the others. An empty found[] for a well-formed ID means the variant is not in the chosen dataset — pair with gnomad_get_coverage to confirm the position is callable before concluding true absence.
gnomad_get_gene_constraintFetch gnomAD loss-of-function constraint for a gene — pLI (probability of LoF intolerance; >0.9 intolerant), LOEUF (oe_lof_upper, the headline metric; <0.6 intolerant in v4, <0.35 in v2) plus its lower bound, observed/expected ratios for LoF, missense, and synonymous variation, and the three Z-scores. This is the orthogonal axis to allele frequency: a loss-of-function variant matters far more in a gene intolerant to being broken. Accepts an HGNC symbol (PCSK9) or an Ensembl gene ID (ENSG00000169174). Many genes have null constraint (sparse upstream) — null fields are reported as such, never fabricated. v4 constraint is flagged beta by the gnomAD team; constraint_flags surfaces any caveats. Echoes the effective dataset and reference build.
gnomad_list_gene_variantsList every gnomAD variant in a gene, transcript, or region with allele frequencies and predicted consequences, optionally filtered to one consequence class (lof, missense, synonymous, other) and/or a maximum allele frequency. The full result is staged on a DataCanvas table named gene_variants and an inline preview is returned alongside canvas_id and table_name — run gnomad_dataframe_query against them to rank by AF, count by consequence, or group across the complete set rather than the preview. When the canvas is disabled (CANVAS_PROVIDER_TYPE != duckdb) the tool returns a capped inline preview with spilled=false and canvas_id empty; the SQL path is then unavailable. Supply exactly one of gene, transcript_id, or region. Echoes the effective dataset and build.
gnomad_get_coverageFetch gnomAD sequencing-coverage summary across a gene, transcript, or region — mean and median read depth, plus the mean fraction of samples covered at each depth threshold (1× through 100×), separated by exome and genome track. Use this to disambiguate a true absent variant from an uncallable position: a variant missing from a well-covered region is informative, while one missing from a poorly-covered region is not. Supply exactly one of gene, transcript_id, or region. The optional coverage_source narrows to one track; by default both available tracks are returned. Echoes the effective dataset and build.
gnomad_search_clinvarSearch ClinVar (NCBI E-utilities) for a gene and return its classified variants — clinical significance, review status with a 0–4 star rating, associated conditions, molecular consequences, and submission counts — turning the variant-level significance gnomAD joins into a gene-panel curation view. Optionally filter by clinical_significance (e.g. pathogenic) and a minimum star rating. The full set is staged on a DataCanvas table named clinvar_variants with an inline preview; query it with gnomad_dataframe_query to rank or count across the complete set. Keyless, but honors NCBI_API_KEY for a higher rate limit. When the canvas is disabled the tool returns a capped inline preview with spilled=false. Credit: ClinVar, NCBI.
gnomad_dataframe_queryRun 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). Use the canvas_id and table_name those tools returned to rank by allele frequency, group by consequence class, count loss-of-function variants, or filter the full set the inline preview only sampled. SELECT statements only — writes, DDL, and file/HTTP table functions are rejected by the canvas gate. Call gnomad_dataframe_describe first to discover staged table and column names.
gnomad_dataframe_describeList 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 gnomad_list_gene_variants or gnomad_search_clinvar. Returns one entry per table with its row count and column schema.