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MCP live MCP 2026-07-28 http

gnomad-genetics-mcp-server

io.github.cyanheads/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 significance.

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Uptime
100.0%
5 direct probes · 30d
Response
1330ms
last probe
Tools
7
callable
Resources
0
readable
Prompts
1
available
Primary URL
https://gnomad-genetics.caseyjhand.com/mcp
Score: 100/100
Handshake verified by our own probe.
why this score
pass Answers the MCP handshake 50/50
The handshake and the list calls succeeded on the primary URL.
pass Lists tools, resources or prompts 30/30
7 tools, 0 resources, 1 prompts returned.
pass 3 or more catalogue items 10/10
8 items in total; 3 or more earns these points.
pass Describes itself 10/10
167 characters; more than 30 earns these points.

Tools · 7

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 counts, quality flags, tr…

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 lower bound, observed/expected ratios fo…

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, synonymous, other) and/or a …

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 depth threshold (1× through 100×), separat…

gnomad_search_clinvar

Search 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, submission…

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) and return one page of the result. Use the…

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 gnomad_list_gene_variants or gnomad_search_c…

Prompts · 1

gnomad_variant_triage

Guided rare-disease variant-triage workflow over gnomAD: pull the variant population record, weigh it against gene loss-of-function constraint, and — critically — confirm the position is well-covered …

How to use

Add to your Claude Desktop / Cursor / Cline MCP config:

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