A
licenseC
qualityD
maintenanceEnables AI assistants to query gene annotations, expression, pathways, variants, and more via the MyGene.info API, supporting batch operations and multiple biological data sources.
26
MIT
mcp-myvariant
by pipeworx-io
Click on "Install 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., "@mcp-myvariantshow me the variant dataset statistics"
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.
mcp-myvariant
MyVariant.info MCP.
Part of Pipeworx — an MCP gateway connecting AI agents to 1394+ live data sources.
Tools
Tool | Description |
| Search aggregated human genetic-variant annotations on MyVariant.info. Accepts an rsID ("rs58991260"), an HGVS id ("chr1:g.218631822G>A"), or a fielded query ("dbnsfp.genename:CDK2", "clinvar.rcv.clinical_significance:pathogenic"). Each hit merges dbSNP, ClinVar clinical significance, CADD/dbNSFP deleteriousness scores, and gnomAD population allele frequencies. Returns { total, hits }; hit._id is usually the HGVS id you can pass to the variant tool. |
| Get the full merged annotation for a single human genetic variant by its HGVS id (e.g. "chr7:g.140453136A>T"). Returns annotations aggregated from dbSNP, ClinVar (pathogenicity / clinical significance), CADD and dbNSFP (deleteriousness/conservation scores), and gnomAD (population allele frequencies). Use to look up a known variant and read its pathogenicity and population frequency. |
| Returns MyVariant.info build metadata: total indexed variant count, available annotation sources (dbSNP, ClinVar, CADD, dbNSFP, gnomAD), and their current release/build versions. |
Related MCP server: Unofficial BioThings.io MCP Server
Quick Start
Add to your MCP client (Claude Desktop, Cursor, Windsurf, etc.):
{
"mcpServers": {
"myvariant": {
"url": "https://gateway.pipeworx.io/myvariant/mcp"
}
}
}Or connect to the full Pipeworx gateway for access to all 1394+ data sources:
{
"mcpServers": {
"pipeworx": {
"url": "https://gateway.pipeworx.io/mcp"
}
}
}Using with ask_pipeworx
Instead of calling tools directly, you can ask questions in plain English:
ask_pipeworx({ question: "your question about Myvariant data" })The gateway picks the right tool and fills the arguments automatically.
More
License
MIT
This server cannot be installed
Maintenance
–Maintainers
–Response time
–Release cycle
–Releases (12mo)
Commit activity
Resources
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Looking for Admin?
If you are the server author, to access and configure the admin panel.
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- Alicense-qualityCmaintenanceProvides dataset statistics and release metadata for MyDisease.info, enabling users to query disease-related data through natural language via the Pipeworx gateway.7MIT
- Alicense-qualityCmaintenanceProvides access to dataset statistics and metadata for MyChem.info, a chemical database.10MIT
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