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uniprot-mcp

uniprot-mcp

by smaniches
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
Remote

uniprot_resolve_clinvar

Read-only

Resolve a UniProt accession to its gene symbol and query ClinVar for human variant records and classifications, optionally filtering by a protein change such as R175H.

Instructions

Look up ClinVar records for the gene encoded by a UniProt entry. First fetches the human UniProt entry to extract its gene symbol, then queries NCBI eutils ClinVar by gene (and optional protein-change filter, e.g. R175H). Returns submitted human variant records with their classifications, review status, conditions, molecular consequences, and protein changes where present.

ClinVar is a human variation archive. Gene symbols are not species- specific identifiers, so nonhuman or taxonomically unverified entries must not inherit human ClinVar classifications. ClinVar coverage is submission-dependent; a missing record does not establish benignity.

Calls https://eutils.ncbi.nlm.nih.gov — declared in PRIVACY.md.

Input Schema

NameRequiredDescriptionDefault
sizeNoMaximum number of ClinVar records to return; capped at 50.
changeNoOptional HGVS-shorthand protein change to filter to, e.g. 'R175H'. Leave empty to return all ClinVar records for the gene.
accessionYesUniProt accession, e.g. 'P04637' (human TP53) or 'P38398' (human BRCA1). Both reviewed (Swiss-Prot) and unreviewed (TrEMBL) accessions are accepted; case-sensitive.
response_formatNo'markdown' (default) for a human-readable report with a provenance footer, or 'json' for a machine-parseable structured payload with the same data. Any other value is rejected.markdown

Output Schema

NameRequiredDescriptionDefault
resultYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed4 schema fields changedv1.3.0
    • addedInput schema / properties / accession / description
      Added value: +"UniProt accession, e.g. 'P04637' (human TP53) or 'P38398' (human BRCA1). Both reviewed (Swiss-Prot) and unreviewed (TrEMBL) accessions are accepted; case-sensitive."
    • addedInput schema / properties / change / description
      Added value: +"Optional HGVS-shorthand protein change to filter to, e.g. 'R175H'. Leave empty to return all ClinVar records for the gene."
    • addedInput schema / properties / response_format / description
      Added value: +"'markdown' (default) for a human-readable report with a provenance footer, or 'json' for a machine-parseable structured payload with the same data. Any other value is rejected."
    • addedInput schema / properties / size / description
      Added value: +"Maximum number of ClinVar records to return; capped at 50."
  2. First observedv1.1.9

TDQS

A4.1/5.0
Behavior5/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

With annotations already declaring readOnlyHint and openWorldHint, the description still adds substantial context: the two-step fetch, the external NCBI eutils endpoint (declared in PRIVACY.md), submission-dependent coverage, and the interpretive hazard of absent records. It also lists the returned content (classifications, review status, conditions, molecular consequences, protein changes), which goes well past the annotations.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The core purpose and mechanism are front-loaded, and the caveats (human-only, submission-dependent coverage) are each doing real work rather than padding. Slightly long for its payload, but every paragraph earns its place.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

An output schema exists so return-format detail is not required, yet the description still summarizes the returned fields. Combined with the species-scope warning, external-source disclosure, and coverage caveat, an agent has everything needed to call this correctly and interpret gaps.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 100%, so all four parameters (accession, change, size, response_format) are already documented in the schema. The description only restates the optional protein-change filter (e.g. 'R175H'), adding no syntax, format, or edge-case detail beyond what the schema provides. Baseline 3 applies.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description opens with a specific verb+resource ('Look up ClinVar records for the gene encoded by a UniProt entry') and explains the two-step resolution path (UniProt entry → gene symbol → NCBI eutils). It implicitly separates itself from siblings like uniprot_get_variants by being ClinVar-specific, but never names a sibling or states the contrast explicitly.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

It gives clear usage conditions and constraints: human-only scope, nonhuman/taxonomically unverified entries must not inherit these classifications, and a missing record does not establish benignity. What it lacks is an explicit 'use this instead of uniprot_get_variants / uniprot_lookup_variant when…' routing statement.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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