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uniprot_resolve_clinvar

Read-only

Retrieves clinical significance classifications from ClinVar for variants in a UniProt gene, with optional protein-change filter. Combines UniProt variant lookup with population-level clinical data.

Instructions

Look up ClinVar records for the gene encoded by a UniProt entry. First fetches the entry to extract the canonical gene symbol, then queries NCBI eutils ClinVar by gene (and optional protein-change filter, e.g. R175H). Returns clinical-significance classification, review status, condition list (trait_set), molecular consequence, and the protein-change list per record.

Critical for clinical workflows — UniProt's natural-variant annotations stop at literature-described variants. ClinVar carries every variant submitted by clinical labs, with curated significance classifications. Combine uniprot_lookup_variant (UniProt side) with uniprot_resolve_clinvar (population side) for a full variant-effect picture.

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

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
accessionYes
changeNo
sizeNo
response_formatNomarkdown

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior4/5

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

Annotations declare readOnlyHint=true and openWorldHint=true. The description adds that the tool calls https://eutils.ncbi.nlm.nih.gov and references privacy documentation. It also describes the two-step process (fetch entry then query ClinVar), which goes beyond the annotations. No contradiction with annotations.

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

Conciseness5/5

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

The description is well-structured with clear paragraphs: action, process, context, privacy. Every sentence adds value. No unnecessary words. The front-loaded first sentence immediately conveys the tool's purpose.

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?

Given the tool's complexity (two-step process, external API call), annotations (readOnly, openWorld), and the existence of an output schema (so return values are documented elsewhere), the description is complete. It explains the data returned and the external dependency, satisfying the need for context.

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?

The input schema has 0% description coverage, so the description must compensate. It explains 'accession' is the UniProt accession, 'change' is an optional protein-change filter (e.g., R175H), 'size' defaults to 10, and 'response_format' defaults to markdown. However, for size and response_format, the description adds little beyond schema defaults. The explanation for 'change' is helpful, but overall coverage is incomplete.

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

Purpose5/5

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

The description clearly states the tool looks up ClinVar records for a gene encoded by a UniProt entry. It details the process (extract gene symbol, query NCBI ClinVar) and specifies return data (clinical significance, review status, condition list, etc.). It distinguishes from sibling tool uniprot_lookup_variant by contrasting UniProt-side vs population-side variant information.

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?

The description explains the tool is critical for clinical workflows because ClinVar contains every variant submitted by clinical labs, unlike UniProt's literature-described variants. It explicitly recommends combining with uniprot_lookup_variant for a full picture. While it doesn't state when not to use, it provides clear context and a usage scenario.

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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