jean — Molecular Biology & Genomics

lookup_variant

Read-only

Look up a variant: ClinVar clinical interpretation, dbSNP records, gnomAD population frequency and gene constraint, CADD deleteriousness, or GWAS/eQTL associations.

Input Schema

TableJSON Schema

Name	Required	Description
`limit`	No	maximum records (1–20).
`query`	Yes	an rsID, HGVS or chrom-pos-ref-alt id, or a command such as "get_variant:variant_id=19-44908822-C-T" or "gene_constraint:gene_symbol=BRCA2". The eQTL Catalogue is the exception and needs a LOCUS, because its summary statistics are indexed by position and its REST API is retired: "eqtl_list_datasets tissue_label=macrophage" to pick a dataset, then "eqtl_associations dataset_id=QTD000021 region=1:109274570-109279000 gene_id=ENSG00000134243".
`_files`	No	The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
`source`	Yes	which authority to ask.
`_subject`	No	The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.

Output Schema

TableJSON Schema

Name	Required	Description
`count`	Yes	how many records came back, which is a result even when it is zero
`records`	Yes	the records the authority returned, in its own field names — wire them into a tool that takes ids, or read them in the transcript
`envelope`	Yes	the authority's whole answer: paging, totals and the query it actually ran
`provenance`	Yes	the authority, the exact endpoints called and when — what makes an answer re-checkable without re-running it

Schema Changelog

Changes observed during successful MCP inspections.

First observedOct 20, 2026

TDQS

B3.4/5.0

Behavior3/5

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

Annotations already declare readOnlyHint=true, destructiveHint=false, and openWorldHint=true, so the safety profile is covered. The description usefully confirms the open-world nature by naming external authorities queried, but adds no detail on rate limits, caching, latency, or what happens when a source has no record.

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?

A single front-loaded sentence with zero filler; every clause names a distinct data source and the payload it yields. It is appropriately sized for a multi-source lookup tool.

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

Completeness4/5

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

With an output schema present, 100% schema coverage, and annotations covering safety, the description supplies the remaining needed context: which authorities back the tool. It could note that source selection changes the required query shape, but the schema already handles that.

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% and the query parameter's schema text already explains rsID/HGVS/chrom-pos-ref-alt syntax plus the eQTL locus exception in detail. The description's source list loosely maps to the source enum but adds no syntax, format, or constraint information beyond the schema, so the 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 gives a specific verb+resource ("Look up a variant") and enumerates exactly what each source returns (ClinVar interpretation, dbSNP records, gnomAD frequency/constraint, CADD, GWAS/eQTL). It stops short of differentiating itself from siblings such as lookup_gene, lookup_clinical, annotate_region, or score_variant_effect, which an agent could easily confuse it with.

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

Usage Guidelines2/5

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

There is no statement of when to use this tool versus the many related lookups in the sibling list, nor any prerequisite or exclusion. The source enumeration implies the kinds of questions it answers, but the agent must infer routing entirely on its own.

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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