plant-genomics-mcp

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Known Variants

locus_variants

Read-onlyIdempotent

List germline SNPs and indels overlapping a locus by resolving gene coordinates via Ensembl. Returns alleles, consequence class, clinical significance, and true variant count when truncated.

Instructions

List natural (germline) variants overlapping a locus's genomic span via Ensembl (rest.ensembl.org; free, no key). Resolves the locus → gene coordinates, then returns EVA/dbSNP-sourced SNPs and indels with id, source, consequence class, alleles, and clinical significance. variant_count is the true overlap total; the variant list is capped for payload size with truncated flagged. Opens the variation axis (distinct from get_sequence / ensembl_region_query). Works for all 12 organisms. Defaults to arabidopsis_thaliana; pass organism= for other species.

Input Schema

TableJSON Schema

Name	Required	Description	Default
`limit`	No	Max variant rows to return. 'variant_count' always reports the true pre-cap total and 'truncated' says whether the cap bit.
`locus`	Yes	e.g. AT1G01010 (Arabidopsis), Os01g0100100 (rice RAP-DB)
`organism`	No	Plant organism — accepts canonical slug (arabidopsis_thaliana), scientific or common name, or NCBI taxid	arabidopsis_thaliana

Output Schema

TableJSON Schema

Name	Required	Description
`locus`	Yes
`total`	Yes	How many variants overlapping the gene exist upstream for this query, all pages (pre-cap) (#123)
`region`	Yes	Queried gene span, e.g. '1:33666-37840'
`gene_end`	No	Gene span end (1-based)
`organism`	Yes	Resolved Ensembl species slug
`returned`	Yes	Rows in this payload (#123)
`variants`	No	Per-variant {id, source, consequence_type, alleles, …}
`truncated`	Yes	True if the variant list was capped
`gene_start`	No	Gene span start (1-based)
`variant_count`	Yes	Total overlapping variants (pre-cap)

Schema Changelog

Changes observed during successful MCP inspections.

Changed3 schema fields changedv1.22.0Sep 24, 2026

addedOutput schema / properties / returned

Added value: +{
+  "description": "Rows in this payload (#123)",
+  "title": "Returned",
+  "type": "integer"
+}

addedOutput schema / properties / total

Added value: +{
+  "description": "How many variants overlapping the gene exist upstream for this query, all pages (pre-cap) (#123)",
+  "title": "Total",
+  "type": "integer"
+}

changedOutput schema / required

Previous value: -[
-  "locus",
-  "organism",
-  "region",
-  "variant_count",
-  "truncated"
-]New value: +[
+  "total",
+  "returned",
+  "locus",
+  "organism",
+  "region",
+  "variant_count",
+  "truncated"
+]

Changed1 schema field changedv1.20.0Jul 28, 2026

addedInput schema / properties / limit

Added value: +{
+  "default": 500,
+  "description": "Max variant rows to return. 'variant_count' always reports the true pre-cap total and 'truncated' says whether the cap bit.",
+  "maximum": 500,
+  "minimum": 1,
+  "type": "integer"
+}

Addedv1.18.2Jul 24, 2026

TDQS

A4.5/5.0

Behavior5/5

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

Annotations already indicate readOnly, openWorld, idempotent, and non-destructive behavior, and the description adds meaningful context beyond that: the variant list is capped for payload size, variant_count reports the true pre-cap total, truncated flags the cap, and the data source is EVA/dbSNP via a free keyless Ensembl endpoint. 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 dense but every sentence earns its place: source, scope, resolution behavior, output fields, payload cap, sibling distinction, organism coverage, and default behavior. The most important filtering behavior is front-loaded.

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 rich annotations, a 100%-documented input schema, and an output schema, the description covers the remaining practical concerns: data provenance, cap/truncation semantics, organism defaults, and the distinction from related region/sequence tools. Nothing critical for correct invocation is missing.

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 the schema already documents locus, limit, and organism well. The description only restates the organism default and adds that all 12 organisms are supported, which is marginal value beyond the structured field descriptions.

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 states a specific verb and resource: 'List natural (germline) variants overlapping a locus's genomic span via Ensembl'. It also names the variation axis and distinguishes the tool from get_sequence and ensembl_region_query, so an agent can differentiate it from at least its closest siblings.

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 gives clear operational guidance: it works for all 12 organisms, defaults to arabidopsis_thaliana, and tells the caller to pass organism= for other species. It names related tools it is 'distinct from', though it does not enumerate all when-not-to-use conditions relative to the broader sibling set.

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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