GeneBe

get_gene

Read-onlyIdempotent

Look up a human gene: identifiers, location, MANE Select transcript, ClinGen gene-disease validity.

Use for questions about a gene rather than a specific variant. Transcripts are listed with MANE Select first and capped; check total_transcripts.

Tool call template

Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {
      "gene": "<gene>"
    },
    "name": "get_gene"
  }
}

Input Schema

Name	Required	Description	Default
`gene`	Yes	Gene symbol (BRCA1), alias, HGNC id (HGNC:1100), 'entrez:672' or Ensembl id (ENSG...).
`include_transcripts`	No	Also list the gene's transcripts.

Output Schema

Name	Required	Description
`chr`	Yes
`end`	Yes
`link`	Yes
`name`	Yes
`start`	Yes
`symbol`	Yes
`hgnc_id`	Yes
`message`	No	Set when an alias matched several genes
`ncbi_id`	Yes
`omim_id`	Yes
`truncated`	No
`ensembl_id`	Yes
`uniprot_id`	Yes
`transcripts`	Yes
`total_transcripts`	Yes
`mane_select_refseq`	Yes
`mane_select_ensembl`	Yes
`alternative_hgnc_ids`	No
`gene_disease_validity`	Yes
`total_gene_disease_entries`	Yes

Schema Changelog

Changes observed during successful MCP inspections.

First observedOct 22, 2026

TDQS

A4.5/5.0

Behavior4/5

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

Annotations already declare readOnly/openWorld/idempotent/non-destructive, so the safety profile is covered. The description adds real behavioral context the annotations cannot carry: transcripts are capped and ordered MANE Select first, with total_transcripts as the escape hatch for truncation. It says nothing about auth or rate limits, keeping it short of a 5.

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?

Two sentences, zero filler, with the purpose and distinguishing scope front-loaded before the transcript caveat. Nothing repeats the schema or annotations verbatim.

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?

A two-parameter, fully documented read-only lookup with an output schema, so return shapes need no explanation. The only behavioral trap — silent transcript truncation — is disclosed, which is exactly what an agent needs to call this correctly.

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

Parameters4/5

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

Schema coverage is 100%, so the baseline is 3; the description earns extra by explaining what include_transcripts actually yields — a capped, MANE-first list with total_transcripts to detect truncation. That is semantics beyond the schema's bare 'Also list the gene's transcripts.'

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?

States a specific verb and resource ('Look up a human gene') and enumerates the payload: identifiers, location, MANE Select transcript, ClinGen validity. It also explicitly separates itself from variant-oriented siblings with 'a gene rather than a specific variant.'

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?

Gives a clear selection rule: use for gene-level questions, not variant-level ones, which implicitly routes to annotate_variant/get_variant_effects. It stops short of naming the specific sibling tool to pick instead, leaving the agent to map 'specific variant' onto the sibling list.

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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