Skip to main content
Glama
kmaneesh

BioPython MCP Server

by kmaneesh

clinvar_variant_lookup

Search ClinVar for genetic variants and clinical interpretations by variant notation, gene, condition, or clinical significance, returning detailed variant information and match counts.

Instructions

Search ClinVar for genetic variants and their clinical interpretations.

This specialized wrapper combines entrez_search and entrez_summary for convenient ClinVar queries.

Args: variant: Variant notation (e.g., "rs80357906", "NM_000059.3:c.1521_1523del") gene: Gene symbol (e.g., "BRCA1", "TP53") condition: Condition/phenotype (e.g., "breast cancer", "Lynch syndrome") significance: Clinical significance filter: - "pathogenic" - "likely_pathogenic" - "benign" - "likely_benign" - "uncertain" max_results: Maximum results to return (default: 20) use_cache: Whether to use cached results (default: True)

Returns: Dictionary containing: - variants: List of variant dictionaries with clinical information - count: Number of variants returned - total_found: Total matches in ClinVar - query_terms: Dictionary of search terms used - cached: Whether result was from cache (if use_cache=True)

Examples: >>> clinvar_variant_lookup(gene="BRCA1", significance="pathogenic", max_results=5) >>> clinvar_variant_lookup(variant="rs80357906") >>> clinvar_variant_lookup(gene="TP53", condition="cancer", max_results=10)

Notes: - At least one search parameter must be provided - Multiple parameters are combined with AND logic - Rate limited (3 req/sec or 10 req/sec with API key) - Cached results inherit TTL from underlying entrez_search and entrez_summary calls

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
variantNo
geneNo
conditionNo
significanceNo
max_resultsNo
use_cacheNo

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault

No arguments

Behavior4/5

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

With no annotations provided, the description carries the full burden. It discloses rate limits, caching behavior (use_cache and TTL inheritance), and AND logic for parameter combination. It does not explicitly state read-only nature, but it is implied. This is more transparent than typical.

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 Args, Returns, Examples, and Notes sections. Every sentence adds value, and the core purpose is front-loaded. No unnecessary content.

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 6 parameters, no annotations, and an output schema that is described in detail (return dictionary structure), the description covers all necessary aspects: input, output, examples, and behavioral notes. It is fully complete for an AI agent to use correctly.

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

Parameters5/5

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

Input schema has 6 parameters with 0% description coverage, but the description adds full meaning for each: variant notation examples, gene symbol, condition, significance filter list, default max_results, and use_cache. This fully compensates for the lack of schema 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 clearly states it searches ClinVar for genetic variants and clinical interpretations, and specifies it is a specialized wrapper combining entrez_search and entrez_summary. This differentiates it from sibling tools like entrez_search and entrez_summary.

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

Usage Guidelines3/5

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

The Notes section explains that at least one search parameter is required and multiple parameters are combined with AND logic. Examples demonstrate typical use cases. However, it does not explicitly state when to use this tool versus alternatives like entrez_search or entrez_summary, nor does it describe when NOT to use it.

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

Install Server

Other Tools

Latest Blog Posts

MCP directory API

We provide all the information about MCP servers via our MCP API.

curl -X GET 'https://glama.ai/api/mcp/v1/servers/kmaneesh/biopython-mcp'

If you have feedback or need assistance with the MCP directory API, please join our Discord server