clinvar_variant_lookup
Search ClinVar for genetic variants and their clinical interpretations using variant notation, gene symbols, or condition filters to retrieve clinical significance data.
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
| Name | Required | Description | Default |
|---|---|---|---|
| variant | No | ||
| gene | No | ||
| condition | No | ||
| significance | No | ||
| max_results | No | ||
| use_cache | No |