Lovd Tools

Configuration File: lovd_tools.json Tool Type: Local Tools Count: 3

This page contains all tools defined in the lovd_tools.json configuration file.

Available Tools

LOVD_get_gene (Type: LOVDTool)

Get gene information from LOVD (Leiden Open Variation Database). Returns HGNC ID, Entrez ID, chro…

LOVD_get_gene tool specification

Tool Information:

  • Name: LOVD_get_gene

  • Type: LOVDTool

  • Description: Get gene information from LOVD (Leiden Open Variation Database). Returns HGNC ID, Entrez ID, chromosomal location, RefSeq transcript(s), genomic build, curation details, and dates. LOVD hosts curated variant databases for over 23,000 genes used in clinical diagnostics.

Parameters:

  • gene_symbol (string) (required) HGNC gene symbol (e.g., ‘TP53’, ‘BRCA1’, ‘BRCA2’, ‘EGFR’).

Example Usage:

query = {
    "name": "LOVD_get_gene",
    "arguments": {
        "gene_symbol": "example_value"
    }
}
result = tu.run(query)

LOVD_get_variants (Type: LOVDTool)

Get all curated variants for a gene from LOVD. Returns variant details including HGVS DNA/RNA/pro…

LOVD_get_variants tool specification

Tool Information:

  • Name: LOVD_get_variants

  • Type: LOVDTool

  • Description: Get all curated variants for a gene from LOVD. Returns variant details including HGVS DNA/RNA/protein notation, genomic positions (hg19), LOVD variant DBID, and reporting count. Note: some genes may have hundreds or thousands of variants.

Parameters:

  • gene_symbol (string) (required) HGNC gene symbol (e.g., ‘TP53’, ‘BRCA1’).

Example Usage:

query = {
    "name": "LOVD_get_variants",
    "arguments": {
        "gene_symbol": "example_value"
    }
}
result = tu.run(query)

LOVD_search_variants (Type: LOVDTool)

Search variants in LOVD by DBID or HGVS DNA notation. Use variant_dbid for exact LOVD variant IDs…

LOVD_search_variants tool specification

Tool Information:

  • Name: LOVD_search_variants

  • Type: LOVDTool

  • Description: Search variants in LOVD by DBID or HGVS DNA notation. Use variant_dbid for exact LOVD variant IDs (e.g., ‘TP53_010464’) or dna_notation for HGVS notation without RefSeq prefix (e.g., ‘c.*2609C>A’). At least one search parameter is required.

Parameters:

  • gene_symbol (string) (required) HGNC gene symbol (e.g., ‘TP53’, ‘BRCA1’).

  • variant_dbid (string) (optional) LOVD variant DBID (e.g., ‘TP53_010464’). Unique identifier assigned by LOVD.

  • dna_notation (string) (optional) HGVS DNA notation without RefSeq prefix (e.g., ‘c.*2609C>A’, ‘c.742C>T’). Use coding ‘c.’ notation.

Example Usage:

query = {
    "name": "LOVD_search_variants",
    "arguments": {
        "gene_symbol": "example_value"
    }
}
result = tu.run(query)