Variant Validator Tools

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

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

Available Tools

VariantValidator_format_genomic_to_transcripts (Type: BaseRESTTool)

Project a genomic variant onto EVERY overlapping RefSeq transcript in one call using the VariantV…

VariantValidator_format_genomic_to_transcripts tool specification

Tool Information:

  • Name: VariantValidator_format_genomic_to_transcripts

  • Type: BaseRESTTool

  • Description: Project a genomic variant onto EVERY overlapping RefSeq transcript in one call using the VariantValidator VariantFormatter endpoint. Given a genomic-level variant (g.HGVS like ‘NC_000017.11:g.50198002C>A’ or a pseudo-VCF string like ‘17-50198002-C-A’) on GRCh37 or GRCh38, returns the per-transcript coding (c.) HGVS, predicted protein (p.) consequence in three- and single-letter codes, gene info (HGNC id + symbol), the pseudo-VCF representation, and MANE Select / RefSeq Select flags for each transcript. Use this when you need all transcript projections for a genomic variant; the standard VariantValidator_validate_variant endpoint no longer accepts select_transcripts=’all’ for genomic input (it returns HTTP 404 directing callers to VariantFormatter), so this is the only way to reach this capability in ToolUniverse. Public API, no key required.

Parameters:

  • genome_build (string) (optional) Reference genome assembly: ‘GRCh37’ (hg19) or ‘GRCh38’ (hg38).

  • variant_description (string) (required) Genomic-level variant description. Accepts genomic HGVS (e.g. ‘NC_000017.11:g.50198002C>A’) or a pseudo-VCF string (e.g. ‘17-50198002-C-A’).

Example Usage:

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

VariantValidator_gene2transcripts (Type: BaseRESTTool)

Get all transcripts for a gene using VariantValidator. Returns MANE Select and MANE Plus Clinical…

VariantValidator_gene2transcripts tool specification

Tool Information:

  • Name: VariantValidator_gene2transcripts

  • Type: BaseRESTTool

  • Description: Get all transcripts for a gene using VariantValidator. Returns MANE Select and MANE Plus Clinical transcript annotations, Ensembl and RefSeq transcript identifiers, genomic coordinates, and cross-references. Useful for identifying the correct transcript for variant annotation. Supports filter for MANE transcripts only or all transcripts.

Parameters:

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

  • gene (string) (optional) Alias for gene_symbol.

  • gene_name (string) (optional) Alias for gene_symbol.

  • transcript_set (string) (optional) Transcript filter: ‘mane’ for MANE Select/Plus Clinical only, ‘refseq’ for RefSeq transcripts, ‘ensembl’ for Ensembl, ‘all’ for everything

  • genome_build (string) (optional) Reference genome assembly: ‘GRCh37’ or ‘GRCh38’ (default: GRCh38)

Example Usage:

query = {
    "name": "VariantValidator_gene2transcripts",
    "arguments": {
        "gene_symbol": "example_value"
    }
}
result = tu.run(query)

VariantValidator_validate_variant (Type: BaseRESTTool)

Validate and convert genetic variant descriptions using VariantValidator. Takes HGVS-formatted va…

VariantValidator_validate_variant tool specification

Tool Information:

  • Name: VariantValidator_validate_variant

  • Type: BaseRESTTool

  • Description: Validate and convert genetic variant descriptions using VariantValidator. Takes HGVS-formatted variant notation and returns validated variant descriptions with genomic context, transcript context, protein consequence, and cross-references. Validates variant nomenclature against current RefSeq sequences and LOVD syntax checker. Supports substitutions, deletions, insertions, duplications, inversions. Reference assemblies: GRCh37 (hg19) or GRCh38 (hg38).

Parameters:

  • genome_build (string) (required) Reference genome assembly: ‘GRCh37’ (hg19) or ‘GRCh38’ (hg38)

  • variant_description (string) (required) HGVS variant description (e.g., ‘NM_007294.4:c.5266dup’ for BRCA1 c.5266dupC, ‘NM_000179.3:c.943C>T’, ‘chr17:g.43092919del’)

  • select_transcripts (string) (required) Transcript to validate against (e.g., ‘NM_007294.4’). Use ‘all’ to get all transcripts for a genomic variant.

Example Usage:

query = {
    "name": "VariantValidator_validate_variant",
    "arguments": {
        "genome_build": "example_value",
        "variant_description": "example_value",
        "select_transcripts": "example_value"
    }
}
result = tu.run(query)