Mutalyzer Tools

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

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

Available Tools

Mutalyzer_back_translate (Type: MutalyzerTool)

Convert a protein-level HGVS variant to possible DNA-level variant descriptions using Mutalyzer. …

Mutalyzer_back_translate tool specification

Tool Information:

  • Name: Mutalyzer_back_translate

  • Type: MutalyzerTool

  • Description: Convert a protein-level HGVS variant to possible DNA-level variant descriptions using Mutalyzer. Given a protein change like NP_002993.1:p.Asp92Tyr, returns the corresponding coding DNA change(s) like NM_003002.4:c.(274G>T). Useful for finding the DNA-level representation of a known amino acid change, accounting for codon degeneracy.

Parameters:

  • variant (string) (required) Protein-level HGVS variant description. Examples: ‘NP_002993.1:p.Asp92Tyr’ (SDHD), ‘NP_000537.3:p.Pro72Arg’ (TP53), ‘NP_000050.2:p.Tyr32Cys’ (BRCA2). Format: NP_accession:p.AminoAcidChange

Example Usage:

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

Mutalyzer_normalize_variant (Type: MutalyzerTool)

Validate and normalize an HGVS variant description using Mutalyzer. Returns the corrected/normali…

Mutalyzer_normalize_variant tool specification

Tool Information:

  • Name: Mutalyzer_normalize_variant

  • Type: MutalyzerTool

  • Description: Validate and normalize an HGVS variant description using Mutalyzer. Returns the corrected/normalized HGVS notation, predicted protein effect, RNA description, and gene symbol. Essential for clinical variant interpretation - ensures HGVS nomenclature compliance and predicts amino acid changes. Accepts coding DNA (c.), genomic (g.), protein (p.), or RNA (r.) variant descriptions. Example: ‘NM_003002.4:c.274G>T’ normalizes to a SDHD missense variant with protein prediction p.(Asp92Tyr).

Parameters:

  • variant (string) (required) HGVS variant description. Examples: ‘NM_003002.4:c.274G>T’ (SDHD missense), ‘NM_000546.6:c.215C>G’ (TP53 p.Pro72Arg), ‘NM_000059.4:c.7397C>T’ (BRCA2). Format: reference:coordinate_system.change

Example Usage:

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

Mutalyzer_parse_hgvs (Type: MutalyzerTool)

Parse an HGVS variant description into a structured model using Mutalyzer. Returns the reference …

Mutalyzer_parse_hgvs tool specification

Tool Information:

  • Name: Mutalyzer_parse_hgvs

  • Type: MutalyzerTool

  • Description: Parse an HGVS variant description into a structured model using Mutalyzer. Returns the reference sequence ID, coordinate system (c./g./p./r.), variant type (substitution, deletion, insertion, etc.), and exact positions. Useful for programmatically extracting components of HGVS notation without regex parsing.

Parameters:

  • variant (string) (required) HGVS variant description to parse. Examples: ‘NM_003002.4:c.274G>T’, ‘NC_000017.11:g.7674220C>G’, ‘NM_000546.6:c.215C>G’. Supports coding (c.), genomic (g.), protein (p.), and RNA (r.) coordinates.

Example Usage:

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