Alphamissense Tools#

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

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

Available Tools#

AlphaMissense_get_protein_scores (Type: AlphaMissenseTool)#

Get AlphaMissense pathogenicity scores across a protein. The upstream hegelab API only exposes pe…

AlphaMissense_get_protein_scores tool specification

Tool Information:

  • Name: AlphaMissense_get_protein_scores

  • Type: AlphaMissenseTool

  • Description: Get AlphaMissense pathogenicity scores across a protein. The upstream hegelab API only exposes per-residue queries; this tool looks up the UniProt length and concurrently fetches a recoverable page of positions. Returns per-position records, protein length, attempted/returned counts, thresholds, and explicit pagination metadata. Use max_residues > 0 for a bounded page and pass next_residue_offset back as residue_offset until has_more is false; max_residues=0 fetches all remaining positions.

Parameters:

  • uniprot_id (string) (required) UniProt accession ID (e.g., ‘P00533’ for EGFR, ‘P01116’ for KRAS, ‘P04637’ for TP53).

  • max_residues ([‘integer’, ‘null’]) (optional) Maximum positions to attempt in this page. 0 / null / omitted fetches all positions at or after residue_offset. A positive value returns at most N positions and exposes next_residue_offset when more remain.

  • residue_offset (integer) (optional) Zero-based number of protein positions to skip before this page. Start with 0 and, when has_more is true, continue with next_residue_offset.

Example Usage:

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

AlphaMissense_get_residue_scores (Type: AlphaMissenseTool)#

Get the AlphaMissense class breakdown for substitutions at a specific protein position: which res…

AlphaMissense_get_residue_scores tool specification

Tool Information:

  • Name: AlphaMissense_get_residue_scores

  • Type: AlphaMissenseTool

  • Description: Get the AlphaMissense class breakdown for substitutions at a specific protein position: which residues fall in each class (benign/ambiguous/pathogenic), reported separately for the SNV-accessible substitutions and for all 19, plus the residue mean scores. NOTE: the upstream hotspot API does not expose a numeric score per individual substitution, so this returns class membership rather than 20 scores.

Parameters:

  • uniprot_id (string) (required) UniProt accession ID (e.g., ‘P00533’ for EGFR)

  • position (integer) (required) Amino acid position in the protein (1-indexed)

Example Usage:

query = {
    "name": "AlphaMissense_get_residue_scores",
    "arguments": {
        "uniprot_id": "example_value",
        "position": 10
    }
}
result = tu.run(query)

AlphaMissense_get_variant_score (Type: AlphaMissenseTool)#

Classify a specific missense variant with AlphaMissense. Input: UniProt ID and variant (e.g., ‘p….

AlphaMissense_get_variant_score tool specification

Tool Information:

  • Name: AlphaMissense_get_variant_score

  • Type: AlphaMissenseTool

  • Description: Classify a specific missense variant with AlphaMissense. Input: UniProt ID and variant (e.g., ‘p.R123H’). Returns the variant’s AlphaMissense class (pathogenic/ambiguous/benign) and whether it came from the SNV-accessible or the all-substitutions set. NOTE: the upstream hotspot API publishes per-residue class membership, not a numeric score per substitution, so pathogenicity_score is null and score_available is false; the residue_mean_score_* fields are residue-level averages, NOT this variant’s score. For a numeric per-variant score use GenomeNexus_annotate_variant.

Parameters:

  • uniprot_id (string) (required) UniProt accession ID (e.g., ‘P00533’ for EGFR)

  • variant (string) (required) Variant in protein notation: p.X123Y or X123Y where X is reference amino acid, 123 is position, Y is variant (e.g., ‘p.R123H’, ‘V600E’)

Example Usage:

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