Vep Pathogenicity Tools

Configuration File: vep_pathogenicity_tools.json Tool Type: Local Tools Count: 1

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

Available Tools

VEP_predict_pathogenicity (Type: VEPPathogenicityTool)

Predict missense variant pathogenicity via the Ensembl VEP REST API with AlphaMissense (DeepMind …

VEP_predict_pathogenicity tool specification

Tool Information:

  • Name: VEP_predict_pathogenicity

  • Type: VEPPathogenicityTool

  • Description: Predict missense variant pathogenicity via the Ensembl VEP REST API with AlphaMissense (DeepMind 2023) + SIFT + PolyPhen-2 per transcript, in one call. Provide ONE of: a dbSNP rsID (‘rsid’), HGVS notation (‘hgvs_notation’), or a genomic locus (‘chrom’+’pos’+’alt’). Returns per-transcript predictions (gene, amino_acids, alphamissense_class/score, sift, polyphen, most_severe_consequence). No API key.

Parameters:

  • rsid ([‘string’, ‘null’]) (optional) dbSNP rsID, e.g. ‘rs699’ (one input mode)

  • hgvs_notation ([‘string’, ‘null’]) (optional) HGVS notation, e.g. ‘ENST00000269305.9:c.524G>A’ (one input mode)

  • chrom ([‘string’, ‘null’]) (optional) Chromosome for region input, e.g. ‘17’ (with pos+alt)

  • pos ([‘integer’, ‘null’]) (optional) 1-based position for region input

  • alt ([‘string’, ‘null’]) (optional) Alternate allele for region input, e.g. ‘T’

  • genome_build ([‘string’, ‘null’]) (optional) GRCh38 (default) or GRCh37

Example Usage:

query = {
    "name": "VEP_predict_pathogenicity",
    "arguments": {
    }
}
result = tu.run(query)