Match Genes Linked to Phenotypes

This algorithm determines matches between the gene annotations of each variant and list of genes associated with a group of user-specified phenotypes.


This algorithm requires first annotating and classifying variants using a gene annotation source.

After clicking OK you will be prompted to select a Gene Names field to be used for matching.

After clicking OK a second time you will be prompted to enter a delimited list of phenotypes to use for selecting a gene list.


This dialog allows the user to specify the following options:

  • New Field Name: Name to be used for the newly created field.
  • Enhance with OMIM phenotypes: Specifies that OMIM terms may be used.
  • Gene Association: Determines how many nodes may be traversed in the ontology to reach a gene.
    • HPO gene association The matched genes must be directly related to the term in the HPO ontology
    • HPO +1 hop in GO Genes will be matched if they share a neighbor with one of the entered phenotype terms in the ontology. This allows for genes indirectly related through GO terms to be included in the gene list.
  • Linked Genes: The computed set of gene names to match.


A boolean column indicating whether the gene annotation for each variant matches at least one of the genes.