Updated G2P terms supported in Ensembl VEP

Recent changes to the terms used in the G2P database are aligned with global standards, but are not compatible with old versions of the VEP G2P plugin. We’ve updated the latest version of the VEP G2P plugin (Ensembl 105) to be compatible with both the old and new formats.

We have previously talked about the Ensembl VEP G2P plugin, which uses gene-phenotype association data from the G2P database to filter genotypes and identify potential causative variants. In the latest G2P release, there are changes to the terms used to describe allelic requirements and confidence levels which impact VEP analysis.

The terms used in G2P data exports after November 2021 are not compatible with old versions of the VEP G2P plugin but from the current Ensembl release (105) onwards, the plugin supports both the original and new terms.  

The Gene Curation Coalition (GenCC) brings together groups engaged in the evaluation of gene-disease validity to develop consistent terminology for gene curation and to facilitate the consistent assessment of gene-disease association from different resources. 

The G2P project is a member of GenCC and has changed the terms it uses to align with GenCC standards. 

Terms describing the confidence of the reported association have been directly mapped:

  • confirmed  =>  definitive
  • probable    =>  strong
  • possible     =>  limited 

Terms describing allelic requirement now reflect slightly different groupings: 

Former GroupingsNew Groupings
x-linked dominant  
x-linked over-dominance

Additional GenCC terms are supported in both categories for future use. Full details of the changes are available on the G2P website. Final data exports using the former terms are available on the G2P FTP site.