Cool stuff Ensembl VEP can do – provide evidence of protein interaction impact

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Ensembl VEP integrates information from many different resources to help you interpret the functional impact of your variants. It now reports when variants fall in sites with evidence of impact on protein interactions, as described in the IntAct database.

Molecular interactions underlie most cellular processes, so it is important to know when a variant changes normal activity. The literature contains detailed information on the observed effects of variants, but it can be difficult to find and extract. To make it accessible, expert curators extract standardised information to populate the IntAct database. Ensembl VEP integrates IntAct data to report when a variant falls in a site investigated for impact on interactions.

IntAct logo

Using the VEP web interface, select the IntAct option in the ‘Protein Annotation’ section and select the attributes you would like to see from the list. The results table has links to the IntAct site from the interaction accession and links to any journals via the PubMed identifier so you can find further information.

Part of the VEP results table for NC_000022.11:g.29678301T>G showing protein interaction information from the IntAct database.

The Ensembl VEP REST service returns IntAct ids and feature type information and the IntAct plugin is available for command line analysis.