Interpreting the effects of genetic variants on protein structure and function

Genetic variation between individuals results in a range of human phenotypes. Variants that fall within coding regions of genes generally have direct effects on the proteins encoded by the genes with which they overlap. 

This six-hour virtual workshop will provide participants with an opportunity to gain hands-on experience of using EMBL-EBI tools and resources to assess the effects of genetic variants on the structure and function of proteins in a common workflow. 

During the course, a single example will be used throughout. It will involve running a Variant Call Format (VCF) file through the Ensembl Variant Effect Predictor (VEP), then following links to other relevant EMBL-EBI resources and tools.

Interpreting the effects of genetic variants on protein structure and function 2027 is currently under development. For reference, you can visit the 2026 course edition webpage.

Virtual course

This course will take place on Zoom. Trainers will be available to assist during practical sessions, answer questions, and provide further explanations during the Zoom.

To join the course you will need to create an EMBL-EBI Training website account.

Who is this course for?

This course is aimed at wet-lab scientists and bioinformaticians who would like to use EMBL-EBI data resources to explore the effects of genetic variants on protein structure and function.

What will I learn?

Course content

• Ensembl genome browser and the VEP tool
• Analysis of a VCF file
• Variant information in UniProt and how it is linked to from  Ensembl VEP
• The link between UniProt and PDBe-KB to identify experimental structures for those variants and compare structural conformations through the superposition tool
• The link between UniProt/PDBe-KB and AlphaFoldDB, where data/resources are showcased for variant/protein interpretation

Learning outcomes

After the course you should be able to:

• Describe the main functionality and options available for the Ensembl Variant Effect Predictor (VEP)
• Annotate a variation dataset using the web-based Ensembl VEP tool
• Interpret the output of EnsemblVEP and navigate to other EMBL-EBI resources to further assess variant effects on proteins
• Access variant information in UniProt
• Identify and evaluate experimental and predicted structures representing protein variants using PDBe-KB and AlphaFoldDB (AFDB)
• Interpret the functional implications of variant-induced changes in protein structure

Registration opens for this workshop on 21 June 2027. Click to register your interest using the button on the right-hand side of this course website to hear as the event develops. 

Whilst you wait, we encourage you to read our payment support page for advice before submitting and paying for your registration. Incomplete and unpaid registrations will be removed by the system.

If you have any questions regarding the application process, please contact your Events Officer Toke Labiyi.

The EMBL-EBI Training team is committed to making our events inclusive and accessible to all participants, whether attending onsite or virtually. Please read our dedicated support page to find out how we may be able to support you with any accessibility requirements.