Feature Request: Support protein sequence annotation for small structural variants (SVs) #804
Description
Hi VEP team,
Thank you for the excellent work on VEP and the VEP_plugins repository — it's an incredibly valuable resource for the community.
I’ve been using the ProteinSeq.pm plugin to retrieve reference and mutated protein sequences for variants with non-synonymous consequences. However, for structural variants (SVs), particularly those with coding impact, there is no plugin can provide mutated protein sequences. I understand that for larger SVs (e.g., kilobase-scale deletions or complex rearrangements) protein consequence annotation can be highly challenging or even ambiguous.
That said, I believe there could be value in supporting protein sequence annotation for small SVs, particularly those under a few hundred base pairs, where a full transcript and protein-level interpretation may still be feasible (e.g., small deletions/duplications within coding regions).
Would the team consider developing a plugin (or extending ProteinSeq.pm) to support this type of functionality? I think it could be a useful addition for researchers studying the functional consequences of SVs at the protein level.
Happy to discuss further or help test if needed.