What does canonical transcript mean in the context of VEP

Question

[curious]

Just looking at this documentation:

https://useast.ensembl.org/info/docs/tools/vep/script/vep_options.html

and seeing:

--canonical
    Adds a flag indicating if the transcript is the canonical transcript for the gene. Not used by default

Does anyone know what this means? Does that mean the fully functional gene most folks think of when thinking of their favorite gene?

[Ram]

Does that mean the fully functional gene most folks think of when thinking of their favorite gene?

That ... doesn't make much sense. Did you even Google the term before creating a post here? You could have even asked ChatGPT!

Answer 1

[Pierre Lindenbaum]

https://www.ensembl.org/info/genome/genebuild/canonical.html

The Ensembl Canonical transcript is a single, representative transcript identified at every locus. For accurate analysis, we recommend that more than one transcripts at a locus may need to be considered, however, we designate a single Ensembl Canonical transcript per locus to provide consistency when only one transcript is required e.g. for initial display on the Ensembl (or other) website and for use in genome-wide calculations e.g. the Ensembl gene tree analysis.. etc...

[LauferVA]

curious - The only thing I have to add to Pierre Lindenbaum 's precise answer is that, while you are considering and reading about Ensembl canonical transcripts, I would go ahead and read about MANE select transcripts (Morales et al., Nature, 2022; PMID: 35388217) and the methodology used to devise it as well. There is no substitute for the manuscript, but it could be helpful to consider a primer as well: https://www.ncbi.nlm.nih.gov/refseq/MANE/.

I think this will help give you key insight and background into related bioinformatic issues.