Question: Functional Relevance Of Stop Retained Variants?
1
gravatar for Rubal7
6.6 years ago by
Rubal7770
Rubal7770 wrote:

Hello Everyone,

I am looking for functional variants in population genomic data. I have identified a candidate variant (high frequency and highly conserved across mammals). The variant is classified by VEP as a stop retained variant, meaning that "A sequence variant where at least one base in the terminator codon is changed, but the terminator remains". Does anyone know of any cases where such a variant has been associated with phenotype variation of any kind? I am wondering if such a variant is only as likely to be functional as any other synonymous variant, or if being in the terminator codon is associated with any increased chance of having a functional effect. If anyone has any experience or ideas on this or a reference to a paper with a functional variant of this kind that would be great. So far I haven't found any examples.

Thanks in advance, Rubal

ADD COMMENTlink modified 6.6 years ago by Emily_Ensembl21k • written 6.6 years ago by Rubal7770
1
gravatar for Emily_Ensembl
6.6 years ago by
Emily_Ensembl21k
EMBL-EBI
Emily_Ensembl21k wrote:

If such a variant does cause a phenotype I would assume that is part of a regulatory region, not due to changes in the stop codon.

ADD COMMENTlink written 6.6 years ago by Emily_Ensembl21k

Could you expand a little on what you mean, I am a little unclear how a synonymous change in a stop codon can be classified as a regulatory region? Thanks very much, probably just my confusion

ADD REPLYlink modified 6.6 years ago • written 6.6 years ago by Rubal7770

There might be a regulatory region that overlaps the stop codon.

ADD REPLYlink written 6.6 years ago by Emily_Ensembl21k
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