interpretation of intronic variant detected by WES

Question

[jonessara770]

Hi

I detected a variant in the intron of a gene that is predicted by MutationFinder to affect splicing by activation of an intronic cryptic acceptor site.

What is the method to check if this variant produces truncating proteins or not?

btw, my data is WES.

Thanks Sara

[Kevin Blighe]

Hey Sara, please take a look at my previous answer: A: pathogenicity predictors of cancer mutations

In particular, note the Splice predictions section. Those are tools that are being currently used by clinical geneticists to gauge alternate splicing.

Kevin

[jonessara770]

Thank Kevin,

The tools in your previous post are for predicting if a variant affects splicing. right? I did this step before and I know it affects splicing but I don't know how to check if it produces truncating protein.

[Kevin Blighe]

I see. I am not aware of any program / algorithm that does this. However, if the protein is truncated, then it should undergo the process of non-sense mediated decay (NMD), and not be expressed. However, this depends on where exactly the mutation is located in the gene. In that light, you could take a read of this: NMD Classifier: A reliable and systematic classification tool for nonsense-mediated decay events.