intron mutations making a new start codon or affecting a stop codon will have an effect on gene expression even though these changes are not in the coding regions

Just to add to Paul Rutland answer, most mutations in introns will NOT have an effect on expression. However there are some that can have an effect, such as those that change the translation start or stop or mutations that impact splicing of the intron.

This is because the intron is removed from the RNA so the expressed mRNA does not normally have the intron sequence present.

Hi all

please add to the list all enhancer and silencer sites, intronic splice sites (read through translation) and so on...without forgetting that the sequence itself can change DNA conformation and therefore access to enzymes and factors...

there are also intron retention, nested splicing events, splicing polyA sites..

Vlasenok M, Margasyuk S, Pervouchine DD.

Transcriptome sequencing suggests that pre-mRNA splicing counteracts widespread intronic cleavage and polyadenylation.

BioRxiv. January 17, 2023.

the way from DNA to matured RNA is a long way and we're still at the beginning in the understanding of all events.

all the best

fred

Just to add a bit more complexity, unless you have very strong molecular evidence to back up the gene model, any PREDICTED introns/exons/promotors/etc are just predictions. Bioinformatics tools use "generally true, most of the time" rules. But if you care about a particular gene, you'll have to spend time either in the literature or at the bench to see the evidence that supports/refutes that model for that specific gene.

The "intron" might not even actually be an intron.