I'm working with some exome-sequencing data that's been run through a mutation calling pipeline. My goal is determine which samples have deactivating mutations within a subset of genes. Using the MAF column "Variant_Classification", I've already decided to mutations with values like "stop_gained" and "start_lost" are indications that the gene is effectively knocked-out. But I don't know what to do about splice-site values like: "splice_acceptor_variant" "splice_donor_variant" "splice_region_variant"
Should I just treat all splice-site mutations as an indication that the gene product won't function properly and therefore it's effectively been knocked out? Are some types of splice-site mutations more likely than others to prevent the gene product from functioning?
I haven't been able to find any literature addressing this question so I thought I'd ask here.
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written
by
sviatoslav.kendall
1 answer
Without any supporting literature at hand: no.
Splice sites mutations may:
- just reduce correct splicing and therefore expression by a bit without creating a full knock out
- result in alternative splicing in which another transcript is produced (e.g. exon skipping), which can be not, partially or fully functional
- indeed result in a knock out
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