Question: Can splice-site mutations be treated as gene knock-outs?
gravatar for sviatoslav.kendall
3 months ago by
United States
sviatoslav.kendall440 wrote:

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.

sequencing snp • 168 views
ADD COMMENTlink modified 3 months ago by WouterDeCoster29k • written 3 months ago by sviatoslav.kendall440
gravatar for WouterDeCoster
3 months ago by
WouterDeCoster29k wrote:

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
ADD COMMENTlink written 3 months ago by WouterDeCoster29k
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