Hello,
I am struggling to interpret couple of splice site mutations I have encountered and I would like to ask if there is a way to predict the outcome of a given splice site mutation (does it lead to exon skipping, or truncation, for example). I have a splice site mutation I need to interpret which occured in the exon 14 splice site of the MET gene. MET exon 14 skipping is critical parameter in cancer patients for therapy decisions. The mutation I am working on has not been shown in the literature however, a splice site mutation just 1 nucleotide upstream was detected and classified as pathogenic in some studies. I am aware there are some in silico tools for prediction however I am not sure which one would be the best fit for my purposes (predicting the outcome of the mutation on the protein level, does it lead to exon skipping? truncation? etc). I understand that in vitro testing is the gold standard however I have no access to lab at this moment.
Thank you very much in advance and please let me know if something is not clear.
Cheers!
Hi Eylül Özgü
you can test VEP from Ensemble to test its prediction on RNA and protein structures (https://www.ensembl.org/info/docs/tools/vep/index.html), but there is no way to predict the impact of a variation on RNA and protein levels. those levels depends of course on the genomics, but also on cell states, pathologies, compensation and regulation phenomenon, copy number of the gene in the genome.....lab is the only way to be sure on what you're thinking it should, sorry.
stay safe
fred
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