Information theory-based analysis of CYP2C19, CYP2D6 and CYP3A5 splicing mutations.

Several mutations are known or suspected to affect mRNA splicing of CYP2C19, CYP2D6 and CYP3A5 genes; however, little experimental evidence exists to support these conclusions. The present study applies mathematical models that measure changes in information content of splice sites in these genes to demonstrate the relationship between the predicted phenotypes of these variants to the corresponding genotypes. Based on information analysis, the CYP2C192 variant activates a new cryptic site 40 nucleotides downstream of the natural splice site. CYP2C197 abolishes splicing at the exon 5 donor site. The CYP2D64 allele similarly inactivates splicing at the acceptor site of exon 4 and activates a new cryptic site one nucleotide downstream of the natural acceptor. CYP2D611 inactivates the acceptor site of exon 2. The CYP3A53 allele activates a new cryptic site 236 nucleotides upstream of the exon 4 natural acceptor site. CYP3A55 inactivates the exon 5 donor site and CYP3A56 strengthens a site upstream of the natural donor site, resulting in skipping of exon 7. Other previously described missense and nonsense mutations at terminal codons of exons in these genes affected splicing. CYP2D68 and CYP2D6*14 both decrease the strength of the exon 3 donor site, producing transcripts lacking this exon. The results of information analysis are consistent with the poor metabolizer phenotypes observed in patients with these mutations, and illustrate the potential value of these mathematical models to quantitatively evaluate the functional consequences of new mutations suspected of altering mRNA splicing.