Recognition of functional genetic polymorphism using ESE motif definition: a conservative evolutionary approach to CYP2D6/CYP2C19 gene variants

• Published in: Genetica 2022-10, Vol.150 (5), p.289-297
• Main Authors: Samadi, Mitra, Beigi, Laleh, Yadegari, Fatemeh, Ansari, Alireza Madjid, Majidzadeh-A, Keivan, Eskordi, Maryam, Farahmand, Leila
• Format: Article
• Language: English
• Subjects: Animal Genetics and Genomics; Biomedical and Life Sciences; Conserved sequence; CYP2D6 protein; Cytochrome P450; Drug metabolism; Enhancers; Evolutionary Biology; Evolutionary conservation; Filters; Functional analysis; Gene polymorphism; Genes; Human Genetics; Life Sciences; Microbial Genetics and Genomics; Mutation; Original Paper; Plant Genetics and Genomics; Polymorphism; Splicing
• ISSN: 0016-6707; 1573-6857
• DOI: 10.1007/s10709-022-00161-x

Although predicting the effects of variants near intron-exon boundaries is relatively straightforward, predicting the functional Exon Splicing Enhancers (ESEs) and the possible effects of variants within ESEs remains a challenge. Considering the essential role of CYP2D6/CYP2C19 genes in drug metabolism, we attempted to identify variants that are most likely to disrupt splicing through their effect on these ESEs. ESEs were predicted in these two genes using ESEfinder 3.0, incorporating a series of filters (increased threshold and evolutionary conservation). Finally, reported mutations were evaluated for their potential to disrupt splicing by affecting these ESEs. Initially, 169 and 243 ESEs were predicted for CYP2C19/CYP2D6 , respectively. However, applying the filters, the number of predicted ESEs was reduced to 26 and 19 in CYP2C19/CYP2D6 , respectively. Comparing prioritized predicted ESEs with known sequence variants in CYP2C 19/ CYP2D6 genes highlights 18 variations within conserved ESEs for each gene. We found good agreement in cases where such predictions could be compared to experimental evidence. In total, we prioritized a subset of mutational changes in CYP2C19 / CYP2D6 genes that may affect the function of these genes and lead to altered drug responses. Clinical studies and functional analysis for investigating detailed functional consequences of the mentioned mutations and their phenotypic outcomes is mostly recommended.