Proof of principle concept for the analysis and functional prediction of rare genetic variants in the CYP2C19 and CYP2D6 genes
Abstract
BACKGROUND: Variations in pharmacogenes that regulate drug absorption, distribution, metabolism, and excretion (ADME) contribute to approximately 20-30% of interindividual differences in drug response. While many common variants are successfully utilized in clinical settings to predict individual drug responses, a significant portion of the genetic basis underlying this variability remains unidentified. This includes rare variants, which are estimated to account for 4-6% of drug response variability. RESULTS: To comprehensively elucidate the functional consequences and molecular mechanisms of rare variants, we conducted in vitro enzyme expression studies combined with in silico structure-function analyses. We selected 11 rare variants in the CYP2C19 and CYP2D6 genes identified among participants within the Estonian Biobank. Variant cDNAs were heterologously expressed in HEK-293 cells, and detailed enzyme activity analyses were performed. The experimental results were further validated against average scores from five optimized in silico prediction models: LRT, Mutation Assessor, PROVEAN, VEST3, and CADD. To explore structure-activity relationships, we performed in silico docking of substrates into available 3D enzyme structures. Our findings reveal that most of the rare genetic variants caused significant functional alterations, including: (i) Likely impairments in substrate transport to the active site due to narrowing of access channels; (ii) Changes in catalytic rates;…
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