Integrative In Silico Analysis of Synonymous Variants in ABCG2 and PPARA: Implications for Valproate Resistance in Epilepsy

<title>Abstract</title> <p> Epilepsy affects millions worldwide, and approximately one-third of patients develop resistance to antiseizure medications such as valproic acid (VPA). The <italic>ABCG2</italic> transporter and its transcriptional regulator <italic>PPARA</italic> have been implicated in VPA response, yet the contribution of synonymous single nucleotide polymorphisms (sSNPs) in these genes to VPA resistance remains poorly understood. Here, we performed an integrative in silico analysis of 262 <italic>ABCG2</italic> and 109 <italic>PPARA</italic> sSNPs to evaluate their potential effects on pre-mRNA splicing, mRNA structure, and translational kinetics. Several variants were predicted to disrupt normal splicing through activation of cryptic splice sites or loss of splicing regulatory elements. Additional variants were associated with significant alterations in mRNA secondary structure and translational efficiency, while others were located within regions important for co-translational protein folding. Overall, a subset of synonymous variants in both genes showed a potential influence on multiple layers of gene regulation despite preserving the encoded amino acid sequence, challenging the long-held assumption that synonymous variants are functionally neutral. These findings support the emerging view that synonymous variants can have functional consequences and suggest that <italic>ABCG2</italic> and <italic>PPARA</italic> sSNPs may contribute to variability in VPA response. The identified variants represent promising candidates for future experimental validation and pharmacogenomic studies aimed at improving precision medicine approaches in epilepsy. </p>