In silico analysis of missense variants in functional domains of PWWP2A and PWWP2B proteins.

Epigenetic regulatory activity through chromatin remodelling is essential for maintaining gene expression integrity, and alterations in chromatin-associated proteins can cause pathological consequences. The conserved PWWP domain in PWWP2A and PWWP2B, which are Royal family of chromatin readers, can recognize methylated histones and regulate transcriptional mechanisms. Beyond their biological significance, the structural effects of missense mutations in the PWWP2A and PWWP2B domains remain unknown. No previous study has been done on the effect of missense mutations in PWWP2A and PWWP2B that affect their stability, folding, chromatin-interacting functions. To predict pathogenicity and structural disruption, in silico characterization of missense mutations was conducted in both genes using SIFT, PolyPhen-2, GERP, Mutation Assessor, MutPred, I-Mutant 2.0, Project HOPE. As a result, 354 and 352 missense variants were obtained from 1712 and 1301 SNPs in PWWP2A and PWWP2B, respectively. Of which, fifteen missense variants were recognized as highly pathogenic: 11 in PWWP2A (R195W, G650D, V655A, D657H/G, A661D, L674V, R680W, W695R, F716V, Y728C) and 4 in PWWP2B (P505L, A506V, Y563C, R564W). These mutations changed the protein's hydrophobic and electrostatic properties and reduced stability. They occur on conserved residues of the PWWP domain, indicating possible link to disease mechanisms. Furthermore, AlphaFold2-based 3D modelling and Ramachandran plot analysis indicated potential misfolding and domain perturbations. To conclude, this study proposes a predictive structural framework to understand the impact of missense mutations in the PWWP2A and PWWP2B domains on transcriptional regulation and chromatin binding; further experimental validation will be required to confirm the effects predicted in this study. The integrative computational approach of this study provides a foundation for experimental validation and therapeutic investigation of PWWP2-associated disorders.