In silico analysis of the effects of non-synonymous SNPs associated with human GSK3B gene on its structure and function

Abstract

Single Nucleotide Polymorphisms (SNPs) are abundantly identified by next generation sequencing (NGS) technology. Glycogen synthase kinase-3 beta (GSK3B), a widely expressed protein kinase, plays pivotal roles in cellular pathways. However, study on SNPs associated with GSK3B and their functional consequences is lacking. In this study, we analysed non-synonymous SNPs of GSK3B gene and their implications using computational tools. From NCBI dbSNP, 103,087 SNPs of GSK3B were initially gathered, later narrowed down to 255 unique nsSNPs. Around one-third of the nsSNPs resulted in charge and polarity change of the amino acids of the protein. 41 nsSNPs were found to significantly alter the stability of GSK3B protein (ΔΔG ≤ -1 or ≥ 1 kcal/mol) and few of them also affected the disorderness at the mutation site. Evolutionary conservation of the nsSNPs in the protein revealed 25 nsSNP may be deleterious to GSK3B protein function. Finally, 4 critical nsSNPs (Y161C, R167G, P225L and Y234D) were identified that can significantly alter both the stability and function of GSK3B. Furthermore, this study predicted 60 post-translational modification sites in GSK3B among which 26 sites contained nsSNPs. Interestingly, 7 upstream ORFs (uORFs) with high ribosomal occupancy were also detected in GSK3B mRNA that can reduce the expression of GSK3B protein. Altogether, this study has employed various in silico methods to characterize GSK3B nsSNPs, but they have limitations. These tools often overlook the cellular context, interacting partners, PTMs and the dynamic nature of proteins, which can affect protein behaviour and function. Despite these limitations, in silico tools are valuable for initial screening and prioritizing SNPs. The prioritized SNPs obtained in this study (Y161C, R167G, P225L and Y234D) should be experimentally validated using techniques like genome editing, biochemical assays, interactome analysis in cell lines and animal models to confirm their biological relevance.

Clinical trial registration: Not Applicable.