In Silico Functional and Structural Analysis of Non-synonymous Single Nucleotide Polymorphisms (nsSNPs) in Human Paired Box 4 Gene

Md Mostafa Kamal; Md Numan Islam; Md Golam Rabby; Md Ashrafuzzaman Zahid; Md Mahmudul Hasan

doi:10.1007/s10528-023-10589-1

In Silico Functional and Structural Analysis of Non-synonymous Single Nucleotide Polymorphisms (nsSNPs) in Human Paired Box 4 Gene

Biochem Genet. 2023 Dec 7. doi: 10.1007/s10528-023-10589-1. Online ahead of print.

Authors

Md Mostafa Kamal¹, Md Numan Islam^{1

2}, Md Golam Rabby¹, Md Ashrafuzzaman Zahid¹, Md Mahmudul Hasan³

Affiliations

¹ Department of Nutrition and Food Technology, Jashore University of Science and Technology, Jashore, Bangladesh.
² Department of Food Engineering, North Pacific International University of Bangladesh, Dhaka, Bangladesh.
³ Department of Nutrition and Food Technology, Jashore University of Science and Technology, Jashore, Bangladesh. hasanm_agb@yahoo.com.

PMID: 38062275
DOI: 10.1007/s10528-023-10589-1

Abstract

In human genome, members of Paired box (PAX) transcription factor family are highly sequence-specific DNA-binding proteins. Among PAX gene family members, PAX4 gene has significant role in growth, proliferation, differentiation, and insulin secretion of pancreatic β-cells. Single nucleotide polymorphisms (SNPs) in PAX4 gene progress in the pathogenesis of various human diseases. Hence, the molecular mechanism of how these SNPs in PAX4 gene significantly progress diseases pathogenesis needs to be elucidated. For the reason, a series of bioinformatic analyzes were done to identify the SNPs of PAX4 gene that contribute in diseases pathogenesis. From the analyzes, 4145 SNPs (rsIDs) in PAX4 gene were obtained, where, 362 missense (8.73%), 169 synonymous (4.08%), and 2323 intron variants (56.04%). The rest SNPs were unspecified. Among the 362 missense variants, 118 nsSNPs were found as deleterious in SIFT analysis. Among those, 25 nsSNPs were most probably damaging and 23 were deleterious as observed in PolyPhen-2 and PROVEAN analyzes, respectively. Following all analyzes, 14 nsSNPs (rs149708455, rs115887120, rs147279315, rs35155575, rs370095957, rs373939873, rs145468905, rs121917718, rs2233580, rs3824004, rs372751660, rs369459316, rs375472849, rs372497946) were common and observed as deleterious, probably damaging, affective and diseases associated. Following structural analyzes, 11 nsSNPs guided proteins were found as most unstable and highly conserved. Among these, R20W, R39Q, R45Q, R60H, G65D, and A223D mutated proteins were highly harmful. Hence, the results from above-mentioned integrated comprehensive bioinformatic analyzes guide how different nsSNPs in PAX4 gene alter structural and functional characteristics of the protein that might progress diseases pathogenesis in human including type 2 diabetes.

Keywords: Paired box 4; Protein characteristics; Single nucleotide polymorphisms.

Grants and funding

24IF16463/Information and Communication Technology Division