Potentially Deleterious Nonsynonymous Single Nucleotide Polymorphisms (nsSNPs) in the Human MCPH1 Gene: Systematic In Silico Predictions and Implications for Structure and Function.

BACKGROUND: The microcephalin 1/BRITI1 (MCPH1) gene has been implicated in microcephaly (MCPH), primary ciliary dyskinesia (PCD) syndrome, enlarged cranial volume, and pancreatic and breast cancers. It functions as a tumor suppressor and shows reduced expression in various cancer types. Therefore, the identification of MCPH1 polymorphisms is of paramount importance. AIMS AND OBJECTIVES: Considering the multifaceted role of MCPH1, this study is aimed at examining the structural and functional impact of nonsynonymous single nucleotide polymorphisms (nsSNPs) on MCPH1 using in silico tools to understand its potential role in pathogenesis. METHODOLOGY: In the present investigation, a wide array of in silico tools was deployed to explicate putative pathogenic missense/nsSNPs that might impact the structural integrity and molecular functions of MCPH1. The mining of damaging nsSNPs was carried out based on the evolutionary conservation of sequence information, prediction of protein stability, interaction analysis, and their potential impact was assessed using structure prediction and 3D modeling, and interaction with other genes/pathways. RESULTS: In the initial screening, SIFT, PolyPhen-2, SNAP2, Align GVGD, PhD-SNP, PANTHER, and SNPs&GO revealed 23 potential deleterious SNPs in MCPH1. Population frequency analysis using gnomAD revealed that the prioritized variants were extremely rare in the global population. I-mutant and ConSurf further revealed that 16 nsSNPs exhibited a decrease in protein stability due to changes in size and charge. I-TASSER was used to predict wild-type and mutant protein 3D structures. The potential effect of variation on 3D protein structure was assessed using the Chimera tool, which presented the probable structural loss in eight variants, including p.A11D, p.H49D, p.T59I, p.W60S, p.W60C, p.L74P, p.C79G, and p.L781P. Most of these potential variants resided in the N-terminal BRCT domain, which is implicated in neurodevelopment, and thus may lead to the pathogenesis of primary microcephaly. Furthermore, single-cell transcriptomic mapping of MCPH1 against dataset of 33,206 cells from malformations of cortical development detected MCPH1 expression across multiple cellular populations. This broad distribution suggested potential MCPH1 function across several neural and glial cell populations. CONCLUSION: The potentially deleterious nsSNPs predicted in this study can be of great significance in understanding MCPH1-related diseases and may serve as potential targets for future functional validation and therapeutic interventions.