In Silico Analysis of CYP1B1 Gene Mutations in Pakistani Families Reveals Structural and Functional Characteristics

Mutations in the CYP1B1 gene have been associated with primary congenital glaucoma (PCG), a developmental visual disorder. CYP1B1 mutations have been linked to increased lipid peroxidation and abnormalities in trabecular meshwork. In this study, protein modeling was utilized to analyze the pathogenicity of hotspot mutations in the CYP1B1 gene in Pakistani families with PCG. Methods: A comprehensive literature survey was conducted to identify CYP1B1 mutations in Pakistani Patients. Ensemble was used to identify missense mutations. 3-D modeling of the mutants was done using ITasser. Potential deleterious effects and pathogenicity were evaluated using PolyPhen-2. The effects of amino acid substitutions on protein function were assessed using SIFT analysis, scoring pathogenic mutations from 0.0 to 1.0 in decreasing order. The secondary structure of the mutated protein was predicted using PSIRED. MusiteDeep server identified potential phosphorylation sites, while Pfam database examined the potentially mutated domains. The potential effects on other genes were evaluated using Gene MANIA server and STRING databases. Results: A total of 5 hotspot mutations—4 missense (c.716C>G/p. A115P, c.988G>T/p. A330F, c.355G>T/p. A119S, and c.1058C>T/p. E229K) and 1 frameshift mutation (c.1325delC/p. P442Efs*15)—were identified among Pakistani patients. A119S was the most common mutation. 3-D modeling of the mutant proteins using i-Tasser revealed the global topology of the variants. Moreover, the phylogenetic tree of the CYP1B1 gene revealed its closest association with Phodopus roborovskii. Secondary structure of the mutant had six alpha helices, six coils, and six extracellular structures. Potential phosphorylation was identified in two nsSNP residues. Conclusion: This in silico analysis contributes to understanding the structural and functional implications of CYP1B1 gene mutations. These insights can potentially help in the development of new targeted and personalized treatments for PCG patients.