In silico prediction and functional analysis of non-synonymous single-nucleotide polymorphisms (nsSNPs) in human ACTL7A gene associated with spermatogenesis

Actin-like 7A (ACTL7A) is considered to play an important role in acrosome formation, fertilization, and early embryo development. Several single-nucleotide polymorphisms (SNPs) in ACTL7A have been reported to be associated with male infertility. However, the functional consequences of the most non-synonymous SNPs (nsSNPs) in ACTL7A remain largely unclear. Here, a total of 489 nsSNPs in the ACTL7A gene were retrieved from the Database of Single-Nucleotide Polymorphism (dbSNP) and systematically analyzed using a series of computational tools. Among these, 44 nsSNPs were predicted to be potentially deleterious. Further in vitro validation identified eight nsSNPs associated with significantly decreased ACTL7A protein levels, which were therefore considered candidate functional variants, including rs534593253, rs775405375, rs768576884, rs1308056655, rs779034458, rs779515458, rs1827186853, and rs1827186891. In addition, one deletion variant and three nonsense variants were identified. Structural modeling further suggested that these nsSNP-derived variants may induce conformational alterations in the ACTL7A protein. Overall, this study provides a framework for prioritizing functionally relevant ACTL7A nsSNPs for future investigation.