Whole-genome sequencing identifies a potentially causative homozygous splicing variant in RAD54 like in non-obstructive azoospermia

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Background: Non-obstructive azoospermia (NOA) is a severe form of male infertility characterized by impaired spermatogenesis. Although chromosomal abnormalities and Y-chromosome microdeletions are known causes, many cases remain idiopathic, suggesting that other genetic factors may be involved. RAD54 like (RAD54L) is a key component of the homologous recombination pathway required for DNA double-strand break repair and meiotic progression. Objective: To identify the potential genetic cause of NOA using whole-genome sequencing (WGS) in affected individuals from consanguineous families. Materials and Methods: For performing this experimental study, 10 NOA men who were referred to Infertility Center of the Yazd Reproductive Sciences Institute, Yazd, Iran underwent clinical, hormonal, and genetic evaluations. Genomic DNA was extracted from peripheral blood and was subjected to WGS. Variants were filtered and prioritized based on allele frequency, predicted pathogenicity, inheritance pattern, and gene expression data. In silico splicing analyses were performed using SpliceAI and Human Splicing Finder. Results: WGS identified an ultrarare homozygous splice-site variant, c.1375+1G>T, in the RAD54L gene. The variant affects a canonical donor splice site and is predicted to cause loss of normal splicing, likely resulting in exon 12 skipping, frameshift, and premature termination codon formation. RAD54L shows the highest expression in testicular tissue and plays a critical role in homologous recombination and meiotic DNA repair. The patient exhibited hormonal findings consistent with primary testicular failure. Conclusion: This study proposes RAD54L as a potential novel candidate gene linked to NOA and underscores the efficacy of WGS in identifying rare genetic etiologies of idiopathic male infertility. Further functional and clinical studies are needed to validate this association.

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