Application of Whole-Exome Sequencing in Identifying the Molecular Basis of Idiopathic Male Infertility

Male infertility represents a major clinical challenge. Despite standard genetic testing (karyotyping, Y-chromosome azoospermia factor (AZF) microdeletion testing, and CFTR variant analysis), the molecular cause remains unidentified in a substantial proportion of patients. These patients are consequently diagnosed with idiopathic male infertility. This review provides a comprehensive overview of the current evidence regarding the application of whole-exome sequencing (WES) in the molecular diagnosis and clinical management of idiopathic male infertility. WES can identify pathogenic variants associated with quantitative spermatogenic defects, qualitative abnormalities of sperm motility and morphology, and pre-testicular causes related to hypogonadotropic hypogonadism. When defining the cohort strictly as patients with true idiopathic non-obstructive azoospermia (NOA) who remain undiagnosed after standard testing, the pooled diagnostic yield of WES is approximately 10–15%. Estimates vary due to differences in cohort selection, variant interpretation, and the range of genes analysed. Establishing a precise molecular diagnosis improves genetic counselling, helps predict the likelihood of successful sperm retrieval via testicular sperm extraction (TESE) or microdissection TESE (micro-TESE), and informs treatment planning for assisted reproductive technologies. However, routine clinical implementation remains limited by the high frequency of variants of uncertain significance, the absence of standardised diagnostic pipelines, unequal access to testing, and ethical concerns. Emerging “all-in-one” diagnostic strategies, multi-omics integration, and whole-genome or long-read sequencing hold promise for improving genomic diagnostics. However, broader adoption will ultimately require ongoing standardisation and functional validation of identified variants.