Gene set enrichment analysis of curated monogenic loci highlights key pathways and multisystem involvement in male infertility

Male infertility affects approximately 10% of men globally, yet approximately 70% of cases lack a definitive genetic diagnosis. Next-generation sequencing has identified numerous monogenic causes, many of which are linked to broader systemic conditions. We curated a list of 596 candidate genes associated with male infertility from the literature and clinical genetics panels. Gene set enrichment analyses were performed on the strong-evidence genes using g: Profiler, REVIGO, and PANTHER to identify overrepresented Gene Ontology (GO) terms, and Reactome pathways. Gene–tissue expression profiles were assessed using GTExv8.

Among the 178 strong-evidence genes, enrichment analyses revealed significant overrepresentation of terms related to ciliary and flagellar function (e.g., cilium movement, dynein complex), endocrine signaling (e.g., hormone receptor binding, steroid biosynthesis), and DNA repair mechanisms, particularly the Fanconi anemia nuclear complex. Reactome pathway analysis identified overrepresentation of androgen, glucocorticoid, and mineralocorticoid biosynthesis, BBSome-mediated ciliary transport, and meiosis. Tissue expression clustering identified extra-gonadal expression patterns, implicating adrenal, hypothalamic, and systemic involvement in genetic forms of male infertility.

Our gene set enrichment and tissue expression analyses suggest that monogenic causes of male infertility are enriched in pathways in ciliary motility, endocrine regulation, and DNA repair which also have roles in extra-gonadal organ systems. These findings are consistent with epidemiological observations linking male infertility to broader health conditions and support multidisciplinary evaluation and care for affected individuals.