Novel NR5A1 variants associated with hypospadias and disorders of sex development: A series case report of 4 patients.

rationaleNuclear receptor subfamily 5 group A member 1 (NR5A1), also known as steroidogenic factor 1 (SF-1), is a master regulator of gonadal development and steroidogenesis. Pathogenic variants in NR5A1 are increasingly recognized as a significant cause of 46,XY disorders of sex development (DSD) and hypospadias, yet the mutational spectrum - particularly in pediatric populations - remains incompletely characterized, hindering early diagnosis and personalized management. PATIENT CONCERNS: Four unrelated pediatric patients presented with a spectrum of genital anomalies: a 2-year-old 46,XY male with penoscrotal hypospadias; an 8-year-old 46,XY boy with micropenis and delayed puberty; a 5-month-old 46,XX infant with virilized genitalia and inguinal gonads; and a 2-year-old 46,XY child with severe genital ambiguity. Families expressed concerns about atypical genital appearance, uncertain sex assignment, future fertility, and the need for surgical or hormonal intervention. DIAGNOSES: All patients were diagnosed with DSD based on clinical, hormonal, and histopathological findings. Whole-exome sequencing identified four novel NR5A1 variants: a splice-site variant (c.1138 + 5G>A), a DNA-binding domain missense variant (c.308G>A; p.Arg103Gln), a deep intronic variant (c.990 + 20C>T), and a ligand-binding domain missense variant (c.1352T>G; p.Leu451Arg). Biochemical profiles consistently showed hypergonadotropic hypogonadism (elevated follicle-stimulating hormone, low testosterone/dehydroepiandrosterone sulfate), and gonadal biopsies confirmed dysgenesis.

interventionsOne patient (Case 1) underwent a novel one-stage sealed Y-shaped penile foreskin vascular protection surgery for hypospadias repair. The other patients received multidisciplinary care, including genetic counseling, endocrine monitoring, and planning for future hormone replacement or reconstructive surgery as needed. OUTCOMES: The surgical intervention in Case 1 achieved excellent cosmetic and functional outcomes with preserved vascular integrity. All patients remain under long-term follow-up. No complications related to interventions were reported during the observation period. LESSONS: This case series expands the pathogenic landscape of NR5A1 and demonstrates its capacity to disrupt sexual development across diverse karyotypes (46,XY and 46,XX). Early genetic diagnosis enables accurate classification, informs surgical and endocrine decision-making, guides gonadoblastoma surveillance, and facilitates family counseling. NR5A1 should be included in first-tier genetic testing for children with unexplained hypospadias or DSD, especially when accompanied by biochemical evidence of primary gonadal failure.