The term “disorders/differences of sex development” (DSD) indicates a group of congenital conditions with atypical development of chromosomal, gonadal, or anatomical sex. The 46, XY DSD are characterized by ambiguous external genitalia with a 46, XY karyotype (1). Advances in genomics, particularly NGS, have helped identify multiple genes associated with 46, XY DSD, including NR5A1. Steroidogenic factor 1 (SF-1), encoded by the NR5A1 gene, is a transcription factor crucial for adrenal and gonadal organogenesis (2, 3). NR5A1 mutations have been detected in about 10%–20% of 46, XY DSD cases as the major causes of gonadal dysgenesis with a wide range of clinical phenotypes (4, 5). We present the case of a patient with ambiguous genitalia at birth who was investigated for DSD genetic panel conditions, emphasizing the importance of genetic analysis in understanding and managing DSD cases. This individualized approach is crucial for ensuring the well-being of patients and their families, both physically and mentally (6).

DSDs include a spectrum of phenotypes defined by congenital conditions in which chromosomal, gonadal, or anatomical sex is atypical. Hypospadias is the most frequent form of DSD due to a disruption of the development of the ventral face of the penis in which, the most evident feature is the urethral meatus in an ectopic position. Most often, hypospadias is relatively mild and a genetic cause is not searched or identified (9). However, severe forms, such as posterior and perineal hypospadias with micropenis and significant chordee, represent some of the most severe 46,XY DSDs and may result in ambiguous genitalia at birth. DSDs with a genital appearance that is sufficiently atypical to prompt evaluation occur in approximately 1 in 1,000–4,500 live births (10). The clinical and psychosocial impact of hypospadias is significant, requiring surgical correction typically around one year of age. In severe cases, hypospadias may compromise sexual function, affect quality of life, and impair psychosocial development (11). While most cases are isolated, some are associated with a more complex genetic syndrome involving anomalies of genital development. Moreover, hypospadias may present alongside other abnormalities such as undescended testis, bifid scrotum or inguinal hernia. Overall, less than 10% of cases may be related to genetic defects (12). Familial clustering is present in about 10% of patients with hypospadias. The inheritability is estimated between 57% and 77% of affected patients. Severe hypospadias are generally seen as isolated cases, while milder variants are more often familial (13). The etiology of hypospadias is multifactorial (14, 15). Several genes have been founded to link with hypospadias such as DGKK, ESRs, HOX, ATF3 and VAMP. The precise role of androgen and estrogen signaling that interact in a temporal and tissue-specific manner during genital tubercle development may explain the wide range of meatal/urethral defects. Significant alterations in DNA methylation of sex hormone receptor genes (ESR1 and AR) and fibroblast growth factor (FGFR2 FGF8) may correlate with abnormal expression of these genes in patients with hypospadias. These findings suggest a potential role for epigenetic modifications in hypospadias etiology that, potentially, can be transmitted to future generations. In our case, the patient presented with severe genital malformation, characterized by perineal hypospadias, micropenis, bifid scrotum, and penoscrotal transposition, linked to a heterozygous missense variant in the NR5A1 gene. Although the variant was classified as a variant of uncertain significance (VUS), its identification necessitated a multidisciplinary approach that guided surgical interventions and emphasized the need for long-term follow-up. Mutations in NR5A1 are associated with a broad spectrum of phenotypes, including testicular dysgenesis, progressive endocrine dysfunction and reproductive challenges (3). These factors may also contribute to the risk of gender dysphoria in later life, particularly in cases of severe genital ambiguity. The interplay between physical characteristics, hormonal influences, and psychosocial factors requires ongoing monitoring and psychosocial support. Moreover, the development of gender identity in individuals with NR5A1 mutations may progress over time, necessitating adaptability in management approaches. Comprehensive follow up, including endocrine, psychological, and surgical assessments, is crucial to ensure holistic care and address any emerging concerns, such as declining testosterone production, fertility preservation, or the risk of germ cell tumors (3). Genetic counseling remains essential for the patient and their family, as NR5A1 variants can have implications for female relatives, including the potential for primary ovarian insufficiency (16). The limitations of the studies trying to correlate hypospadias and genetics are that the etiology of hypospadias is obviously multifactorial. These studies are often conducted on a limited number of cases and on a single ethnic group or race. In addition, the various cases of hypospadias are not the same, and the results of the studies are often discordant. To overcome these problems, multicenter studies are needed.

This case underscores the significance of genetic testing in severe hypospadias, highlighting its contribution to multidisciplinary management and long-term monitoring. The identification of an NR5A1 variant, classified as a variant of uncertain significance (VUS), informed surgical decisions and heightened awareness of possible endocrine complications.

Comprehensive care must emphasize endocrine monitoring, psychosocial support, and fertility preservation. Genetic counseling is essential for addressing familial implications and customizing patient-specific strategies. Additional research is required to delineate more precise correlations between genetic findings and clinical outcomes in severe DSD cases.