Refining the diagnosis of 46,XY disorders of sex development: insight from whole-exome sequencing

Differences in sex development (DSD) with 46,XY karyotype are a group of rare congenital conditions affecting the structure and function of the urogenital system. Published data indicate, that despite the increasingly widespread use of genetic testing, the etiology remains unclear in approximately half of cases.

To clarify the molecular causes of 46,XY DSD by performing whole-exome sequencing (WES) in a precisely phenotyped and clinically comprehensively evaluated group of patients.

WES was performed in a consecutive cohort of 39 children diagnosed in our center as 46,XY DSD (aged 0.2-17.9 years). 32 were assigned male, 6 female, and 1 was a transgender boy. All patients underwent detailed clinical, hormonal and biochemical evaluation prior to genetic testing.

A genetic cause explaining DSD phenotype was identified in 8 children. Pathogenic variants were detected in 3 patients, including variants in the AR and DHX37 genes. Likely pathogenic variants were found in 5 patients, affecting the AR and HSD17B3 genes. Variants of uncertain significance (VUSs) were identified in 7 patients, involving genes with well-established relevance to DSD- NR5A1, DHX37, AR, MAMLD1, SOS2andFAM111A. Although classified as VUSs these variants represent plausible contributors to the patients' phenotypes. In the remaining children, no variants currently known or suspected to be associated with 46,XY DSD were identified. The most common confirmed etiology in the cohort was androgen insensitivity syndrome (AIS). In addition, pathogenic variants in genes not linked to DSD were identified in 7 patients, demonstrating the broader clinical utility of WES.

Our findings confirm that even a broad, high-throughput method such as WES fails to establish the molecular cause of 46,XY DSD in a substantial proportion of well-phenotyped patients, while at the same time enabling the identification of pathogenic variants in genes unrelated to DSD. We observed frequent genotype-phenotype discordance: similar clinical phenotypes could be associated with different genotypes, whereas the same gene variant could present with variable clinical expression. Re-analysis of WES data after 12-24 months should be considered in patients without a definitive diagnosis or in those who develop additional clinical features.