STARD9 and CDK5RAP2—Novel Candidate Genes for 46,XY Complete Gonadal Dysgenesis

46,XY gonadal dysgenesis, characterised by absent or defective testicular development in individuals with a 46,XY karyotype, results from disruptions in the genetic programme governing testis determination and differentiation during embryogenesis. While monogenic causes explain approximately 50% of cases, emerging evidence suggests an oligogenic basis in some patients. However, many cases remain without a definitive molecular diagnosis. In this study, we investigated a patient with 46,XY gonadal dysgenesis to explore the underlying genetic aetiology. Whole-exome sequencing in the patient did not reveal any pathogenic variants in genes previously associated with this condition. Instead, it detected rare variants in <i>STARD9</i> and <i>CDK5RAP2</i>, which encode centrosomal proteins known to interact with each other. Gene expression analysis of embryonic gonads revealed that <i>STARD9</i> is sexually dimorphic, with the highest expression in testis-specific Sertoli cells, while <i>CDK5RAP2</i> is ubiquitously expressed, including in Sertoli cells. These findings suggest a role for both genes in Sertoli cell development, implicating them in the pathogenesis of 46,XY gonadal dysgenesis. To evaluate the functional relevance of the identified variants, we performed molecular dynamics simulations, which suggest that these variants may impair the individual and/or combined functions of STARD9 and CDK5RAP2 proteins. This study is the first to propose a role for <i>STARD9</i> and <i>CDK5RAP2</i> genes in human Sertoli cell development and highlights their potential contribution to 46,XY gonadal dysgenesis.