In this report, we present the case of a 14-year-old male with a complex constellation of neurological, gastrointestinal, endocrine, and dysmorphic features, in whom two clinically relevant and genetically distinct diagnoses were identified, CTX and Klinefelter syndrome, responsible for the clinical phenotype, as well as an incidental pathogenic variant in BRCA2. The gene discussed is BRCA2; the disease is Klinefelter syndrome.