We observed a patient with a cryptic subtelomeric de novo balanced translocation 46,XY.ish t(11;20)(p15.4;q13.2) presenting with severe mental retardation, muscular hypotonia, seizures, bilateral sensorineural hearing loss, submucous cleft palate, persistent ductus Botalli, unilateral cystic kidney dysplasia and frequent infections. Fluorescence in situ hybridization mapping and sequencing of the translocation breakpoints showed that no known genes are disrupted at 20q13.2 and that ST5 (suppression of tumorigenicity 5; MIM 140750) is disrupted on 11p15.4. By quantitative PCR from different human tissues we found ST5 relatively evenly expressed in fetal tissues. ST5 expression was more pronounced in adult brain, kidney and muscle than in the corresponding fetal tissues, whereas expression in other tissues was generally lower than in the fetal tissue. Using RNA in situ hybridization in mouse we found that St5 is expressed in the frontal cortex during embryonic development. In adult mouse brain expression of St5 was especially high in the hippocampal area and cerebellum. Hence we suppose that ST5 plays an important role in central nervous system development probably due to disturbance of DENN-domain mediated vesicle formation and neurotransmitter trafficking. Thus, our findings implicate ST5 in the etiology of mental retardation, seizures and multiple congenital anomalies.