Schaaf–Yang syndrome (SYS) was recently identified as a genetic condition resembling Prader–Willi syndrome. It is caused by mutations on the paternal allele of the MAGEL2 gene, a gene that has been mapped in the Prader–Willi critical region. Here, we present an infant with SYS who sadly died because of the combination of hypotonia, sleep apnea, and obesity. A heterozygous premature stop mutation in MAGEL2 was identified in the patient. The main factors reported in the mortality of SYS are lethal arthrogryposis multiplex congenita, fetal akinesia, and pulmonary problems. Our clinical report indicates that obesity and its complications are an important additional factor in the mortality associated with SYS. Therefore, we advise to strictly monitor weight and intensively treat overweight and obesity in SYS.