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Balanced translocations affecting the paternal copy of 15q11–q13 are a rare cause of Prader–Willi syndrome (PWS) or PWS-like features. Here we report on the cytogenetic and molecular characterization of a  de novo  balanced reciprocal translocation t(X;15)(q28;q12) in a female patient with atypical PWS. The translocation breakpoints in this patient and two previously reported patients map 70 – 80 kb distal to the  SNURF - SNRPN  gene and define a breakpoint cluster region. The breakpoints disrupt one of several hitherto unknown 3′ exons of this gene. Using RT–PCR we demonstrate that sequences distal to the breakpoint, including the recently identified C/D box small nucleolar RNA (snoRNA) gene cluster  HBII-85  as well as  IPW  and  PAR1 , are not expressed in the patient. Our data suggest that lack of expression of these sequences contributes to the PWS phenotype.

A translocation breakpoint cluster disrupts the newly defined 3′ end of the SNURF - SNRPN transcription unit on chromosome 15