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J Med Genet 49:380-385 doi:10.1136/jmedgenet-2011-100686
  • Developmental defects
  • Short report

Whole exome sequencing identifies a splicing mutation in NSUN2 as a cause of a Dubowitz-like syndrome

  1. Joseph G Gleeson1
  1. 1Department of Neurosciences and Pediatrics, Neurogenetics Laboratory, Institute for Genomic Medicine, Howard Hughes Medical Institute, University of California, San Diego, California, USA
  2. 2Wellcome Trust Centre for Stem Cell Research, University of Cambridge, Cambridge, UK
  3. 3The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
  4. 4Department of Paediatrics Faculty of Medicine & Health Sciences United Arab Emirates University Al Ain, United Arab Emirates
  1. Correspondence to Dr Joseph G Gleeson, Department of Neurosciences and Pediatrics, Neurogenetics Laboratory, Institute for Genomic Medicine, Howard Hughes Medical Institute, University of California, San Diego, CA 92093, USA; jogleeson{at}ucsd.edu Dr Lihadh Al-Gazali, Department of Pediatrics, United Arab Emirates University, School of Medicine and Health Sciences, 17666 Al Ain, United Arab Emirates.
  1. Contributors JGG designed the experiments with FJM and JHL. FM and JHL completed the experiments and analysed the data. JEL assisted in the experiments. EN and SG contributed whole exome sequencing data. LA-G conceived the study, examined patients and contributed all clinical information and patient samples. SB and MF generated m5C bisulfite sequencing data. JGG wrote the manuscript with FJM and JHL.

  • Received 12 December 2011
  • Revised 22 March 2012
  • Accepted 23 March 2012
  • Published Online First 10 May 2012

Abstract

Background Dubowitz syndrome (DS) is an autosomal recessive disorder characterized by the constellation of mild microcephaly, growth and mental retardation, eczema and peculiar facies. Over 140 cases have been reported, but the genetic basis is not understood.

Methods We enrolled a multiplex consanguineous family from the United Arab Emirates with many of the key clinical features of DS as reported in previous series. The family was analyzed by whole exome sequencing. RNA splicing was evaluated with reverse-transcriptase PCR, immunostaining and western blotting was performed with specific antibodies, and site-specific cytosine-5-methylation was studied with bisulfite sequencing.

Results We identified a homozygous splice mutation in the NSUN2 gene, encoding a conserved RNA methyltransferase. The mutation abolished the canonical splice acceptor site of exon 6, leading to use of a cryptic splice donor within an AluY and subsequent mRNA instability. Patient cells lacked NSUN2 protein and there was resultant loss of site-specific 5-cytosine methylation of the tRNA(Asp GTC) at C47 and C48, known NSUN2 targets.

Conclusion Our findings establish NSUN2 as the first causal gene with relationship to the DS spectrum phenotype. NSUN2 has been implicated in Myc-induced cell proliferation and mitotic spindle stability, which might help explain the varied clinical presentation in DS that can include chromosomal instability and immunological defects.

Footnotes

  • FJM and JHL contributed equally to this work.

  • Competing interests None.

  • Patient consent Obtained.

  • Ethics approval Ethics approval was provided by the UCSD Institutional Review Board.

  • Provenance and peer review Not commissioned; externally peer reviewed.