Characterization of a novel transcript of the EHMT1 gene reveals important diagnostic implications for Kleefstra syndrome

Willy M. Nillesen, Helger G. Yntema, Marco Moscarda, Nienke E. Verbeek, Louise C. Wilson, Frances Cowan, Marga Schepens, Annick Raas-Rothschild, Orly Gafni-Weinstein, Marcella Zollino, Raymon Vijzelaar, Giovanni Neri, Marcel Nelen, Hans Van Bokhoven, Jacques Giltay, Tjitske Kleefstra*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


The core phenotype of Kleefstra syndrome (KS) is characterized by intellectual disability, childhood hypotonia, and a characteristic facial appearance. This can be caused by either submicroscopic 9q34 deletions or loss of function mutations of the EHMT1 gene. Remarkably, in three patients with a clinical suspicion of KS, molecular cytogenetic analysis revealed an interstitial 9q34 microdeletion proximal to the coding region of the EHMT1 gene based on the NM- 024757.3 transcript. Because we found a mono-allelic EHMT1 transcript suggestive for haploinsufficiency of EHMT1 in two of these patients tested, we hypothesized that a deletion of regulatory elements or so far unknown coding sequences in the 5' region of the EHMT1 gene, might result in a phenotype compatible with KS. We further characterized the molecular content of deletions proximal to the transcript NM- 024757.3 and confirmed presence of a novel predicted open reading frame comprising 27 coding exons (NM- 024757.4). Further analysis showed that all three deletions included the presumed novel first exon of the EHMT1 gene. Subsequent testing of 75 individuals without previously detectable EHMT1 aberrations showed one additional case with a deletion comprising only this 5' part of the gene. These results have important implications for the genetic screening of KS and for studies of the functional significance of EHMT1.

Original languageEnglish
Pages (from-to)853-859
Number of pages7
JournalHuman Mutation
Issue number7
StatePublished - Jul 2011
Externally publishedYes


FundersFunder number
Seventh Framework Programme241995


    • 9qSTDS
    • Chromosome 9q
    • EHMT1
    • Kleefstra syndrome
    • Subtelomere deletion


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