A complex structural variant near SOX3 causes X-linked split-hand/foot malformation

Elke de Boer, Carlo Marcelis, Kornelia Neveling, Ellen van Beusekom, Alexander Hoischen, Willemijn M. Klein, Nicole de Leeuw, Tuomo Mantere, Uirá S. Melo, Jeroen van Reeuwijk, Dominique Smeets, Malte Spielmann, Tjitske Kleefstra, Hans van Bokhoven, Lisenka E.L.M. Vissers*

*Corresponding author for this work


Split-hand/foot malformation (SHFM) is a congenital limb defect most typically presenting with median clefts in hands and/or feet, that can occur in a syndromic context as well as in isolated form. SHFM is caused by failure to maintain normal apical ectodermal ridge function during limb development. Although several genes and contiguous gene syndromes are implicated in the monogenic etiology of isolated SHFM, the disorder remains genetically unexplained for many families and associated genetic loci. We describe a family with isolated X-linked SHFM, for which the causative variant could be detected after a diagnostic journey of 20 years. We combined well-established approaches including microarray-based copy number variant analysis and fluorescence in situ hybridization coupled with optical genome mapping and whole genome sequencing. This strategy identified a complex structural variant (SV) comprising a 165-kb gain of 15q26.3 material ([GRCh37/hg19] chr15:99795320-99960362dup) inserted in inverted position at the site of a 38-kb deletion on Xq27.1 ([GRCh37/hg19] chrX:139481061-139518989del). In silico analysis suggested that the SV disrupts the regulatory framework on the X chromosome and may lead to SOX3 misexpression. We hypothesize that SOX3 dysregulation in the developing limb disturbed the fine balance between morphogens required for maintaining AER function, resulting in SHFM in this family.

Original languageEnglish
Article number100200
JournalHuman Genetics and Genomics Advances
Issue number3
Pages (from-to)100200
Publication statusPublished - 13.07.2023

Research Areas and Centers

  • Research Area: Medical Genetics


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