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Background  KBG syndrome, a rare autosomal disorder characterised by distinctive craniofacial and skeletal features and developmental delay, is caused by haploinsufficiency of the  ANKRD11  gene.    Results  Here we describe two siblings with multiple symptoms characteristic of KBG and their mother with a milder phenotype. In the siblings, array-based comparative genomic hybridization (array CGH) identified an intragenic microduplication affecting  ANKRD11  that was absent from the parents’ array CGH profiles. Microsatellite analysis revealed the maternal origin of the rearrangement and interphase fluorescent  in situ  hybridization (i-FISH) experiments identified the rearrangement in low-level mosaicism in the mother. Molecular characterisation of the duplication allele demonstrated the presence of two mutant  ANKRD11  transcripts containing a premature stop codon and predicting a truncated non-functional protein.    Conclusions  Similarly to deletions and point mutations, this novel pathogenetic rearrangement causes haploinsufficiency of  ANKRD11 , resulting in KBG syndrome.    Electronic supplementary material  The online version of this article (doi:10.1186/s13039-015-0126-7) contains supplementary material, which is available to authorized users.

Familial intragenic duplication of ANKRD11 underlying three patients of KBG syndrome