BackgroundHereditary multiple exostoses (HME) is an autosomal dominant skeletal disorder characterized by the development of multiple, circumscript and usually symmetric bony protuberances called osteochondromas. Most HME are caused byEXT1andEXT2loss of function mutations. Most pathogenic mutations are nonsense followed by missense mutations and deletions.Case presentationHere we report on a patient with a rare and complex genotype resulting in a typical HME phenotype. Initial point mutation screening inEXT1andEXT2genes by Sanger sequencing did not reveal any pathogenic variants. The patient along with the healthy parents was subsequently referred for karyotype and array-Comparative Genomic Hybridization (CGH) analyses.Chromosomal analysis revealed two independent de novo apparently balanced rearrangements: a balanced translocation between the long arms of chromosomes 2 and 3 at breakpoints 2q22 and 3q13.2 and a pericentric inversion with breakpoints at 8p23.1q24.1. Both breakpoints were confirmed by Fluorescence In Situ Hybridization (FISH). Subsequently, array-CGH revealed a novel heterozygous deletion within theEXT1gene at one of the inversion breakpoints, rendering the inversion unbalanced. The mode of inheritance, as well as the size of the deletion were further investigated by Quantitative Real-time PCR (qPCR), defining the deletion as de novo and of 3.1 kb in size, removing exon 10 ofEXT1. The inversion in combination with the 8p23.1 deletion most likely abolishes the transcription ofEXT1downstream of exon 10 hence resulting in a truncated protein.ConclusionsThe identification of a rare and novel genetic cause of HME, highlights the importance of additional comprehensive investigation of patients with typical clinical manifestations, even whenEXT1andEXT2mutation analysis is negative.