We present an 8-year-old girl with cleidocranial dysplasia, psychomotor developmental delay, poor wound healing and a 6p21.2–p12.3 deletion detected by aCGH. The patient was previously found to have a normal karyotype on conventional cytogenetic analysis and no RUNX2 mutation on sequence analysis. We discuss the genotype–phenotype correlation and the consequence of haploinsufficiency of CUL7, VEGFA, NFKBIE and RUNX2 in this case.