Abstract The 22q11.2 region is a hotspot for chromosomal rearrangements mediated by LCR22A-D low-copy repeats. Sequence motifs and homology-driven mechanisms have been suggested to mediate rearrangements. Nevertheless, recent evidence has emphasized the role of functional properties in genome instability, suggesting that replication timing transition regions could be peculiarly prone to genetic damage. In this work, we show that an early-late replication-transition zone is localised within LCR22A, the shared proximal endpoint of the majority of deletions and duplications of 22q11.2 region. Transition zone is characterized by asynchronous replication and by a DNA flexibility peak, features which are relevant for double-strand breaks and rearrangements at fragile sites. This and other flexibility peaks, associated with less relevant replication anomalies, are present in clusters inside LCR22A, B and D. All of them are composed of modules of AT-rich sequences, DNA satellites, and a HIV-1 integration site; moreover, they have coincidental position with boundaries of duplicons inside segmental duplications and with breakpoints of recurrent translocations. Noteworthy, flexibility peaks also lay at breakpoints of translocation partner chromosomes, three of which, 1p21.2, 8q24.13 and 11q23.3, have been positioned inside known common fragile sites. In many cases peaks are associated with potential matrix attachment regions (MARs). We propose that, similarly to fragile sites, replication perturbation and flexibility peaks may mediate strand breakage and rearrangements. Consistently with this view we show that the replication timing transition zone detected inside LCR22A is susceptible to replicative stress by aphidicolin, known inducer of fragile sites. These findings emphasize the significance of mutagenic exposure for the constitutional syndrome origin.