Large non-coding deletions and translocation breakpoints over 1.2 megabases (Mb) upstream of SOX9 are implicated in Pierre Robin sequence (PRS) (Tan and Farlie, 2013; Paletta et al., 1994), a malformation characterised by underdevelopment of the lower jaw, backwards displacement of the tongue, airway obstruction and frequent incidence of cleft palate (Amarillo et al., 2013; Benko et al., 2009; Gordon et al., 2009, 2014). Here, SOX9 is linked to cleft palate.