The maxillary and mandibular ICW in the Saethre-Chotzen syndrome or the TCF12-related craniosynostosis were statistically significantly smaller than those of the control group (β = − 1.99, 95% CI − 3.37, − 0.60; β = − 2.24, 95% CI − 3.41, − 1.07, respectively). Here, TCF12 is linked to Saethre-Chotzen syndrome.