UCSF

Background: Cleft lip with or without cleft palate (CL/P) results from failed fusion of the facial prominences during embryogenesis. The cranial base, shaped largely by intrinsic developmental controls, serves as a practical proxy for the embryonic brain morphology that governs facial prominence positioning and fusion timing. Its relationship to CL/P severity in humans remains incompletely characterized.Objectives: To compare basicranial and facial shape between CL/P and non-cleft individuals, quantify their morphological covariation, and determine whether these parameters correlate with cleft severity.Materials and Methods: CBCT images from 30 children with non-syndromic CL/P (ages 7–11), acquired prior to alveolar bone grafting or orthodontic treatment, were compared to 29 age- and sex-matched controls. Thirty-nine basicranial and 29 facial three-dimensional landmarks were placed and analyzed using geometric morphometrics in MorphoJ, including Procrustes superimposition, PCA, CVA, PLS analysis, and multivariate regression against cranial base width and flexure.Results: CL/P individuals had basicrania that were wider anteriorly and in the middle, narrower posteriorly, and shorter in the anterior-to-posterior dimension. Their midfaces were wider and less anteriorly projecting. Anterior and middle cranial base width increased in the cleft group; posterior width was greater in controls. Cranial base flexure explained less variance than the width measures. PLS analysis confirmed significant basicranial-facial covariation: narrower, longer basicrania predicted longer, more projecting faces in controls, while wider, shorter basicrania predicted retruded midfaces in CL/P individuals. Asymmetry trends favored the CL/P group but did not reach significance, and no clear severity-specific relationship was established, likely due to limited subgroup sample sizes.Conclusions: CL/P is associated with a distinct, quantifiable basicranial and facial morphological profile consistent with a wider anterior brain influencing facial prominence fusion. Significant basicranial-facial covariation supports their developmental integration. Early basicranial morphometrics may inform anticipation of midfacial retrusion, interceptive orthodontic timing, and surgical planning in CL/P patients.