A Novel Nonsense Variant in TBX15 Transcription Factor Suggests an Expanded Genetic Spectrum Of Submucous Cleft Palate

Introduction and aims: Submucous cleft palate (SMCP) is a congenital craniofacial malformation. While TBX22 is a known pathogenic gene, the potential role of TBX15 in SMCP remains unclear. This study aimed to investigate the genetic etiology of SMCP in a multigenerational family and explore the possible involvement of TBX15. Methods: Whole-exome sequencing (WES) was performed on a 4-generation Chinese family with SMCP. Functional characterization of the identified variant was conducted through protein localization and transcriptional activity assays. Furthermore, single-nucleus RNA sequencing (snRNA-seq) of developing mouse palate tissues and immunofluorescence staining were employed to analyse the expression and role of Tbx15 during palatogenesis. Results: WES identified a heterozygous nonsense variant (c.C1231T, p.Gln411Ter) in the terminal exon of TBX15. This variant is predicted to produce a truncated protein. Functional analyses demonstrated that the mutant TBX15 protein exhibits aberrant cytoplasmic mis-localization and significantly reduced transcriptional activity. SnRNA-seq revealed high expression of Tbx15 in a specific mesenchymal cell population during mouse palate development, with the highest expression observed at E15.5. Immunofluorescence confirmed colocalization of TBX15 with osteogenic markers in the developing palate, implicating it in intramembranous bone formation. Conclusion: This study provides the first evidence that a loss-of-function variant in TBX15 is associated with SMCP. The findings suggest that TBX15 plays a critical role in palatal osteogenesis, potentially through mechanisms overlapping with TBX22, and implicate TBX15 as a potential novel candidate gene for SMCP, suggesting a possible expansion of the genetic spectrum of this condition. Clinical Relevance: The results suggest a potential expansion of the genetic spectrum of SMCP, offering new insights for molecular diagnosis and genetic counselling. Understanding TBX15's role in palate bone development may inform future research into therapeutic strategies.