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TCF12-related craniosynostosis can be caused by small heterozygous loss-of-function mutations inTCF12. Large intragenic rearrangements, however, have not been described yet. Here, we present the identification of four large rearrangements inTCF12causingTCF12-related craniosynostosis. Whole-genome sequencing was applied on the DNA of 18 index cases with coronal synostosis and their family members (43 samples in total). The data were analyzed using an autosomal-dominant disease model. Structural variant analysis reported intragenic exon deletions (of sizes 84.9, 8.6, and 5.4 kb) inTCF12in three different families. The results were confirmed by deletion-specific PCR and dideoxy-sequence analysis. Separately, targeted sequencing of theTCF12genomic region in a patient with coronal synostosis identified a tandem duplication of 11.3 kb. The pathogenic effect of this duplication was confirmed by cDNA analysis. These findings indicate the importance of screening for larger rearrangements in patients suspected to haveTCF12-related craniosynostosis.