Case report We describe an unusual clinical case with an 11-Mb deletion at 4q27 (chr4: 123094652-134164491), craniosynostosis (CS), mild psychomotor retardation, and facial dysmorphic features. This deletion involves 18 genes; FGF2, NUDT6, and SPRY1 are primarily or secondarily implicated in human cranial bone and sagittal suture development and could play an important role in CS. Conclusions Clinicians should always contemplate genetic studies in patients with syndromic CS. Mutational targeted genetic testing is appropriate for patients with classical or specific CS syndrome. Nevertheless, array comparative genomic hybridization (array CGH) should be considered as a first-line test in nontypical syndromic CS phenotype. Cytogenetic studies are decisive for genetic counseling indeed.