Introduction: Ellis-Van Creveld syndrome is a rare genetic disorder characterised by skeletal abnormalities, cardiac anomalies, and findings of hidrotic ectodermal dysplasia. Cardiac anomalies are common in this syndrome and usually include an atrial septal defect when present. The disorder is caused by homozygous or compound heterozygous pathogenic variants in the EVC and EVC2 genes. A small number of patients with Ellis-Van Creveld syndrome have also been found to have copy number variants associated with these two genes. Case Presentation: A 13-year-old girl patient was referred to the paediatric genetic department with short stature, short extremities, operated post-axial polydactyly, nail hypoplasia, and severe mitral valve insufficiency. Chromosomal microarray analysis identified a 45 kb homozygous deletion encompassing exons 3–11 of the EVC gene at 4p16.2. Conclusion: Herein, we present a case with an intragenic deletion of the EVC gene and expand the clinical and genetic spectrum of Ellis-Van Creveld syndrome.