Dyggve-Melchior-Clausen (DMC) syndrome is an autosomal skeletal dysplasia, caused by mutations in the DYM gene. The features of this condition include developmental delay skeletal deformity, coarse facial features, and skeletal abnormalities. This case report presents a novel mutation association between DMC syndrome and celiac disease, emphasizing unique clinical findings and management strategies. This case report presents the case of an eight-year-old boy from Saudi Arabia, born to consanguineous parents. The patient presented with delayed development, coarse facial features, skeletal deformity, and fused toes. Radiological findings showed hallmark features of DMC syndrome such as a double hump appearance of the spine, short tubular metacarpal bones, and a lacy pattern on the iliac crest. A homozygous pathogenic mutation in the DYM gene was confirmed by whole-exome sequencing. Furthermore, the patient had celiac disease serology positive. To our knowledge, we did not find any case of DMC syndrome and celiac disease. This case expands the clinical spectrum of DMC syndrome by documenting its association with celiac disease, a previously unreported comorbidity. It underscores the importance of comprehensive evaluation, including autoimmune screening, in patients with rare genetic disorders. Further research is needed to explore the potential link between DMC syndrome and autoimmune conditions.