Spondyloepiphyseal dysplasia (SEDKF) is a rare skeletal dysplasia associated with kyphosis and low bone mineral density, significantly delayed growth, and skeletal deformities. Blood lysosomal enzyme levels have also been shown to be elevated with a delay in development. The first variant described was compound heterozygosity for mutations in the MBTPS1 gene: a 1-bp duplication and a missense mutation. In the current study, we examined a Saudi consanguineous family. Clinical features like spondyloepiphyseal dysplasia, indicative of characteristic skeletal abnormalities, and impaired cognitive abilities were observed. Our patient has dysmorphic facial features, short stature, and significant skeletal deformities. A homozygous missense MBTPS1 (c.2634C > A p. (Ser878Arg)) with unknown significance was discovered in the whole exome; pathogenic MBTPS1 variants cause the autosomal recessive Kondo-Fu type of spondyloepiphyseal dysplasia (SEDKF, OMIM®: 618392). The whole exome sequence, which described a homozygous missense variant of unknown clinical significance (VUS, class 3 variant) in the MBTPS1 gene, was heterozygous in both asymptomatic parents. We are mindful that changing the classification of a variant of unknown significance is challenging. Considering clinical phenotypes and radiological findings produced by the pathogenic mutation in the MBTPS1 gene, the identified c.2634C > A variant is supported and may be categorized as likely pathogenic based on clinical symptoms.