Autosomal recessive disorders are the most common forms of hereditary diseases in consanguineous populations. Despite their frequencies, the diagnosis of these disorders continues to be a challenging task given their extreme genetic heterogeneities. However, since the discovery of next generation sequencing-based techniques, the number of pathogenic mutations linked to autosomal recessive disorders has increased dramatically due to the time and cost effectiveness of these methods. Succinyl-CoA:3ketoacid CoA transferase (SCOT) deficiency is considered as one of these rare autosomal recessive genetic disorders. In the present study, whole exome sequencing (WES) revealed a novel 3-oxoacid CoA-transferase 1(OXCT1) frameshift mutation in a consanguineous UAE family with autosomal recessive SCOT deficiency. Sanger sequencing analysis confirmed co-segregation with the disease in the studied family. Using real time PCR, we showed that this new frameshift mutation affects the OXCT1-mRNA by nonsense mediated mRNA decay (NMD). To the best of our knowledge, this is the first study associating SCOT deficiency with an OXCT1 frameshift mutation in the world. In addition, we report for the first time by studying this new OXCT1 mutation evidence for an NMD effect associated with SCOT mutations.