Molybdenum cofactor deficiency type B (MOCODB, #252160) is a rare autosomal recessive metabolic disorder characterized by intractable seizures of neonatal-onset, muscular spasticity, accompanying with hypouricemia, elevated urinary sulfite levels and craniofacial dysmorphism. Thirty-five patients were reported to date. Our paper aimed to delineate the disease genotype by presenting another patient, in whom novel, inframe variant within the MOCS2 gene was identified. Its clinical significance was supported by the medical history and analysis of the possible mutation consequences on a molecular level with the use of the available crystal structure of the human molybdopterin synthase complex. Moreover, potential pathomechanism resulting from molecular defect was presented, giving original insight into current knowledge on this rare disease, including treatment options.