Members of the mitochondrial carrier family (SLC25) transport nucleotides, keto acids, amino acids, fatty acids, co-factors and inorganic ions across the mitochondrial inner membrane. Several inherited diseases with very variable clinical presentations are associated with dysfunctional mitochondrial carriers. We report a patient with childhood-onset spinal muscular atrophy and mitochondrial myopathy caused by a homozygous mutation in SLC25A21, encoding the mitochondrial oxodicarboxylate carrier (ODC). The mutation renders the carrier dysfunctional and, consequently, 2-oxoadipate cannot be imported into the mitochondrial matrix. Computer modelling of the metabolic defect caused by the mutation predicted that the impaired transport leads to accumulation of 2-oxoadipate, pipecolic acid and the known neurotoxin quinolinic acid, which were precisely confirmed by targeted metabolomics in serum and urine. Exposure of 2-oxoadipate and quinolinic acid reduced the level of mitochondrial complexes in SH-SY5Y cells in-vitro suggesting a possible pathomechanism. Here we demonstrate that 2-oxoadipate and quinolinic acid are toxic for spinal motor neurons and their increased levels may contribute to neuropathy.