Numerous cases of limb-girdle muscular dystrophy (LGMD) remain without genetic diagnoses, despite the stunning genetic advances of recent decades. We conducted exome sequencing on a cohort of unsolved LGMD subjects, with follow-up investigations that included Sanger sequencing, quantitative PCR, and zebrafish studies. In two unrelated probands with sporadic LGMD phenotypes, these analyses revealed and confirmed compound heterozygous putative pathogenic mutations for a nuclear mitochondrial gene not previously associated with a human disease. Dramatic reductions in gene expression were confirmed on RNA derived from muscle biopsy samples representing the two probands. Knockdown of the gene in human myoblast culture was associated with abnormal mitochondrial cellular distribution. Knockdown of the homologous gene in zebrafish was associated with reduced motility. In aggregate, these results support the causative role of mutations in this nuclear mitochondrial gene in a subset of patients with LGMD.