Impaired Mitochondrial Translation and Bioenergetic Dysfunction Associated with the MT-RNR1 m.1014A>G Variant

Pathogenic variants in MT-RNR1 are classically associated with aminoglycoside-induced sensorineural hearing loss through disruption of the mitochondrial 12S rRNA decoding center. Their contribution to pediatric neurological disease remains poorly defined. We identified a novel homoplasmic MT-RNR1 variant, m.1014A>G, in a patient with drug-resistant focal epilepsy beginning at 9 months of age who remained undiagnosed after trio whole-exome sequencing filtered using an extensive epilepsy gene panel. The variant was also detected in her mother. Structural modeling suggests that the variant, affecting a highly conserved region of the mitochondrial 12S rRNA, may alter the mitochondrial small ribosomal subunit assembly. To investigate its pathogenicity, we performed comprehensive functional studies in patient-derived fibroblasts. Unlike canonical MT-RNR1 variants, m.1014A>G did not confer aminoglycoside toxicity. Functional in vitro studies on patients’ fibroblasts demonstrated increased 12S/16S rRNA ratios, reduced abundance of both mitoribosomal subunit proteins, decreased levels of mitochondrially encoded respiratory-chain subunits, and impaired oxidative phosphorylation. These abnormalities were accompanied by mitochondrial network fragmentation, increased mitochondria–lysosome colocalization suggestive of enhanced mitophagy and reduced mitochondrial DNA copy number. Altogether, the findings are consistent with defective mitoribosome assembly and altered mitochondrial translation, resulting in a bioenergetic defect. Our study points to a previously unrecognized candidate pathogenic mechanism associated with MT-RNR1 and may expand the phenotypic spectrum of MT-RNR1-related disorders to include maternally inherited infantile-onset epileptic encephalopathy. These findings highlight the importance of dedicated mitochondrial DNA analysis in children with unexplained early-onset epilepsy despite negative nuclear genomic testing.