The m.9952G>A (p.W249Term) variant in MT-CO3 has been reported in one individual with mitochondrial disease to date, in a 36-year-old woman with encephalopathy, myopathy, exercise-induced myalgia, muscle weakness, and migraines, with onset of symptoms at age 17 years (PMID: 9634511). Muscle biopsy showed reduced COX activity and decreased complex IV activity. The variant was present at 57% heteroplasmy in muscle and was undetectable in blood and skin. The variant was absent in muscle from her mother (PM6; PMID: 9634511). This variant causes a premature stop in the MT-CO3 gene resulting in truncation of 5% of the protein (PVS1_moderate). This variant is absent in the MITOMAP GenBank dataset, gnomAD v3.1.2, and the Helix dataset (PM2_supporting). There are no in silico predictors for this type of variant in mitochondrial DNA. Single fiber testing showed higher levels of the variant in COX negative fibers (56.2%, n=24) than in COX positive fibers (10.1%, n=21), p<0.0002 (PS3_supporting, PMID: 9634511). In summary, this variant meets criteria to be classified as likely pathogenic for primary mitochondrial disease inherited in a mitochondrial manner. This classification was approved by the NICHD/NINDS U24 ClinGen Mitochondrial Disease Variant Curation Expert Panel on February 26, 2024. Mitochondrial DNA-specific ACMG/AMP criteria applied (PMID: 32906214): PM6, PVS1_moderate, PM2_supporting, PS3_supporting.