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The numbers listed are the numbers of distinct individual-variant combinations found. Blue and green boxes highlight automated and manual prioritization approaches, respectively, with orange highlighting diagnostic/likely causative mtDNA variants. There were 135 individuals with 136 variants found after MITOMAP, MToolbox, and manual filtering approaches. The phenotype similarity score evaluation utilized results from the phenotype test cohort, which included the 47 previously diagnosed individuals with mtDNA diseases (totaln= 1,507). The thresholds were applied to evaluate the 135 undiagnosed individuals with 136 rare mtDNA variants, and the numbers of individuals with new or likely mtDNA disease diagnoses are shown. HPO, Human Phenotype Ontology term; mtDNA, mitochondrial DNA; PSS, phenotype similarity score; QC, quality control.

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