*2.3. Penetrance Analysis*

We determined penetrance as the proportion of a ffected individuals from all maternally related family members using family pedigrees [19]. Values for both men and women were calculated separately.

#### *2.4. Analysis of Pathogenicity for Non-Synonymous Mutations*

To make sure that the revealed non-synonymous mtDNA mutations were not sequencing errors or to not point out to general population polymorphisms, and in turn to find out the disease-associated polymorphisms among those published earlier, we used several databases: MITOMAP [27]; mtDB (Human Mitochondrial Genome Database, containing 2704 human mitochondrial genomes) [28]; and HmtDB (Human Mitochondrial DataBase), which contains 32922 human mitochondrial genomes [29]. To assess the possible pathogenicity of these mutations, and to predict whether a protein sequence variation a ffects protein function, we used the following web applications: MutPred 1.2 [30], MutPred 2 [31], PolyPhen–2 [32], PROVEAN (Protein Variation E ffect Analyzer) [33], and SIFT (Sorting Intolerant from Tolerant) [34]. All the sources are provided in the public domain.
