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More recently, it has become appreciated that certain pathogenic variants may exist as homoplasmic mutations with variable degrees of penetrance 9. These changes in our appreciation of the elements required for pathogenicity, together with the fact that the data available in databases has grown enormously, makes it imperative to find a new framework for the analysis of mitochondrially encoded rRNA mt-rRNA variations.

The emergence of scoring systems has provided a much needed tool for the evaluation of certain categories of mtDNA mutations and should provide guidance to future research on mt-rRNA variation 6710— With all probability, an important subset of pathogenic mtDNA variations map to the mt-rRNA genes; however, they remain the most difficult genes in which to confirm the pathogenicity of an mtDNA variant.

Since the mitochondrial ribosome mitoribosome translates all 13 proteins encoded by the mitochondrial genome, mutations leading to ribosome dysfunction should result in a respiratory chain defect and, therefore, cause mitochondrial disease.

This prediction was confirmed by the identification of alterations in the nuclear and mitochondrial genome that affect the mitochondrial translational machinery. For example, a small number of highly deleterious mutations have been identified in the nuclear genes encoding protein components of mitoribosomes, mitochondrial translation factors and elements of the apparatus involved in the maturation of mitoribosomes 13— The severity of these mutations clearly indicates that interfering with mitochondrial protein synthesis can lead to highly deleterious phenotypes.

Not surprisingly, deleterious mutations have also been identified in the rRNA component of the mitoribosome. In addition, there is a large list of other mt-rRNA mutations whose pathogenic role is yet to be convincingly proven. Thus, despite the identification of base substitutions in the mt-rRNA of patients, the evidence supporting the pathogenicity of mt-rRNA variations is, at best, circumstantial, except for the two cases mentioned above.

The reasons for this are many. First, ascertaining the magnitude of the actual biochemical defect caused by such variations is often complicated by incomplete penetrance, as well as by the possible existence of nuclear modifiers.

Secondly, the existence of numerous human haplogroups further complicates the correct assignment of mutations, as the penetrance of some variants might change in different genetic contexts Thirdly, the intractability of the mitochondrial translation apparatus and the lack of methods for the manipulation of the mitochondrial genome make it impossible to test the effect of these mutations directly.

Finally, all of this is complicated by the lack of agreement among authors on the criteria that should be used to evaluate pathogenicity in the context of mt-rRNA mutations 5 For all these reasons, it is imperative that a robust system is devised that allows the assessment of the biochemical defect caused by mt-rRNA mutations.

Scoring systems have been developed and validated for the analysis of the potential pathogenicity of both mt-tRNA and mitochondrially encoded complex I subunits 6710— The existence of a substantial number of known mutations and gold-standard experimental procedures, including biochemical and transmitochondrial-cybrid evidence, were important in developing these scoring systems.

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