Interpretation of mitochondrial tRNA variants

  • A Correction to this article was published on 05 March 2020
  • A Correction to this article was published on 09 April 2020



To develop criteria to interpret mitochondrial transfer RNA (mt-tRNA) variants based on unique characteristics of mitochondrial genetics and conserved structural/functional properties of tRNA.


We developed rules on a set of established pathogenic/benign variants by examining heteroplasmy correlations with phenotype, tissue distribution, family members, and among unrelated families from published literature. We validated these deduced rules using our new cases and applied them to classify novel variants.


Evaluation of previously reported pathogenic variants found that 80.6% had sufficient evidence to support phenotypic correlation with heteroplasmy levels among and within families. The remaining variants were downgraded due to the lack of similar evidence. Application of the verified criteria resulted in rescoring 80.8% of reported variants of uncertain significance (VUS) to benign and likely benign. Among 97 novel variants, none met pathogenic criteria. A large proportion of novel variants (84.5%) remained as VUS, while only 10.3% were likely pathogenic. Detection of these novel variants in additional individuals would facilitate their classification.


Proper interpretation of mt-tRNA variants is crucial for accurate clinical diagnosis and genetic counseling. Correlations with tissue distribution, heteroplasmy levels, predicted perturbations to tRNA structure, and phenotypes provide important evidence for determining the clinical significance of mt-tRNA variants.

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Fig. 1

Change history

  • 23 February 2020

    The original version of this Article contained an error in the spelling of "Criteria for mt-tRNA variants" in the top right column header of Table 2, which was incorrectly given as "mt-mRNA". This has now been corrected in both the PDF and HTML versions of the Article.

  • 09 April 2020

    The original version of this Article contained errors in the third row of the last column (PS2) of Table 1. Whereby “>2 different tissues” should read “>=2 different tissues” and the two instances of “0%” should be “not detected”. These have now been corrected in both the PDF and HTML versions of the Article.


  1. 1.

    Smeitink J, van den Heuvel L, DiMauro S. The genetics and pathology of oxidative phosphorylation. Nat Rev Genet. 2001;2:342–352.

    CAS  Article  Google Scholar 

  2. 2.

    DiMauro S, Emmanuele V. The clinical spectrum of nuclear DNA-related mitochondrial disorders. In: Wong L-J C, editor. Mitochondrial disorders caused by nuclear genes. New York: Springer; 2013. p. 3–25 .

  3. 3.

    Frazier AE, Thorburn DR, Compton AG. Mitochondrial energy generation disorders: genes, mechanisms, and clues to pathology. J Biol Chem. 2019;294:5386–5395.

    CAS  Article  Google Scholar 

  4. 4.

    Richards S, Aziz N, Bale S, et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015;17:405.

    Article  Google Scholar 

  5. 5.

    Lott MT, Leipzig JN, Derbeneva O, et al. mtDNA variation and analysis using Mitomap and Mitomaster. Curr Protoc Bioinformatics. 2013;44:1–23.

    Article  Google Scholar 

  6. 6.

    Wong L-JC, Wong H, Liu A. Intergenerational transmission of pathogenic heteroplasmic mitochondrial DNA. Genet Med. 2002;4:78.

    Article  Google Scholar 

  7. 7.

    Wong LJC, Liang MH, Kwon H, Park J, Bai RK, Tan DJ. Comprehensive scanning of the entire mitochondrial genome for mutations. Clin Chem. 2002;48:1901–1912.

    CAS  Article  Google Scholar 

  8. 8.

    Kirchner S, Ignatova Z. Emerging roles of tRNA in adaptive translation, signalling dynamics and disease. Nat Rev Genet. 2015;16:98–112.

    CAS  Article  Google Scholar 

  9. 9.

    Helm M, Brulé H, Degoul F, et al. The presence of modified nucleotides is required for cloverleaf folding of a human mitochondrial tRNA. Nucleic Acids Res. 1998;26:1636–1643.

    CAS  Article  Google Scholar 

  10. 10.

    Yarham JW, Elson JL, Blakely EL, McFarland R, Taylor RW. Mitochondrial tRNA mutations and disease. Wiley Interdiscip Rev RNA. 2010;1:304–324.

    CAS  Article  Google Scholar 

  11. 11.

    Sonney S, Leipzig J, Lott MT, et al. Predicting the pathogenicity of novel variants in mitochondrial tRNA with MitoTIP. PLoS Comput Biol. 2017;13:1–8.

    Article  Google Scholar 

  12. 12.

    Silvestri G, Mongini T, Odoardi F, et al. A new mtDNA mutation associated with a progressive encephalopathy and cytochrome c oxidase deficiency. Neurology. 2000;54:1693–1696.

    CAS  Article  Google Scholar 

  13. 13.

    Zsurka G, Hampel KG, Nelson I, et al. Severe epilepsy as the major symptom of new mutations in the mitochondrial tRNAPhe gene. Neurology. 2010;74:507–512.

    CAS  Article  Google Scholar 

  14. 14.

    Connor TM, Hoer S, Mallett A, et al. Mutations in mitochondrial DNA causing tubulointerstitial kidney disease. PLoS Genet. 2017;13:1–17.

    Article  Google Scholar 

  15. 15.

    Cui H, Li F, Chen D, et al. Comprehensive next-generation sequence analyses of the entire mitochondrial genome reveal new insights into the molecular diagnosis of mitochondrial DNA disorders. Genet Med. 2013;15:388–394.

    CAS  Article  Google Scholar 

  16. 16.

    Cox R, Platt J, Chen LC, et al. Leigh syndrome caused by a novel m.4296G>A mutation in mitochondrial tRNA isoleucine. Mitochondrion. 2012;12:258–261.

    CAS  Article  Google Scholar 

  17. 17.

    McFarland R, Clark KM, Morris AAM, et al. Multiple neonatal deaths due to a homoplasmic mitochondrial DNA mutation. Nat Genet. 2002;30:145–146.

    CAS  Article  Google Scholar 

  18. 18.

    Rorbach J, Yusoff AA, Tuppen H, et al. Overexpression of human mitochondrial valyl tRNA synthetase can partially restore levels of cognate mt-tRNAVal carrying the pathogenic C25U mutation. Nucleic Acids Res. 2008;36:3065–3074.

    CAS  Article  Google Scholar 

  19. 19.

    Del Mar O’Callaghan M, Emperador S, López-Gallardo E, et al. New mitochondrial DNA mutations in tRNA associated with three severe encephalopamyopathic phenotypes: neonatal, infantile, and childhood onset. Neurogenetics. 2012;13:245–250.

    Article  Google Scholar 

  20. 20.

    Bosley TM, Brodsky MC, Glasier CM, et al. Sporadic bilateral optic neuropathy in children: the role of mitochondrial abnormalities. Investig Ophthalmol Vis Sci. 2008;49:5250–5256.

    Article  Google Scholar 

  21. 21.

    Abu-Amero KK, Bosley TM. Mitochondrial abnormalities in patients with LHON-like optic neuropathies. Investig Ophthalmol Vis Sci. 2006;47:4211–4220.

    Article  Google Scholar 

  22. 22.

    Bannwarth S, Procaccio V, Lebre AS, et al. Prevalence of rare mitochondrial DNA mutations in mitochondrial disorders. J Med Genet. 2013;50:704–714.

    CAS  Article  Google Scholar 

  23. 23.

    Garcia-Lozano J-R, Aguilera I, Bautista J, et al. A new mitochondrial DNA mutation in the tRNA leucine 1 gene (C3275A) in a patient with Leber’s hereditary optic neuropathy. Hum Mutat. 2000;15:120.

    CAS  Article  Google Scholar 

  24. 24.

    Zhang W, Cui H, Wong LJC. Comprehensive one-step molecular analyses of mitochondrial genome by massively parallel sequencing. Clin Chem. 2012;58:1322–1331.

    CAS  Article  Google Scholar 

  25. 25.

    Ingman M. mtDB: Human Mitochondrial Genome Database, a resource for population genetics and medical sciences. Nucleic Acids Res. 2005;34:D749–D751.

    Article  Google Scholar 

  26. 26.

    Mimaki M, Hatakeyama H, Ichiyama T, et al. Different effects of novel mtDNA G3242A and G3244A base changes adjacent to a common A3243G mutation in patients with mitochondrial disorders. Mitochondrion. 2009;9:115–122.

    CAS  Article  Google Scholar 

  27. 27.

    Lightowlers RN, Taylor RW, Turnbull DM. What is new in mitochondrial disease, and what challenges remain? Science. 2015;349:1494–1499.

    CAS  Article  Google Scholar 

  28. 28.

    Glatz C, D’Aco K, Smith S, et al. Mutation in the mitochondrial tRNAVal causes mitochondrial encephalopathy, lactic acidosis and stroke-like episodes. Mitochondrion. 2011;11:615–619.

    CAS  Article  Google Scholar 

  29. 29.

    Horváth R, Bender A, Abicht A, et al. Heteroplasmic mutation in the anticodon-stem of mitochondrial tRNA Val causing MNGIE-like gastrointestinal dysmotility and cachexia. J Neurol. 2009;256:810–815.

    Article  Google Scholar 

  30. 30.

    Uittenbogaard M, Wang H, Zhang VW, et al. The nuclear background influences the penetrance of the near-homoplasmic m.1630 A > G MELAS variant in a symptomatic proband and asymptomatic mother. Mol Genet Metab. 2019;126:429–438.

    CAS  Article  Google Scholar 

  31. 31.

    Sacconi S, Salviati L, Nishigaki Y. et al. A functionally dominant mitochondrial DNA mutation. Hum Mol Genet. 2008;17:1814–1820.

    CAS  Article  Google Scholar 

  32. 32.

    Roos S, Darin N, Kollberg G, et al. A novel mitochondrial tRNA Arg mutation resulting in an anticodon swap in a patient with mitochondrial encephalomyopathy. Eur J Hum Genet. 2012;21:571.

    Article  Google Scholar 

  33. 33.

    Anitori R, Manning K, Quan F, et al. Contrasting phenotypes in three patients with novel mutations in mitochondrial tRNA genes. Mol Genet Metab. 2005;84:176–188.

    CAS  Article  Google Scholar 

  34. 34.

    Kirino Y, Suzuki T. Human mitochondrial diseases associated with tRNA wobble modification deficiency. RNA Biol. 2005;2:41–44.

    CAS  Article  Google Scholar 

  35. 35.

    Ibba M, Söll D. Aminoacyl-tRNA synthesis. Annu Rev Biochem. 2000;69:617–650.

    CAS  Article  Google Scholar 

  36. 36.

    Moraes CT, Ciacci F, Bonilla E, et al. A mitochondrial tRNA anticodon swap associated with a muscle disease. Nat Genet. 1993;4:284–288.

    CAS  Article  Google Scholar 

  37. 37.

    Wang J, Venegas V, Li F, et al. Analysis of mitochondrial DNA point mutation heteroplasmy by ARMS quantitative PCR. Curr Protoc Hum Genet. 2011;68:19.6.1–19.6.16.

    Article  Google Scholar 

  38. 38.

    Santibanez-Koref M, Griffin H, Turnbull DM, et al. Assessing mitochondrial heteroplasmy using next generation sequencing: a note of caution. Mitochondrion. 2019;46:302–306.

    CAS  Article  Google Scholar 

  39. 39.

    Cardena MMSG, Mansur AJ, Pereira ADC, et al. A new duplication in the mitochondrially encoded tRNA proline gene in a patient with dilated cardiomyopathy. Mitochondrial DNA. 2013;24:46–49.

    CAS  Article  Google Scholar 

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Correspondence to Lee-Jun C. Wong PhD.

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Wong, L.C., Chen, T., Wang, J. et al. Interpretation of mitochondrial tRNA variants. Genet Med 22, 917–926 (2020).

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Key words

  • mt-tRNA variants interpretation
  • tRNA variants classification criteria
  • MitoTIP

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