The m.3291T>C mt-tRNALeu(UUR) mutation is definitely pathogenic and causes multisystem mitochondrial disease

Abstract

Mitochondrial tRNA point mutations are important causes of human disease, and have been associated with a diverse range of clinical phenotypes. Definitively proving the pathogenicity of any given mt-tRNA mutation requires combined molecular, genetic and functional studies. Subsequent evaluation of the mutation using a pathogenicity scoring system is often very helpful in concluding whether or not the mutation is causing disease. Despite several independent reports linking the m.3291T>C mutation to disease in humans, albeit in association with several different phenotypes, its pathogenicity remains controversial. A lack of conclusive functional evidence and an over-emphasis on the poor evolutionary conservation of the affected nucleotide have contributed to this controversy. Here we describe an adult patient who presented with deafness and lipomas and evidence of mitochondrial abnormalities in his muscle biopsy, who harbours the m.3291T > C mutation, providing conclusive evidence of pathogenicity through analysis of mutation segregation with cytochrome c oxidase (COX) deficiency in single muscle fibres, underlining the importance of performing functional studies when assessing pathogenicity.

A MT-TL1 variant identified by whole exome sequencing in an individual with intellectual disability, epilepsy, and spastic tetraparesis

“…Prioritization of nuclear DNA variants did not yield diagnostically relevant variants, despite analysis of ( de novo ) variants in known disease–genes, particularly those associated with recessive or dominant cortical dysplasia, and in genes not yet implicated in NDD/ID. Variant prioritization from mtDNA revealed a variant in MT-TL1 [ 8 ], NC_012920.1:m.3291T > C (NC_012920.1:n.62T > C), known to affect mitochondrial function, at 22% heteroplasmy. The variant was absent from maternal WES data.…”

“…Multiple small hyperintense areas in subcortical white matter of cerebrum on T2 MRI NA NA NA Family of 5 affected individuals in 4 generations Sunami et al [ 10 ] 36 F Photo-induced myoclonus, atrophy of cerebellum, absence of tendon reflexes, truncal ataxia, normal mental status 16% (peripheral leukocytes) NA NA Family of 5 affected individuals in 4 generations Sunami et al [ 10 ] 15 F Generalized seizures, myoclonic jerks, slight cognitive decline, absence of tendon reflexes 27% (peripheral leukocytes) NA NA Family of 5 affected individuals in 4 generations Emmanuele et al [ 13 ] 43 M Progressive myoclonus epilepsy, cerebellar ataxia, cortical and cerebellar atrophy, hearing loss, myopathic weakness, ophthalmoparesis, pigmentary retinopathy, bifascicular heart block, premature graying (20 years) 92% (muscle) Elevated (serum) Normal respiratory chain enzymes. RRFs and succinate dehydrogenase reactive vessels Yarham et al [ 8 ] 51 M Bilateral sensorineural deafness, falls, speech disturbance, weight loss, diabetes mellitus, macroglossia with fatty infiltration, dysarthria, bilateral pes cavus, lipoma, low tendon reflexes, dysmetria, generalized brain atrophy 39% (muscle) Elevated (cerebrospinal fluid) Dystrophic changes and lipid infiltrates, RRFs, COX-negative fibers, succinate dehydrogenase reactive vessels Unaffected sister shows heteroplasmy levels of 6% in both urine and blood Liu et al [ 11 ] 14 F Progressive cerebellar ataxia, frequent myoclonus seizures, recurrent stroke-like episodes, migraine-like headaches with nausea and vomiting, nystagmus, basal ganglia calcification, brain atrophy, and stroke-like lesions 93% (muscle), 67% (blood), 62% (fibroblasts) Elevated (serum) RRF, COX-negative fibers, succinate dehydrogenase reactive vessels Mother of proband (phenotype: emaciation and short stature) and asymptomatic sister of proband have heteroplasmy levels of 46% and 50%, respectively Keilland et al [ 12 ] 15 F Stat...…”

“…Mitochondrial disorders associated with mitochondrial tRNA genes are characterized by both genotypic and phenotypic heterogeneity, with poor genotype–phenotype correlations [ 8 , 16 , 17 ]. The m.3291T > C variant described here is located in the T-loop of mitochondrial tRNALeu(UUR).…”

The expanding phenotype of MELAS caused by the m.3291T>C mutation in the MT-TL1 gene

“…Kirino et al [8] demonstrated that the functional impact of the m.3291T > C mutation was to reduce the percentage of the 5-taurinomethyluridine (τm5U) modification at the anticodon wobble position of the tRNA Leu(UUR) presumably affecting the accuracy or efficiency of translation in common with other MELAS causing mutations. The question of pathogenicity seems to have been resolved by Yarham et al by identifying that the m.3291T > C transition segregated with cytochrome oxidase deficiency in single muscle fibers in a biopsy from a patient who presented with deafness and lipomas [9] .…”

MitoPhen database: a human phenotype ontology-based approach to identify mitochondrial DNA diseases

“…Four mtSNVs were only reported in one family but were included due to functional evidence of pathogenicity. We did not factor in the evolutionary conservation of amino acid residues given previous evidence that it did not add further weight to determining pathogenicity in mitochondrial disease ( 14 , 15 ). We also did not consider cybrid data where multiple mtSNVs within the same cell line made it difficult to establish the functional effect of each variant (eg.…”