| Literature DB >> 34037856 |
Dagmar Nolte1, Jun-Suk Kang2,3, Amrei Hofmann4,5, Eva Schwaab6, Heidrun H Krämer7, Ulrich Müller4.
Abstract
Adult-onset ataxias are a genetically and clinically heterogeneous group of movement disorders. In addition to nuclear gene mutations, sequence changes have also been described in the mitochondrial genome. Here, we present findings of mutation analysis of the mitochondrial gene MT-ATP6. We analyzed 94 patients with adult-onset spinocerebellar ataxia (SCA), including 34 sporadic cases. In all patients, common sequence changes found in SCAs such as repeat expansions and point mutations had been excluded previously. We found pathogenic MT-ATP variants in five of these patients (5.32%), two of whom were sporadic. Four of the five mutations have not previously been described in ataxias. All but one of these mutations affect transmembrane helices of subunit-α of ATP synthase. Two mutations (p.G16S, and p.P18S) disrupt transmembrane helix 1 (TMH1), one mutation (p.G167D) affects TMH5, and another one (p.L217P) TMH6. The fifth mutation (p.T96A) describes an amino acid change in close proximity to transmembrane helix 3 (TMH3). The level of heteroplasmy was either complete or very high ranging from 87 to 99%. The high prevalence of pathogenic MT-ATP6 variants suggests that analysis of this gene should be included in the routine workup of both hereditary and sporadic ataxias.Entities:
Keywords: ATP synthase; Adult-onset ataxia; Complex V defect; MT-ATP6
Mesh:
Substances:
Year: 2021 PMID: 34037856 PMCID: PMC8563540 DOI: 10.1007/s00415-021-10607-5
Source DB: PubMed Journal: J Neurol ISSN: 0340-5354 Impact factor: 6.682
Prediction, MitoMap frequency, and ACMG classification of MT-ATP6 missense variants detected in a cohort of 94 SCA patients
| mDNA/cDNA/protein change/ cases in cohort | SNV number | MutationTaster | Polyphen-2 (Score) | PROVEAN (Score) | SIFT (Score) | VEP/ Ensembl | MitoMap frequency | ACMG Classification criteria | |
|---|---|---|---|---|---|---|---|---|---|
rs28502681 A = 0.0009 | Disease causing (0.9961) | Probably damaging (0.895) | Deleterious (− 4.623) | not tolerated (0.02) | 0.03 | 0.498 | 0.344% | Class 3 (variant of uncertain significance) PM1, PP3 | |
rs1556423492 T = 0.0004 | Polymorphism (0.9517) | Probably damaging (0,999) | Deleterious (− 6.594) | Tolerated (0.17) | 0.03 | 0.996 | 0.058% | Class 4 (likely pathogenic) PS4, PM1, PP3 | |
m.8584G > A c.58G > A, p.A20T, 2 | rs3135028 A = 0.0067 | Polymorphism (0.9999) | Benign (0.004) | Neutral (− 0.404) | Tolerated (0.21) | 0.24 | 0.012 | 5.558% | Class 1 (benign) BA1 |
m.8701A > G c.175A > G, p.T59A, 3 | rs2000975 G = 0.06433 | Polymorphism (0.9999) | Benign (0.002) | Neutral (− 0.935) | Tolerated (0.66) | 0.51 | 0.005 | 32.975% | Class 1 (benign) BA1 |
m.8705 T > C c.179 T > C, p.M60T, 2 | rs878959404 C = 0.0043 | Polymorphism (0,9999) | benign (0.000) | Neutral (0.320) | tolerated (0.30) | 0.68 | 0.0 | 0.383% | Class 2 (likely benign) BP4, BP6 |
m.8723G > A c.197G > A, p.R66Q, 1 | rs unknown | Polymorphism (0.9997) | Benign (0.021) | Neutral (− 0.523) | Tolerated (0.51) | 0.55 | 0.012 | 0.159% | Class 2 (likely benign) BP4, BP6 |
m.8764G > A c.238G > A, p.A80T 1 | rs1556423534 A = 0.0018 | Polymorphism (0.9999) | Benign (0.001) | Neutral (− 1.221) | Tolerated (0.26) | 0.12 | 0.007 | 0.207% | Class 2 (likely benign) BP4, BP6 |
rs1556423543 G = 0.0018 | Polymorphism (0.9266) | Probably damaging (0.994) | Deleterious (− 3.891) | Not tolerated (0.03) | 0.05 | 0.988 | 0.118% | Class 3 (variant of uncertain significance) PM1, PP3 | |
m.8950G > A c.424G > A, p.V142I, 1 | rs1556423574 A = 0.0008 | Polymorphism (0.9999) | Benign (0.0) | Neutral (0.118) | Tolerated (1.0) | 1.0 | 0.0 | 0.151% | Class 2 (likely benign) BP4, BP6 |
| COSV62293160 | Disease causing (0.9999) | Probably damaging (1.0) | Deleterious (− 6.275) | Not tolerated (0.00) | 0.0 | 0.999 | 0.006% | Class 5 (pathogenic) PS1, PM1, PM2, PM5 | |
m.9055G > A c.529G > A, p.A177T, 7 | rs193303045 A = 0.1556 | Polymorphism (0.9988) | Probably damaging (0.845) | Deleterious (− 2.606) | Tolerated (0.16) | 0.1 | 0.399 | 4.244% | Class 1 (benign) BS1, BS4 |
m.9067A > G c.541A > G, p.M181V, 2 | rs unknown | Polymorphism (0.9999) | Benign (0.003) | Neutral (− 0.967) | Not tolerated (0.01) | 0.01 | 0.007 | 0.070% | Class 2 (likely benign) BP4, BP6 |
m.9070 T > G c.544 T > G, p.S182A, 1 | rs879190502 G = 0.0020 | Polymorphism (0.9999) | Benign (0.225) | Neutral (− 0.122) | Tolerated (0.57) | 0.12 | 0.182 | 0.126% | Class 2 (likely benign) BP4, BP6 |
rs199476135 C = MAF unknown | Disease causing (0.9999) | Probably damaging (0.999) | Deleterious (− 6.258) | Not tolerated (0.00) | 0.0 | 0.998 | 0.006% | Class 5 (pathogenic) PS1, PS3, PS4 | |
SCA spinocerebellar ataxia, MAF minor allele frequency, underline: likely pathogenic variants; ALFA database: (https://www.ncbi.nlm.nih.gov/snp/docs/gsr/alfa) [36]; ACMG classification, detailed information is given in [24]
Fig. 1a Pedigrees of the German adult-onset SCA cases. Black symbols indicate affected probands. Index patients are marked by arrow. Probands for whom no clinical information was available are highlighted by an asterisk. b Electropherograms of sequences of index patients and controls. The relevant base changes are indicated by arrow. c Amino acid sequence alignments of ATP synthase subunit-α orthologs. Name of species and protein identifier numbers are given on the left. Amino acids mutated in patients are evolutionarily highly conserved and are highlighted in green. Non-conserved amino acid residues are given in red. H., Homo; P., Pan; M., Macaca; R., Rattus; M., Mus; G., Gallus; X., Xenopus; T., Takifugu
Mutations in MT-ATP6 associated with adult-onset ataxia, prediction analysis, and clinical features
| Family/patient (sex, current age, identifier) | mtDNA/cDNA change | Deduced aa change/localization | Prediction | Age at onset/first symptoms | Age at examination/clinical symptoms | MRI |
|---|---|---|---|---|---|---|
| II-1 (M, 65) | m.8578C > T; c.52C > T | p.P18S TMH1 | Prob. damaging (0.999), deleterious (-6.594), tolerated (0.17) | Umbilical cord prolapse, 45, dystonia | 58, generalized dystonia, dystonic dysarthria, dysphagia, mild psychomotor developmental delay | Hyperintensity of bilateral putamen and precentral gyrus |
| II-2 (M, 63) index patient (#982) | m.8578C > T; c.52C > T | p.P18S TMH1 | Prob. damaging (0.999), deleterious (-6.594), tolerated (0.17) | 53, gait abnormality, frequent falls | 56, mild and slowly progressive gait ataxia, horizontal nystagmus | Cerebellar atrophy |
| II-3 (M, deceased) | n.d | n.i | obsessive–compulsive disorder, imbalance problems, deceased at 51 | n.d | ||
| II-4 (F, 55) | m.8578C > T; c.52C > T | p.P18S TMH1 | Prob. damaging (0.999), deleterious (-6.594), tolerated (0.17) | Asymptomatic | 48, (last examination), asymptomatic | n.d |
| I-1 (F, deceased) | n.d | 50, gait abnormality | n.d | |||
| II-1 (F, deceased) | n.d | 54, head and hand tremor | n.d | |||
| III-1 (M, 73) index patient (#873) | m.9026G > A; c.500G > A | p.G167D TMH5 | Prob. damaging (1.0), deleterious (-6.275), not tolerated (0.00) | 46, progressive head and hand tremor | 62, mild gait ataxia, undirected falls, tremor with lateral shift to the right and rotation to the left side, dysmetric finger-to-nose and knee–heel test, lifted saccades, mild cognitive impairment | Colliquative necrosis of the temporal lobe |
(F, 85) (#960) | m.8572G > A c.46G > A; | p.G16S TMH1 | Prob. damaging (0.895), deleterious (-4.623), not tolerated (0.02) | 65, mild gait ataxia | 75, mild but progressive gait ataxia, dysmetria, dysarthria, restless-legs-syndrome | Global brain atrophy, incl. Cerebellum |
(M, 61) (#1115) | m.8812A > G c.286A > G; | p.T96A adjacent to TMH3 (aa 97–117) | Prob. damaging (0.994), deleterious (-3.891), not tolerated (0.03) | 46, gait abnormality | 56, progressive gait ataxia | Cerebellar atrophy |
(F, 79) (#1174) | m.9176T> C; c.650T > C | p.L217P TMH6 | Prob. damaging (0.999), deleterious (-6.258), not tolerated (0.00) | 46, frequent falls, gait insecurity | 75, severe progressive gait ataxia, cerebellar dysarthria, saccadic gaze | Moderate cerebellar atrophy |
F female, M male, aa amino acid, m. mitochondrial genomic DNA, TMH transmembrane helix domain, n.d. not done/unavailable for testing; n.i.: no information