OBJECTIVE: ATP synthase (ATPase) is responsible for the majority of ATP production. Nevertheless, disease phenotypes associated with mutations in ATPase subunits are extremely rare. We aimed at expanding the spectrum of ATPase-related diseases. METHODS: Whole-exome sequencing in cohorts with 2,962 patients diagnosed with mitochondrial disease and/or dystonia and international collaboration were used to identify deleterious variants in ATPase-encoding genes. Findings were complemented by transcriptional and proteomic profiling of patient fibroblasts. ATPase integrity and activity were assayed using cells and tissues from 5 patients. RESULTS: We present 10 total individuals with biallelic or de novo monoallelic variants in nuclear ATPase subunit genes. Three unrelated patients showed the same homozygous missense ATP5F1E mutation (including one published case). An intronic splice-disrupting alteration in compound heterozygosity with a nonsense variant in ATP5PO was found in one patient. Three patients had de novo heterozygous missense variants in ATP5F1A, whereas another 3 were heterozygous for ATP5MC3 de novo missense changes. Bioinformatics methods and populational data supported the variants' pathogenicity. Immunohistochemistry, proteomics, and/or immunoblotting revealed significantly reduced ATPase amounts in association to ATP5F1E and ATP5PO mutations. Diminished activity and/or defective assembly of ATPase was demonstrated by enzymatic assays and/or immunoblotting in patient samples bearing ATP5F1A-p.Arg207His, ATP5MC3-p.Gly79Val, and ATP5MC3-p.Asn106Lys. The associated clinical profiles were heterogeneous, ranging from hypotonia with spontaneous resolution (1/10) to epilepsy with early death (1/10) or variable persistent abnormalities, including movement disorders, developmental delay, intellectual disability, hyperlactatemia, and other neurologic and systemic features. Although potentially reflecting an ascertainment bias, dystonia was common (7/10). INTERPRETATION: Our results establish evidence for a previously unrecognized role of ATPase nuclear-gene defects in phenotypes characterized by neurodevelopmental and neurodegenerative features. ANN NEUROL 2022;91:225-237.

Broad Center for Mendelian Genomics Broad Institute of MIT and Harvard Cambridge MA

Children's Hospital Kreiskliniken Reutlingen Germany

Département de Biochimie et Génétique Centre Hospitalier Universitaire d'Angers Angers France

Department of General Pediatrics Neonatology and Pediatric Cardiology University Children's Hospital Medical Faculty Heinrich Heine University Düsseldorf Germany

Department of Genetics Washington University School of Medicine St Louis MO

Department of Medical Genetic Diskapi Yildirim Beyazit Training and Research Hospital Ankara Turkey

Department of Neurology Charles University 1st Faculty of Medicine and General University Hospital Prague Prague Czech Republic

Department of Neurology Medical University of Innsbruck Innsbruck Austria

Department of Neuropediatrics and Muscle Disorders University Medical Center Faculty of Medicine University of Freiburg Freiburg Germany

Department of Pediatric Neurology University Children's Hospital Zurich University of Zurich Zurich Switzerland

Department of Pediatrics Washington University School of Medicine St Louis MO

Departments of Child Health Neurology and Cellular and Molecular Medicine and Program in Genetics University of Arizona College of Medicine Phoenix Phoenix AZ

Harvard Medical School and Center for Genomic Medicine Massachusetts General Hospital Boston and Laboratory for Molecular Medicine Partners Healthcare Personalized Medicine Cambridge MA

Institute of Neurogenomics Helmholtz Zentrum München Munich Germany

Kinderkrankenhaus St Marien gGmbH Zentrum für Kinder und Jugendmedizin Landshut Germany

Lehrstuhl für Neurogenetik Technische Universität München Munich Germany

Munich Cluster for Systems Neurology Munich Germany

Pediatric Movement Disorders Program Division of Pediatric Neurology Barrow Neurological Institute Phoenix Children's Hospital Phoenix AZ

Pediatric Neurology Department CHU Clocheville Tours France

Program in Medical and Population Genetics Broad Institute Cambridge MA

Radboud Center for Mitochondrial Medicine Department of Pediatrics Amalia Children's Hospital Radboud UMC Nijmegen The Netherlands

Radboud Centre for Mitochondrial Medicine Department of Paediatrics Radboud Institute for Molecular Life Sciences Radboud University Nijmegen Medical Centre Nijmegen Nijmegen The Netherlands

Technical University of Munich School of Medicine Institute of Human Genetics Munich Germany

Unité Mixte de Recherche MITOVASC CNRS 6015 INSERM 1083 Université d'Angers Angers France

University Children's Hospital Paracelsus Medical University Salzburg Austria

See more in PubMed

Gorman GS, Chinnery PF, DiMauro S, et al. Mitochondrial diseases. Nat Rev Dis Primers. 2016. Oct 20;2:16080. PubMed

Yoshida M, Muneyuki E, Hisabori T. ATP synthase--a marvellous rotary engine of the cell. Nat Rev Mol Cell Biol. 2001. Sep;2(9):669–77. PubMed

He J, Ford HC, Carroll J, et al. Assembly of the membrane domain of ATP synthase in human mitochondria. Proc Natl Acad Sci U S A. 2018. Mar 20;115(12):2988–93. PubMed PMC

Jonckheere AI, Smeitink JA, Rodenburg RJ. Mitochondrial ATP synthase: architecture, function and pathology. J Inherit Metab Dis. 2012. Mar;35(2):211–25. PubMed PMC

Schlieben LD, Prokisch H. The Dimensions of Primary Mitochondrial Disorders. Front Cell Dev Biol. 2020;8:600079. PubMed PMC

Galber C, Carissimi S, Baracca A, Giorgio V. The ATP Synthase Deficiency in Human Diseases. Life (Basel). 2021. Apr 8;11(4). PubMed PMC

Dautant A, Meier T, Hahn A, Tribouillard-Tanvier D, di Rago JP, Kucharczyk R. ATP Synthase Diseases of Mitochondrial Genetic Origin. Front Physiol. 2018;9:329. PubMed PMC

Neilson DE, Zech M, Hufnagel RB, et al. A Novel Variant of ATP5MC3 Associated with Both Dystonia and Spastic Paraplegia. Mov Disord. 2021. Oct 11. PubMed PMC

Mayr JA, Havlickova V, Zimmermann F, et al. Mitochondrial ATP synthase deficiency due to a mutation in the ATP5E gene for the F1 epsilon subunit. Hum Mol Genet. 2010. Sep 1;19(17):3430–9. PubMed

Jonckheere AI, Renkema GH, Bras M, et al. A complex V ATP5A1 defect causes fatal neonatal mitochondrial encephalopathy. Brain. 2013. May;136(Pt 5):1544–54. PubMed

Lieber DS, Calvo SE, Shanahan K, et al. Targeted exome sequencing of suspected mitochondrial disorders. Neurology. 2013. May 7;80(19):1762–70. PubMed PMC

Olahova M, Yoon WH, Thompson K, et al. Biallelic Mutations in ATP5F1D, which Encodes a Subunit of ATP Synthase, Cause a Metabolic Disorder. Am J Hum Genet. 2018. Mar 1;102(3):494–504. PubMed PMC

Barca E, Ganetzky RD, Potluri P, et al. USMG5 Ashkenazi Jewish founder mutation impairs mitochondrial complex V dimerization and ATP synthesis. Hum Mol Genet. 2018. Oct 1;27(19):3305–12. PubMed PMC

Stenton SL, Shimura M, Piekutowska-Abramczuk D, et al. Diagnosing pediatric mitochondrial disease: lessons from 2,000 exomes. medRxiv [Preprint] 10.1101/2021.06.21.21259171. DOI

Zech M, Jech R, Boesch S, et al. Monogenic variants in dystonia: an exome-wide sequencing study. Lancet Neurol. 2020. Nov;19(11):908–18. PubMed PMC

Sobreira N, Schiettecatte F, Valle D, Hamosh A. GeneMatcher: a matching tool for connecting investigators with an interest in the same gene. Hum Mutat. 2015. Oct;36(10):928–30. PubMed PMC

Duzkale N, Oz O, Turkmenoglu TT, Cetinkaya K, Eren T, Yalcin S. Investigation of Hereditary Cancer Predisposition Genes of Patients with Colorectal Cancer: Single-centre Experience. J Coll Physicians Surg Pak. 2021. Jul;30(7):811–6. PubMed

Jin SC, Lewis SA, Bakhtiari S, et al. Mutations disrupting neuritogenesis genes confer risk for cerebral palsy. Nat Genet. 2020. Oct;52(10):1046–56. PubMed PMC

Ziegler A, Bader P, McWalter K, et al. Confirmation that variants in TTI2 are responsible for autosomal recessive intellectual disability. Clin Genet. 2019. Oct;96(4):354–8. PubMed

The UniProt C UniProt: the universal protein knowledgebase. Nucleic Acids Res. 2017. Jan 4;45(D1):D158–D69. PubMed PMC

Sievers F, Wilm A, Dineen D, et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol. 2011. Oct 11;7:539. PubMed PMC

Ng PC, Henikoff S. Predicting deleterious amino acid substitutions. Genome Res. 2001. May;11(5):863–74. PubMed PMC

Adzhubei IA, Schmidt S, Peshkin L, et al. A method and server for predicting damaging missense mutations. Nat Methods. 2010. Apr;7(4):248–9. PubMed PMC

Kircher M, Witten DM, Jain P, O'Roak BJ, Cooper GM, Shendure J. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet. 2014. Mar;46(3):310–5. PubMed PMC

Berman HM, Westbrook J, Feng Z, et al. The Protein Data Bank. Nucleic Acids Res. 2000. Jan 1;28(1):235–42. PubMed PMC

Feichtinger RG, Olahova M, Kishita Y, et al. Biallelic C1QBP Mutations Cause Severe Neonatal-, Childhood-, or Later-Onset Cardiomyopathy Associated with Combined Respiratory-Chain Deficiencies. Am J Hum Genet. 2017. Oct 5;101(4):525–38. PubMed PMC

Charif M, Gueguen N, Ferre M, et al. Dominant ACO2 mutations are a frequent cause of isolated optic atrophy. Brain Commun. 2021;3(2):fcab063. PubMed PMC

Kremer LS, Bader DM, Mertes C, et al. Genetic diagnosis of Mendelian disorders via RNA sequencing. Nat Commun. 2017. Jun 12;8:15824. PubMed PMC

Invernizzi F, Legati A, Nasca A, et al. Myopathic mitochondrial DNA depletion syndrome associated with biallelic variants in LIG3. Brain. 2021. Jun 24. PubMed PMC

Kopajtich R, Smirnov D, Stenton SL, et al. Integration of proteomics with genomics and transcriptomics increases the diagnostic rate of Mendelian disorders. bioRxiv [Preprint] doi:10.1101/2021.03.09.21253187. DOI

Ritchie ME, Phipson B, Wu D, et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015. Apr 20;43(7):e47. PubMed PMC

Gueguen N, Piarroux J, Sarzi E, et al. Optic neuropathy linked to ACAD9 pathogenic variants: A potentially riboflavin-responsive disorder? Mitochondrion. 2021. Jul;59:169–74. PubMed

Karczewski KJ, Francioli LC, Tiao G, et al. The mutational constraint spectrum quantified from variation in 141,456 humans. Nature. 2020. May;581(7809):434–43. PubMed PMC

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. May;17(5):405–24. PubMed PMC

Landrum MJ, Lee JM, Benson M, et al. ClinVar: public archive of interpretations of clinically relevant variants. Nucleic Acids Res. 2016. Jan 4;44(D1):D862–8. PubMed PMC

Kaplanis J, Samocha KE, Wiel L, et al. Evidence for 28 genetic disorders discovered by combining healthcare and research data. Nature. 2020. Oct;586(7831):757–62. PubMed PMC

Gusic M, Prokisch H. Genetic basis of mitochondrial diseases. FEBS Lett. 2021. Apr;595(8):1132–58. PubMed

Kucharczyk R, Zick M, Bietenhader M, et al. Mitochondrial ATP synthase disorders: molecular mechanisms and the quest for curative therapeutic approaches. Biochim Biophys Acta. 2009. Jan;1793(1):186–99. PubMed

Stenton SL, Prokisch H. Genetics of mitochondrial diseases: Identifying mutations to help diagnosis. EBioMedicine. 2020. Jun;56:102784. PubMed PMC

Variability of Clinical Phenotypes Caused by Isolated Defects of Mitochondrial ATP Synthase

Dystonia and mitochondrial disease: the movement disorder connection revisited in 900 genetically diagnosed patients

In vitro human cell culture models in a bench-to-bedside approach to epilepsy