Palindrome-mediated 16p13.3 triplications cause a recognizable neurodegenerative disorder with ataxia
Year: 2025
Type: article
Study design: Observational Study
Abstract: Complex neurodegenerative conditions have occasionally been associated with copy-number gains. Using microarray and genome sequencing on DNA samples from eleven individuals from nine unrelated families, we show that copy-number gains at 16p13.3 cause a severe, recognizable disorder characterized by early-onset progressive ataxia and cognitive decline (9–32 years). Most affected individuals also displayed peripheral neuropathy and scoliosis. Optic atrophy, nystagmus, and dystonia were more variable features. The neuroradiological phenotype comprises a distinctive combination of atrophy of the cerebellum and caudate nuclei. Co-segregation data showed that the structural variant (SV) had occurred de novo in 5 individuals and, for one other individual, had been inherited from a mosaic, unaffected parent. Triplicated segments of 16p13.3 were identified within the duplications. Although these varied in size (30–811 kb), the minimal region of overlap included a single gene ( ATP6V0C ) that is highly expressed in the cerebellum. RNA sequencing (RNA-seq) using whole-blood and fibroblast/lymphoblast cultures indicated increased expression of several genes within the SV, with ATP6V0C showing the most significant increase (up to 4-fold). In most cases, the central segment of the SV was proven to be inverted and lay immediately distal to a 144 kb palindrome. Across 500,000 individuals from the UK Biobank, we identified 19 duplications but no triplications at this locus. Further analysis of the consequences of ATP6V0C overexpression on the stoichiometry within the vacuolar H + -ATPase heteromer and on neurological function will provide valuable pathomechanistic insights. Together, our findings define palindrome-mediated triplication on 16p13.3 as the cause of a clinically distinct childhood-onset neurodegenerative disorder.
Authors: James Fasham, Julia Rankin, Rachel Schot, Susan M. White, Katrina M. Bell, Matthew N. Wakeling, Lucy J. Mallin, Alex Shah, Michelle G. de Silva, David I. Francis, Maie Walsh, Emily E. Jones, Kayal Vijayakumar, Katie Johnson, Francis H. Sansbury, Johann te Water Naudé, Paola Giunti, Marios Hadjivassiliou, Andrea H. Nemeth, George K. Tofaris, Carlo Rinaldi, Benito Banos-Pinero, Marianna Selikhva, Nishanka Ubeyratna, Anneke Kievit, Frank Sleutels, Joey van Giessen, Tahsin Stefan Barakat, Timothy S. Hall, Alan Whone, Eleanor Thomas, Joseph S. Leslie, Rosemary A. Bamford, Aaron R. Jeffries, Jenny Lord, Susan Walker, Tjakko J. van Ham, Sue L. Hill, Lucy McGavin, Andrew Parrish, Andrew H. Crosby, Emma L. Baple, Alistair T. Pagnamenta
Institutions: University of Exeter, Royal Devon University Healthcare NHS Foundation Trust, Royal Devon and Exeter Hospital, Erasmus MC, The University of Melbourne, Victorian Clinical Genetics Services, Murdoch Children's Research Institute, University Hospitals Plymouth NHS Trust, The Royal Melbourne Hospital, North Bristol NHS Trust, University Hospitals Bristol NHS Foundation Trust, Nottingham City Hospital, Cardiff and Vale University Health Board, National Health Service Wales, Cardiff University, University Hospital of Wales, UCL Queen Square Institute of Neurology, Sheffield Teaching Hospitals NHS Foundation Trust, University of Sheffield, University of Oxford, Oxford University Hospitals NHS Trust, Southmead Hospital, Genomics England, NHS England, University of Plymouth
Language: English
Subfield: Genetics
Domain: Life Sciences
Open Access status: hybrid
Estimated APC paid: $5,150
Funders: Wellcome Trust, Children's Hospital Foundation, European Bioinformatics Institute, Heart of England NHS Foundation Trust, Royal Children's Hospital Foundation, Cancer Research UK, National Institute for Health and Care Research, Department of Health and Social Care, ZonMw, Nederlandse Organisatie voor Wetenschappelijk Onderzoek, Medical Research Council, NIHR Imperial Biomedical Research Centre
OpenAlex ID: W4416997224