Identification of GGC Repeat Expansions in ZFHX3 among Chilean Movement Disorder Patients

Paula Saffie-Awad¹, Abraham Moller², Kensuke Daida³, Pilar Alvarez Jerez^{2

4}, Zhongbo Chen^{4

5

6}, Zachary B Anderson⁷, Mariam Isayan⁸, Kimberly Paquette², Sophia B Gibson^{7

9}, Madison Fulcher³, Abigail Miano-Burkhardt³, Laksh Malik², Breeana Baker², Paige Jarreau², Henry Houlden¹⁰, Mina Ryten^{11

12

13

14}, Bida Gu¹⁵, Mark J P Chaisson¹⁵, Danny E Miller^{9

16

17}, Pedro Chaná-Cuevas¹⁸, Cornelis Blauwendraat^{2

3}, Andrew B Singleton^{2

3}, Kimberley J Billingsley²

Affiliations

¹ Clínica Santa María, Santiago, Chile.
² Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA.
³ Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA.
⁴ Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, UK.
⁵ Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK.
⁶ NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK.
⁷ Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington, USA.
⁸ Department of Neurology and Neurosurgery, National Institute of Health, Yerevan, Armenia.
⁹ Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
¹⁰ Department of Neuromuscular Disease, Queen Square Institute of Neurology, UCL, London, UK.
¹¹ Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, UCL, London, UK.
¹² NIHR Great Ormond Street Hospital Biomedical Research Centre, UCL, London, UK.
¹³ UK Dementia Research Institute, University of Cambridge, Cambridge, UK.
¹⁴ Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge, UK.
¹⁵ Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California, USA.
¹⁶ Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA.
¹⁷ Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, Washington, USA.
¹⁸ Centro de Trastornos del Movimiento, Facultad de Ciencias M ́edicas, Universidad de Santiago de Chile, Santiago, Chile.

PMID: 40459184
PMCID: PMC12273613
DOI: 10.1002/mds.30242

Identification of GGC Repeat Expansions in ZFHX3 among Chilean Movement Disorder Patients

Paula Saffie-Awad et al. Mov Disord. 2025 Jul.

. 2025 Jul;40(7):1433-1441.

doi: 10.1002/mds.30242. Epub 2025 Jun 3.

Authors

Affiliations

¹ Clínica Santa María, Santiago, Chile.
² Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA.
³ Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA.
⁴ Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, UK.
⁵ Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK.
⁶ NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK.
⁷ Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington, USA.
⁸ Department of Neurology and Neurosurgery, National Institute of Health, Yerevan, Armenia.
⁹ Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
¹⁰ Department of Neuromuscular Disease, Queen Square Institute of Neurology, UCL, London, UK.
¹¹ Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, UCL, London, UK.
¹² NIHR Great Ormond Street Hospital Biomedical Research Centre, UCL, London, UK.
¹³ UK Dementia Research Institute, University of Cambridge, Cambridge, UK.
¹⁴ Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge, UK.
¹⁵ Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California, USA.
¹⁶ Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA.
¹⁷ Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, Washington, USA.
¹⁸ Centro de Trastornos del Movimiento, Facultad de Ciencias M ́edicas, Universidad de Santiago de Chile, Santiago, Chile.

PMID: 40459184
PMCID: PMC12273613
DOI: 10.1002/mds.30242

Abstract

Background: Hereditary ataxias are genetically diverse, yet up to 75% remain undiagnosed due to technological and financial barriers. The GGC repeat expansion in ZFHX3, responsible for spinocerebellar ataxia type 4 (SCA4), has only been described in individuals of Northern Europeandescent.

Objective: Uncover the genetic etiology of suspected hereditary movement disorders.

Methods: We performed Oxford Nanopore long-read genome sequencing on 15 individuals with suspected hereditary movement disorders. Using variant calling and ancestry inference tools.

Results: We identified ZFHX3 GGC expansions (47-55 repeats) in 4 patients with progressive ataxia, polyneuropathy, and vermis atrophy. One presented with rapidly progressive parkinsonism-ataxia, expanding the known phenotype. Longer expansions correlated with earlier onset and severity. All carriers shared single nucleotide variants (SNVs) associated with the Swedish founder haplotype, and methylation analysis confirmed allele-specific hypermethylation.

Conclusion: These represent the first SCA4 cases identified outside Northern Europe. Our findings highlight the value of long-read sequencing in resolving undiagnosed movement disorders. Published 2025. This article is a U.S. Government work and is in the public domain in the USA. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.

Keywords: Latin American Population; Long Read Sequencing; Spinocerebellar Ataxias; Tandem Repeat Expansions; ZFHX3 gene.

Published 2025. This article is a U.S. Government work and is in the public domain in the USA. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.

PubMed Disclaimer

Figures

**FIG. 1**
(A) Schematic overview of the study design. (B) Waterfall plots displaying Oxford Nanopore Technologies (ONT) long‐read sequencing data for the four predicted *ZFHX3* GGC repeat carriers. The red dotted line marks the pathogenic threshold. Created using BioRender.com.

**FIG. 2**
(I) Haplotype analysis of *ZFHX3* GGC repeat expansion carriers. Out of the six rare single nucleotide variants (SNVs) reported as part of the distance common founder event, four were found in our samples within the repeat region (highlighted by the pink box) and compared to the Utah index patient from Chen et al. ¹⁸ These SNVs are missing in the unaffected Chilean individual. (II) Haplotype‐specific differential methylation around the expansion. (a–d) Modbamtools plots of methylation frequency for the four heterozygous expansion carriers. Methylation frequency is plotted at the top where haplotype 1 (blue) represents the non‐expanded allele and haplotype 2 (orange) represents the expanded allele. The *ZFHX3* gene track is overlaid at the top, showing the last two exons. Haplotype‐specific reads are shown at the bottom with blue sections of the reads denoting hypomethylation and red sections of the reads denoting hypermethylation. Purple box indicates repeat region. For all four carriers, the expanded allele is hypermethylated compared to the non‐expanded allele. (e) Modbamtools plot of an unaffected related individual, homozygous non‐repeat carrier, showing that hypomethylation in this region is expected under normal conditions.

See this image and copyright information in PMC

Update of

Identification of GGC Repeat Expansions in ZFHX3 Among Chilean Movement Disorder Patients.
Saffie-Awad P, Moller A, Daida K, Jerez PA, Chen Z, Anderson ZB, Isayan M, Paquette K, Gibson SB, Fulcher M, Miano-Burkhardt A, Malik L, Baker B, Jarreau P, Houlden H, Ryten M, Gu B, Chaisson MJ, Miller DE, Chaná-Cuevas P, Blauwendraat C, Singleton AB, Billingsley KJ. Saffie-Awad P, et al. medRxiv [Preprint]. 2025 Mar 19:2025.03.17.25323863. doi: 10.1101/2025.03.17.25323863. medRxiv. 2025. Update in: Mov Disord. 2025 Jul;40(7):1433-1441. doi: 10.1002/mds.30242. PMID: 40166539 Free PMC article. Updated. Preprint.

References

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1. Flanigan K, Gardner K, Alderson K, Galster B, Otterud B, Leppert MF, et al. Autosomal dominant spinocerebellar ataxia with sensory axonal neuropathy (SCA4): clinical description and genetic localization to chromosome 16q22.1. Am J Hum Genet 1996;59(2):392–399. - PMC - PubMed
1. Figueroa KP, Gross C, Buena‐Atienza E, Paul S, Gandelman M, Kakar N, et al. A GGC‐repeat expansion in ZFHX3 encoding polyglycine causes spinocerebellar ataxia type 4 and impairs autophagy. Nat Genet 2024;56(6):1080–1089. - PubMed
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Identification of GGC Repeat Expansions in ZFHX3 among Chilean Movement Disorder Patients

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Identification of GGC Repeat Expansions in ZFHX3 among Chilean Movement Disorder Patients

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