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Sultan T, Scorrano G, Panciroli M, Christoforou M, Raza Alvi J, Di Ludovico A, Qureshi S, Efthymiou S, Salpietro V, Houlden H. Clinical and molecular heterogeneity of VPS13D-related neurodevelopmental and movement disorders. Gene 2024; 899:148119. [PMID: 38160741 DOI: 10.1016/j.gene.2023.148119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/25/2023] [Accepted: 12/28/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND The VPS13 family of proteins has been implicated in lipid transport and trafficking between endoplasmic reticulum and organelles, to maintain homeostasis of subcellular membranes. Recently, pathogenic variants in each human VPS13S gene, have been linked to distinct human neurodevelopmental or neurodegenerative disorders. Within the VPS13 family of genes, VPS13D is known to be implicated in mitochondria homeostasis and function. METHODS We investigated a Pakistani sibship affected with neurodevelopmental impairment and severe hyperkinetic (choreoathetoid) movements. Whole exome sequencing (WES) and Sanger sequencing were performed to identify potential candidate variants segregating in the family. We described clinical phenotypes and natural history of the disease during a 3-year clinical follow-up and summarized literature data related to previously identified patients with VPS13D-related neurological disorders. RESULTS We identified by WES an homozygous non-synonymous variant in VPS13D (c.5723 T > C; p.Ile1908Thr) as the potential underlying cause of the disease in our family. Two young siblings developed an early-onset neurological impairment characterized by global developmental delay, with impaired speech and motor milestones, associated to hyperkinetic movement disorders as well as progressive and non-progressive neurological abnormalities. CONCLUSION In this study we delineated the heterogeneity of VPS13D-related clinical phenotypes and described a novel VPS13D homozygous variant associated with severe neurological impairment. Further studies will be pivotal to understand the exact VPS13D function and its impact on mitochondria homeostasis, brain development and regulation of movements, to further clarify genotype-phenotype correlations and provide crucial prognostic information and potential therapeutic implications.
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Affiliation(s)
- Tipu Sultan
- Department of Pediatric Neurology, Children Hospital Lahore, Main Boulevard Gulberg, Nishtar Town, Lahore, Punjab 54000, Pakistan
| | | | - Marta Panciroli
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London WC1N 3BG, United Kingdom
| | - Marilena Christoforou
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London WC1N 3BG, United Kingdom
| | - Javeria Raza Alvi
- Department of Pediatric Neurology, Children Hospital Lahore, Main Boulevard Gulberg, Nishtar Town, Lahore, Punjab 54000, Pakistan
| | | | - Sameen Qureshi
- Department of Pediatric Neurology, Children Hospital Lahore, Main Boulevard Gulberg, Nishtar Town, Lahore, Punjab 54000, Pakistan
| | - Stephanie Efthymiou
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London WC1N 3BG, United Kingdom
| | - Vincenzo Salpietro
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London WC1N 3BG, United Kingdom.
| | - Henry Houlden
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London WC1N 3BG, United Kingdom
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Chang YM, Pan YW, Chou YY, Yu WH, Tsai MC. A boy with a progressive neurologic decline harboring two coexisting mutations in KMT2D and VPS13D. Brain Dev 2023; 45:603-607. [PMID: 37599126 DOI: 10.1016/j.braindev.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 06/25/2023] [Accepted: 08/05/2023] [Indexed: 08/22/2023]
Abstract
INTRODUCTION Kabuki syndrome (KS) and spinocerebellar ataxia (SCA) are both rare conditions with neurodevelopmental abnormalities. Approaching a patient with complex phenotypes and differentiating the role of mutations may be beneficial but challenging in predicting the disease prognosis. CASE PRESENTATION A boy presented with progressive ataxia, developmental regression, and myoclonus since 4 years of age. Additional features included growth hormone deficiency, excessive body hair, dysmorphic facies, hypoparathyroidism, and bilateral sensorineural hearing impairment. Brain magnetic resonance imaging depicted T2-weighted hyperintensities over bilateral globus pallidus, thalamus, subcortical white matter, and brainstem. The results of tandem mass spectrometry, mitochondrial deletion, and mitochondrial DNA sequencing were inconclusive. Whole-exome sequencing (WES) on genomic DNA obtained from peripheral blood cells revealed a known pathogenic variant at KMT2D gene (c.5993A > G, p.Tyr1998Cys) related to KS and two compound heterozygous, likely pathogenic variants at VPS13D gene (c.908G > A, p.Arg303Gln and c.8561T > G, p.Leu2854Arg) related to autosomal recessive SCA type 4 (SCAR4). DISCUSSION SCAR4 is mainly adult-onset, but a few pediatric cases have recently been reported with progressive gait instability and developmental delay. The VPS13D gene has been suggested to play a role in mitochondrial size, autophagy, and clearance, thus explaining the clinical and imaging phenotypes. CONCLUSION Our case showed a rare co-existence of KS and SCAR4, highlighting the utility of WES in atypical cases that a single-gene disease cannot fully explain.
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Affiliation(s)
- Yu-Ming Chang
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yu-Wen Pan
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yen-Yin Chou
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Genomic Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Wen-Hao Yu
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Meng-Che Tsai
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Genomic Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
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Baker EK, Han J, Langley WA, Reott MA, Hallinan BE, Hopkin RJ, Zhang W. RNA sequencing reveals a complete picture of a homozygous missense variant in a patient with VPS13D movement disorder: a case report and review of the literature. Mol Genet Genomics 2023:10.1007/s00438-023-02044-y. [PMID: 37340120 DOI: 10.1007/s00438-023-02044-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 06/04/2023] [Indexed: 06/22/2023]
Abstract
RNA sequencing (RNA-seq) is a complementary diagnostic tool to exome sequencing (ES), only recently clinically available to undiagnosed patients post-ES, that provides functional information on variants of unknown significance (VUS) by evaluating its effect on RNA transcription. ES became clinically available in the early 2010s and promised an agnostic platform for patients with a neurological disease, especially for those who believed to have a genetic etiology. However, the massive data generated by ES pose challenges in variant interpretation, especially for rare missense, synonymous, and deep intronic variants that may have a splicing effect. Without functional study and/or family segregation analysis, these rare variants would be likely interpreted as VUS which is difficult for clinicians to use in clinical care. Clinicians are able to assess the VUS for phenotypic overlap, but this additional information alone is usually not enough to re-classify a variant. Here, we report a case of a 14-month-old male who presented to clinic with a history of seizures, nystagmus, cerebral palsy, oral aversion, global developmental delay, and poor weight gain requiring gastric tube placement. ES revealed a previously unreported homozygous missense VUS, c.7406A > G p.(Asn2469Ser), in VPS13D. This variant has not been previously reported in genome aggregation database (gnomAD), ClinVar, or in any peer-reviewed published literature. By RNA-seq, we demonstrated that this variant mainly impacts splicing and results in a frameshift and early termination. It is expected to generate either a truncated protein, p.(Val2468fs*19), or no protein from this transcript due to nonsense-mediated mRNA decay leading to VPS13D deficiency. To our knowledge, this is the first case utilizing RNA-seq to further functionally characterize a homozygous novel missense VUS in VPS13D and confirm its impact on splicing. This confirmed pathogenicity gave the diagnosis of VPS13D movement disorder to this patient. Therefore, clinicians should consider utilizing RNA-seq to clarify VUS by evaluating its effect on RNA transcription.
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Affiliation(s)
- Elizabeth K Baker
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, ML7016, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Jingfen Han
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, ML7016, Cincinnati, OH, 45229, USA
| | | | | | - Barbara E Hallinan
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Neurology, Cincinnati Children's Hospital Medicine, Cincinnati, OH, USA
| | - Robert J Hopkin
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, ML7016, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Wenying Zhang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, ML7016, Cincinnati, OH, 45229, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
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Dekker J, Schot R, Bongaerts M, de Valk WG, van Veghel-Plandsoen MM, Monfils K, Douben H, Elfferich P, Kasteleijn E, van Unen LMA, Geeven G, Saris JJ, van Ierland Y, Verheijen FW, van der Sterre MLT, Sadeghi Niaraki F, Smits DJ, Huidekoper HH, Williams M, Wilke M, Verhoeven VJM, Joosten M, Kievit AJA, van de Laar IMBH, Hoefsloot LH, Hoogeveen-Westerveld M, Nellist M, Mancini GMS, van Ham TJ. Web-accessible application for identifying pathogenic transcripts with RNA-seq: Increased sensitivity in diagnosis of neurodevelopmental disorders. Am J Hum Genet 2023; 110:251-72. [PMID: 36669495 DOI: 10.1016/j.ajhg.2022.12.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 12/21/2022] [Indexed: 01/20/2023] Open
Abstract
For neurodevelopmental disorders (NDDs), a molecular diagnosis is key for management, predicting outcome, and counseling. Often, routine DNA-based tests fail to establish a genetic diagnosis in NDDs. Transcriptome analysis (RNA sequencing [RNA-seq]) promises to improve the diagnostic yield but has not been applied to NDDs in routine diagnostics. Here, we explored the diagnostic potential of RNA-seq in 96 individuals including 67 undiagnosed subjects with NDDs. We performed RNA-seq on single individuals' cultured skin fibroblasts, with and without cycloheximide treatment, and used modified OUTRIDER Z scores to detect gene expression outliers and mis-splicing by exonic and intronic outliers. Analysis was performed by a user-friendly web application, and candidate pathogenic transcriptional events were confirmed by secondary assays. We identified intragenic deletions, monoallelic expression, and pseudoexonic insertions but also synonymous and non-synonymous variants with deleterious effects on transcription, increasing the diagnostic yield for NDDs by 13%. We found that cycloheximide treatment and exonic/intronic Z score analysis increased detection and resolution of aberrant splicing. Importantly, in one individual mis-splicing was found in a candidate gene nearly matching the individual's specific phenotype. However, pathogenic splicing occurred in another neuronal-expressed gene and provided a molecular diagnosis, stressing the need to customize RNA-seq. Lastly, our web browser application allowed custom analysis settings that facilitate diagnostic application and ranked pathogenic transcripts as top candidates. Our results demonstrate that RNA-seq is a complementary method in the genomic diagnosis of NDDs and, by providing accessible analysis with improved sensitivity, our transcriptome analysis approach facilitates wider implementation of RNA-seq in routine genome diagnostics.
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Pauly MG, Brüggemann N, Efthymiou S, Grözinger A, Diaw SH, Chelban V, Turchetti V, Vona B, Tadic V, Houlden H, Münchau A, Lohmann K. Not to Miss: Intronic Variants, Treatment, and Review of the Phenotypic Spectrum in VPS13D-Related Disorder. Int J Mol Sci 2023; 24:ijms24031874. [PMID: 36768210 PMCID: PMC9953040 DOI: 10.3390/ijms24031874] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 12/28/2022] [Indexed: 01/21/2023] Open
Abstract
VPS13D is one of four human homologs of the vacuolar sorting protein 13 gene (VPS13). Biallelic pathogenic variants in the gene are associated with spastic ataxia or spastic paraplegia. Here, we report two patients with intronic pathogenic variants: one patient with early onset severe spastic ataxia and debilitating tremor, which is compound-heterozygous for a canonical (NM_018156.4: c.2237-1G > A) and a non-canonical (NM_018156.4: c.941+3G>A) splice site variant. The second patient carries the same non-canonical splice site variant in the homozygous state and is affected by late-onset spastic paraplegia. We confirmed altered splicing as a result of the intronic variants and demonstrated disturbed mitochondrial integrity. Notably, tremor in the first patient improved significantly by bilateral deep brain stimulation (DBS) in the ventralis intermedius (VIM) nucleus of the thalamus. We also conducted a literature review and summarized the phenotypical spectrum of reported VPS13D-related disorders. Our study underscores that looking for mutations outside the canonical splice sites is important not to miss a genetic diagnosis, especially in disorders with a highly heterogeneous presentation without specific red flags.
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Affiliation(s)
- Martje G. Pauly
- Institute of Neurogenetics, University of Lübeck, 23562 Lübeck, Germany
- Department of Neurology, University Hospital Schleswig Holstein, 23562 Lübeck, Germany
- Institute of Systems Motor Science, University of Lübeck, 23562 Lübeck, Germany
| | - Norbert Brüggemann
- Institute of Neurogenetics, University of Lübeck, 23562 Lübeck, Germany
- Department of Neurology, University Hospital Schleswig Holstein, 23562 Lübeck, Germany
| | - Stephanie Efthymiou
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Anne Grözinger
- Institute of Neurogenetics, University of Lübeck, 23562 Lübeck, Germany
| | | | - Viorica Chelban
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Valentina Turchetti
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Barbara Vona
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, 37075 Göttingen, Germany
- Institute of Human Genetics, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Vera Tadic
- Institute of Neurogenetics, University of Lübeck, 23562 Lübeck, Germany
- Department of Neurology, University Hospital Schleswig Holstein, 23562 Lübeck, Germany
| | - Henry Houlden
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Alexander Münchau
- Institute of Systems Motor Science, University of Lübeck, 23562 Lübeck, Germany
| | - Katja Lohmann
- Institute of Neurogenetics, University of Lübeck, 23562 Lübeck, Germany
- Correspondence:
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Durand CM, Angelini C, Michaud V, Delleci C, Coupry I, Goizet C, Trimouille A. Whole-exome sequencing confirms implication of VPS13D as a potential cause of progressive spastic ataxia. BMC Neurol 2022; 22. [PMID: 35151251 PMCID: PMC8840315 DOI: 10.1186/s12883-022-02553-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 01/09/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
VPS13D is a large ubiquitin-binding protein playing an essential role in mitophagy by regulating mitochondrial fission. Recently, VPS13D biallelic pathogenic variants have been reported in patients displaying variable neurological phenotypes, with an autosomic recessive inheritance.
The objectives of the study were to determine the genetic etiology of a patient with early onset sporadic progressive spastic ataxia, and to investigate the pathogenicity of VPS13D variants through functional studies on patient’s skin fibroblasts.
Case presentation
We report the case of a 51-year-old patient with spastic ataxia, with an acute onset of the disease at age 7. Walking difficulties slowly worsened over time, with the use of a wheelchair since age 26. We have used trio-based whole-exome sequencing (WES) to identify genes associated with spastic ataxia. The impact of the identified variants on mitochondrial function was assessed in patient’s fibroblasts by imaging mitochondrial network and measuring level of individual OXPHOS complex subunits. Compound heterozygous variants were identified in VPS13D: c.946C > T, p.Arg316* and c.12416C > T, p.(Ala4139Val). Primary fibroblasts obtained from this patient revealed an altered mitochondrial morphology, and a decrease in levels of proteins from complex I, III and IV.
Conclusions
Our findings confirmed implication of VPS13D in spastic ataxia and provided further support for mitochondrial defects in patient’s skin fibroblasts with VPS13D variants. This report of long-term follow up showed a slowly progressive course of the spastic paraplegia with cerebellar features. Furthermore, the performed functional studies could be used as biomarker helping diagnosis of VPS13D-related neurological disorders when molecular results are uneasy to interpret.
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