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Aweidah H, Xi Z, Sahel JA, Byrne LC. PRPF31-retinitis pigmentosa: Challenges and opportunities for clinical translation. Vision Res 2023; 213:108315. [PMID: 37714045 PMCID: PMC10872823 DOI: 10.1016/j.visres.2023.108315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/17/2023]
Abstract
Mutations in pre-mRNA processing factor 31 cause autosomal dominant retinitis pigmentosa (PRPF31-RP), for which there is currently no efficient treatment, making this disease a prime target for the development of novel therapeutic strategies. PRPF31-RP exhibits incomplete penetrance due to haploinsufficiency, in which reduced levels of gene expression from the mutated allele result in disease. A variety of model systems have been used in the investigation of disease etiology and therapy development. In this review, we discuss recent advances in both in vivo and in vitro model systems, evaluating their advantages and limitations in the context of therapy development for PRPF31-RP. Additionally, we describe the latest approaches for treatment, including AAV-mediated gene augmentation, genome editing, and late-stage therapies such as optogenetics, cell transplantation, and retinal prostheses.
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Affiliation(s)
- Hamzah Aweidah
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Zhouhuan Xi
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA, USA; Department of Ophthalmology, Eye Center, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - José-Alain Sahel
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA, USA; Department of Neurobiology, University of Pittsburgh, Pittsburgh, PA, USA; Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Leah C Byrne
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA, USA; Department of Neurobiology, University of Pittsburgh, Pittsburgh, PA, USA; Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA.
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2
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Lisbjerg K, Bertelsen M, Grønskov K, Kessel L. Clinical characterization of patients with PRPF31-related retinitis pigmentosa and asymptomatic carriers: a cross-sectional study. Ophthalmic Genet 2023; 44:456-464. [PMID: 37293790 DOI: 10.1080/13816810.2023.2219732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 04/27/2023] [Accepted: 05/25/2023] [Indexed: 06/10/2023]
Abstract
BACKGROUND/AIM To describe the clinical phenotype of retinitis pigmentosa (RP) caused by PRPF31-variants and clinical characterization of asymptomatic PRPF31 carriers. MATERIALS AND METHODS We conducted a descriptive cross-sectional deep phenotyping study. We included subjects with PRPF31 variants predicted to be disease-causing, both individuals with RP and asymptomatic carriers. Participants underwent a comprehensive clinical examination of standard visual function parameters (visual acuity, contrast sensitivity, Goldmann visual field), full-field stimulus threshold (FST), full-field electroretinogram (ff-ERG), and a structural investigation with slit lamp and multimodal imaging. We used Spearman correlation analyses to evaluate associations between quantitative outcomes. RESULTS We included 21 individuals with disease-causing PRPF31-variants: 16 symptomatic and 5 asymptomatic subjects. The symptomatic subjects demonstrated a typical RP phenotype with constricted visual fields, extinguished ff-ERG, and disrupted outer retinal anatomy. FST was impaired and correlated significantly with other outcome measures in RP subjects. Structure-function correlations with Spearman correlation analysis showed moderate correlation coefficients due to a few outliers in each analysis. The asymptomatic individuals had normal best-corrected visual acuity and visual fields, but showed reduced ff-ERG amplitudes, borderline FST sensitivity, and structural abnormalities on OCT and fundoscopy. CONCLUSIONS RP11 has a typical RP phenotype but varies in terms of severity. FST measurements correlated well with other functional and structural metrics and may be a reliable outcome measure in future trials as it is sensitive to a broad range of disease severities. Asymptomatic carriers showed sub-clinical disease manifestations, and our findings underline that reported non-penetrance in PRPF31-related RP is not an all-or-none phenomenon.
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Affiliation(s)
- Kristian Lisbjerg
- Department of Ophthalmology, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Mette Bertelsen
- Department of Clinical Genetics, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Karen Grønskov
- Department of Clinical Genetics, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Line Kessel
- Department of Ophthalmology, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
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3
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Gene augmentation prevents retinal degeneration in a CRISPR/Cas9-based mouse model of PRPF31 retinitis pigmentosa. Nat Commun 2022; 13:7695. [PMID: 36509783 PMCID: PMC9744804 DOI: 10.1038/s41467-022-35361-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 11/29/2022] [Indexed: 12/14/2022] Open
Abstract
Mutations in PRPF31 cause autosomal dominant retinitis pigmentosa, an untreatable form of blindness. Gene therapy is a promising treatment for PRPF31-retinitis pigmentosa, however, there are currently no suitable animal models in which to develop AAV-mediated gene augmentation. Here we establish Prpf31 mutant mouse models using AAV-mediated CRISPR/Cas9 knockout, and characterize the resulting retinal degeneration phenotype. Mouse models with early-onset morphological and functional impairments like those in patients were established, providing new platforms in which to investigate pathogenetic mechanisms and develop therapeutic methods. AAV-mediated PRPF31 gene augmentation restored the retinal structure and function in a rapidly degenerating mouse model, demonstrating the first in vivo proof-of-concept for AAV-mediated gene therapy to treat PRPF31-retinitis pigmentosa. AAV-CRISPR/Cas9-PRPF31 knockout constructs also mediated efficient PRPF31 knockout in human and non-human primate retinal explants, laying a foundation for establishing non-human primate models using the method developed here.
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Jeyabalan N, Ghosh A, Mathias GP, Ghosh A. Rare eye diseases in India: A concise review of genes and genetics. Indian J Ophthalmol 2022; 70:2232-2238. [PMID: 35791102 PMCID: PMC9426079 DOI: 10.4103/ijo.ijo_322_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Rare eye diseases (REDs) are mostly progressive and are the leading cause of irreversible blindness. The disease onset can vary from early childhood to late adulthood. A high rate of consanguinity contributes to India’s predisposition to RED. Most gene variations causing REDs are monogenic and, in some cases, digenic. All three types of Mendelian inheritance have been reported in REDs. Some of the REDs are related to systemic illness with variable phenotypes in affected family members. Approximately, 50% of the children affected by REDs show associated phenotypes at the early stages of the disease. A precise clinical diagnosis becomes challenging due to high clinical and genetic heterogeneity. Technological advances, such as next-generation sequencing (NGS), have improved genetic and genomic testing for REDs, thereby aiding in determining the underlying causative gene variants. It is noteworthy that genetic testing together with genetic counseling facilitates a more personalized approach in the accurate diagnosis and management of the disease. In this review, we discuss REDs identified in the Indian population and their underlying genetic etiology.
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Affiliation(s)
- Nallathambi Jeyabalan
- Molecular Signaling and Gene Therapy Unit, GROW Research Laboratory, Narayana Nethralaya Foundation, Narayana Nethralaya Eye Hospital, Bengaluru, Karnataka, India
| | - Anuprita Ghosh
- Molecular Signaling and Gene Therapy Unit, GROW Research Laboratory, Narayana Nethralaya Foundation, Narayana Nethralaya Eye Hospital, Bengaluru, Karnataka, India
| | - Grace P Mathias
- Molecular Signaling and Gene Therapy Unit, GROW Research Laboratory, Narayana Nethralaya Foundation, Narayana Nethralaya Eye Hospital, Bengaluru, Karnataka, India
| | - Arkasubhra Ghosh
- Molecular Signaling and Gene Therapy Unit, GROW Research Laboratory, Narayana Nethralaya Foundation, Narayana Nethralaya Eye Hospital, Bengaluru, Karnataka, India
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5
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Kannabiran C, Parameswarappa D, Jalali S. Genetics of Inherited Retinal Diseases in Understudied Populations. Front Genet 2022; 13:858556. [PMID: 35295952 PMCID: PMC8919366 DOI: 10.3389/fgene.2022.858556] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 02/03/2022] [Indexed: 11/17/2022] Open
Abstract
Retinitis pigmentosa is one of the major forms of inherited retinal dystrophy transmitted in all Mendelian and non-Mendelian forms of inheritance. It involves the loss of retinal photoreceptor cells with severe loss of vision or blindness within the first 2 decades of life. RP occurs at a relatively high prevalence in India and is often associated with consanguinity in certain South Asian communities where this practice is customary. This review describes the studies that have been published with regard to genetics of retinitis pigmentosa in India and neighboring South Asian countries. These populations have been understudied in these aspects although to a variable degree from one country to another. Genetic studies on RP in India have been carried out with a range of methods aimed at detecting specific mutations, to screening of candidate genes or selected genomic regions, homozygosity mapping to whole genome sequencing. These efforts have led to a molecular genetic characterization of RP in Indian families. Similar studies on large extended families from Pakistan have provided insight into several novel genes underlying the pathogenesis of these diseases. The extreme degree of clinical and genetic heterogeneity of RP renders it challenging to identify the associated genes in these populations, and to translate the research output towards better management of the disease, as there are no unifying genetic features that are characteristic of any population so far.
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Affiliation(s)
- Chitra Kannabiran
- Kallam Anji Reddy Molecular Genetics Laboratory, Prof Brien Holden Eye Research Centre, Hyderabad, India.,L. V. Prasad Eye Institute, Hyderabad, India
| | - Deepika Parameswarappa
- L. V. Prasad Eye Institute, Hyderabad, India.,Smt Kannuri Santhamma Centre for Retina Vitreous Services, Hyderabad, India
| | - Subhadra Jalali
- L. V. Prasad Eye Institute, Hyderabad, India.,Smt Kannuri Santhamma Centre for Retina Vitreous Services, Hyderabad, India
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6
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Fadaie Z, Whelan L, Ben-Yosef T, Dockery A, Corradi Z, Gilissen C, Haer-Wigman L, Corominas J, Astuti GDN, de Rooij L, van den Born LI, Klaver CCW, Hoyng CB, Wynne N, Duignan ES, Kenna PF, Cremers FPM, Farrar GJ, Roosing S. Whole genome sequencing and in vitro splice assays reveal genetic causes for inherited retinal diseases. NPJ Genom Med 2021; 6:97. [PMID: 34795310 PMCID: PMC8602293 DOI: 10.1038/s41525-021-00261-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 10/21/2021] [Indexed: 01/08/2023] Open
Abstract
Inherited retinal diseases (IRDs) are a major cause of visual impairment. These clinically heterogeneous disorders are caused by pathogenic variants in more than 270 genes. As 30-40% of cases remain genetically unexplained following conventional genetic testing, we aimed to obtain a genetic diagnosis in an IRD cohort in which the genetic cause was not found using whole-exome sequencing or targeted capture sequencing. We performed whole-genome sequencing (WGS) to identify causative variants in 100 unresolved cases. After initial prioritization, we performed an in-depth interrogation of all noncoding and structural variants in genes when one candidate variant was detected. In addition, functional analysis of putative splice-altering variants was performed using in vitro splice assays. We identified the genetic cause of the disease in 24 patients. Causative coding variants were observed in genes such as ATXN7, CEP78, EYS, FAM161A, and HGSNAT. Gene disrupting structural variants were also detected in ATXN7, PRPF31, and RPGRIP1. In 14 monoallelic cases, we prioritized candidate noncanonical splice sites or deep-intronic variants that were predicted to disrupt the splicing process based on in silico analyses. Of these, seven cases were resolved as they carried pathogenic splice defects. WGS is a powerful tool to identify causative variants residing outside coding regions or heterozygous structural variants. This approach was most efficient in cases with a distinct clinical diagnosis. In addition, in vitro splice assays provide important evidence of the pathogenicity of rare variants.
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Affiliation(s)
- Zeinab Fadaie
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Laura Whelan
- The School of Genetics and Microbiology, Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Tamar Ben-Yosef
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Adrian Dockery
- The School of Genetics and Microbiology, Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Zelia Corradi
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lonneke Haer-Wigman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jordi Corominas
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Galuh D N Astuti
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Division of Human Genetics, Center for Biomedical Research (CEBIOR), Faculty of Medicine, Diponegoro University, Semarang, Indonesia
| | - Laura de Rooij
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Caroline C W Klaver
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Carel B Hoyng
- Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Niamh Wynne
- Department of Ophthalmology, Royal Victoria Eye and Ear Hospital, Dublin, Ireland
| | - Emma S Duignan
- Department of Ophthalmology, Royal Victoria Eye and Ear Hospital, Dublin, Ireland
| | - Paul F Kenna
- The School of Genetics and Microbiology, Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
- Department of Ophthalmology, Royal Victoria Eye and Ear Hospital, Dublin, Ireland
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - G Jane Farrar
- The School of Genetics and Microbiology, Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
- Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands.
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7
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Song F, Owczarek-Lipska M, Ahmels T, Book M, Aisenbrey S, Menghini M, Barthelmes D, Schrader S, Spital G, Neidhardt J. High-Throughput Sequencing to Identify Mutations Associated with Retinal Dystrophies. Genes (Basel) 2021; 12:genes12081269. [PMID: 34440443 PMCID: PMC8391535 DOI: 10.3390/genes12081269] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 11/16/2022] Open
Abstract
Retinal dystrophies (RD) are clinically and genetically heterogenous disorders showing mutations in over 270 disease-associated genes. Several millions of people worldwide are affected with different types of RD. Studying the relevance of disease-associated sequence alterations will assist in understanding disorders and may lead to the development of therapeutic approaches. Here, we established a whole exome sequencing (WES) pipeline to rapidly identify disease-associated mutations in patients. Sanger sequencing was applied to identify deep-intronic variants and to verify the co-segregation of WES results within families. We analyzed 26 unrelated patients with different syndromic and non-syndromic clinical manifestations of RD. All patients underwent ophthalmic examinations. We identified nine novel disease-associated sequence variants among 37 variants identified in total. The sequence variants located to 17 different genes. Interestingly, two cases presenting with Stargardt disease carried deep-intronic variants in ABCA4. We have classified 21 variants as pathogenic variants, 4 as benign/likely benign variants, and 12 as variants of uncertain significance. This study highlights the importance of WES-based mutation analyses in RD patients supporting clinical decisions, broadly based genetic diagnosis and support genetic counselling. It is essential for any genetic therapy to expand the mutation spectrum, understand the genes' function, and correlate phenotypes with genotypes.
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Affiliation(s)
- Fei Song
- Human Genetics Faculty VI-School of Medicine and Health Sciences, University of Oldenburg, Ammerländer Heerstrasse 114-118, 26129 Oldenburg, Germany; (F.S.); (M.O.-L.)
| | - Marta Owczarek-Lipska
- Human Genetics Faculty VI-School of Medicine and Health Sciences, University of Oldenburg, Ammerländer Heerstrasse 114-118, 26129 Oldenburg, Germany; (F.S.); (M.O.-L.)
- Research Center Neurosensory Science, University of Oldenburg, 26129 Oldenburg, Germany
| | - Tim Ahmels
- Department of Ophthalmology, Pius-Hospital, University of Oldenburg, 26121 Oldenburg, Germany; (T.A.); (S.S.)
| | - Marius Book
- Eye Centre at the St. Franziskus Hospital, 48145 Münster, Germany; (M.B.); (G.S.)
| | - Sabine Aisenbrey
- Department of Ophthalmology, Vivantes Health Network Ltd., Neukölln Hospital, 12351 Berlin, Germany;
| | - Moreno Menghini
- Department of Ophthalmology, Ospedale Regionale di Lugano, 6900 Lugano, Switzerland;
- Department of Ophthalmology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland;
| | - Daniel Barthelmes
- Department of Ophthalmology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland;
| | - Stefan Schrader
- Department of Ophthalmology, Pius-Hospital, University of Oldenburg, 26121 Oldenburg, Germany; (T.A.); (S.S.)
| | - Georg Spital
- Eye Centre at the St. Franziskus Hospital, 48145 Münster, Germany; (M.B.); (G.S.)
| | - John Neidhardt
- Human Genetics Faculty VI-School of Medicine and Health Sciences, University of Oldenburg, Ammerländer Heerstrasse 114-118, 26129 Oldenburg, Germany; (F.S.); (M.O.-L.)
- Research Center Neurosensory Science, University of Oldenburg, 26129 Oldenburg, Germany
- Correspondence: ; Tel.: +49-(0)441-7983810
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Roshandel D, Thompson JA, Heath Jeffery RC, Zhang D, Lamey TM, McLaren TL, De Roach JN, McLenachan S, Mackey DA, Chen FK. Clinical Evidence for the Importance of the Wild-Type PRPF31 Allele in the Phenotypic Expression of RP11. Genes (Basel) 2021; 12:genes12060915. [PMID: 34198599 PMCID: PMC8232116 DOI: 10.3390/genes12060915] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 06/09/2021] [Accepted: 06/12/2021] [Indexed: 11/16/2022] Open
Abstract
PRPF31-associated retinopathy (RP11) is a common form of autosomal dominant retinitis pigmentosa (adRP) that exhibits wide variation in phenotype ranging from non-penetrance to early-onset RP. Herein, we report inter-familial and intra-familial variation in the natural history of RP11 using multimodal imaging and microperimetry. Patients were recruited prospectively. The age of symptom onset, best-corrected visual acuity, microperimetry mean sensitivity (MS), residual ellipsoid zone span and hyperautofluorescent ring area were recorded. Genotyping was performed using targeted next-generation and Sanger sequencing and copy number variant analysis. PRPF31 mutations were found in 14 individuals from seven unrelated families. Four disease patterns were observed: (A) childhood onset with rapid progression (N = 4), (B) adult-onset with rapid progression (N = 4), (C) adult-onset with slow progression (N = 4) and (D) non-penetrance (N = 2). Four different patterns were observed in a family harbouring c.267del; patterns B, C and D were observed in a family with c.772_773delins16 and patterns A, B and C were observed in 3 unrelated individuals with large deletions. Our findings suggest that the RP11 phenotype may be related to the wild-type PRPF31 allele rather than the type of mutation. Further studies that correlate in vitro wild-type PRPF31 allele expression level with the disease patterns are required to investigate this association.
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Affiliation(s)
- Danial Roshandel
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Perth, WA 6009, Australia; (D.R.); (R.C.H.J.); (T.M.L.); (T.L.M.); (J.N.D.R.); (S.M.); (D.A.M.)
- Ocular Tissue Engineering Laboratory, Lions Eye Institute, Nedlands, WA 6009, Australia;
| | - Jennifer A. Thompson
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia;
| | - Rachael C. Heath Jeffery
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Perth, WA 6009, Australia; (D.R.); (R.C.H.J.); (T.M.L.); (T.L.M.); (J.N.D.R.); (S.M.); (D.A.M.)
- Ocular Tissue Engineering Laboratory, Lions Eye Institute, Nedlands, WA 6009, Australia;
- Department of Ophthalmology, Royal Perth Hospital, Perth, WA 6000, Australia
| | - Dan Zhang
- Ocular Tissue Engineering Laboratory, Lions Eye Institute, Nedlands, WA 6009, Australia;
| | - Tina M. Lamey
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Perth, WA 6009, Australia; (D.R.); (R.C.H.J.); (T.M.L.); (T.L.M.); (J.N.D.R.); (S.M.); (D.A.M.)
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia;
| | - Terri L. McLaren
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Perth, WA 6009, Australia; (D.R.); (R.C.H.J.); (T.M.L.); (T.L.M.); (J.N.D.R.); (S.M.); (D.A.M.)
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia;
| | - John N. De Roach
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Perth, WA 6009, Australia; (D.R.); (R.C.H.J.); (T.M.L.); (T.L.M.); (J.N.D.R.); (S.M.); (D.A.M.)
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia;
| | - Samuel McLenachan
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Perth, WA 6009, Australia; (D.R.); (R.C.H.J.); (T.M.L.); (T.L.M.); (J.N.D.R.); (S.M.); (D.A.M.)
- Ocular Tissue Engineering Laboratory, Lions Eye Institute, Nedlands, WA 6009, Australia;
| | - David A. Mackey
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Perth, WA 6009, Australia; (D.R.); (R.C.H.J.); (T.M.L.); (T.L.M.); (J.N.D.R.); (S.M.); (D.A.M.)
- Ocular Tissue Engineering Laboratory, Lions Eye Institute, Nedlands, WA 6009, Australia;
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia;
| | - Fred K. Chen
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Perth, WA 6009, Australia; (D.R.); (R.C.H.J.); (T.M.L.); (T.L.M.); (J.N.D.R.); (S.M.); (D.A.M.)
- Ocular Tissue Engineering Laboratory, Lions Eye Institute, Nedlands, WA 6009, Australia;
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia;
- Department of Ophthalmology, Royal Perth Hospital, Perth, WA 6000, Australia
- Department of Ophthalmology, Perth Children’s Hospital, Nedlands, WA 6009, Australia
- Correspondence: ; Tel.: +61-08-9381-0777
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Diverse Genetic Landscape of Suspected Retinitis Pigmentosa in a Large Korean Cohort. Genes (Basel) 2021; 12:genes12050675. [PMID: 33946315 PMCID: PMC8146864 DOI: 10.3390/genes12050675] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 04/27/2021] [Accepted: 04/27/2021] [Indexed: 12/29/2022] Open
Abstract
We conducted targeted next-generation sequencing (TGS) and/or whole exome sequencing (WES) to assess the genetic profiles of clinically suspected retinitis pigmentosa (RP) in the Korean population. A cohort of 279 unrelated Korean patients with clinically diagnosed RP and available family members underwent molecular analyses using TGS consisting of 88 RP-causing genes and/or WES with clinical variant interpretation. The combined genetic tests (TGS and/or WES) found a mutation in the 44 RP-causing genes and seven inherited retinal disease (IRD)-causing genes, and the total mutation detection rate was 57%. The mutation detection rate was higher in patients who experienced visual deterioration at a younger age (75.4%, age of symptom onset under 10 years) and who had a family history of RP (70.7%). The most common causative genes were EYS (8.2%), USH2A (6.8%), and PDE6B (4.7%), but mutations were dispersed among the 51 RP/IRD genes generally. Meanwhile, the PDE6B mutation was the most common in patients experiencing initial symptoms in their first decade, EYS in their second to third decades, and USH2A in their fifth decades and older. Of note, WES revealed some unexpected genotypes: ABCC6, CHM, CYP4V2, RS1, TGFBI, VPS13B, and WDR19, which were verified by ophthalmological re-phenotyping.
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Roshandel D, Thompson JA, Charng J, Zhang D, Chelva E, Arunachalam S, Attia MS, Lamey TM, McLaren TL, De Roach JN, Mackey DA, Wilton SD, Fletcher S, McLenachan S, Chen FK. Exploring microperimetry and autofluorescence endpoints for monitoring disease progression in PRPF31-associated retinopathy. Ophthalmic Genet 2020; 42:1-14. [PMID: 32985313 DOI: 10.1080/13816810.2020.1827442] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
BACKGROUND Mutations in the splicing factor pre-messenger RNA processing factor 31 (PRPF31) gene cause autosomal dominant retinitis pigmentosa 11 (RP11) through a haplo-insufficiency mechanism. We describe the phenotype and progression of microperimetry and autofluorescence endpoints in an Indigenous Australian RP11 family. PATIENTS AND METHODS Ophthalmic examination, optical coherence tomography, fundus autofluorescence and microperimetry were performed at baseline and every 6-12 months. Baseline and annual change in best-corrected visual acuity (BCVA), microperimetry mean sensitivity (MS) and number of scotoma loci, residual ellipsoid zone (EZ) span and hyperautofluorescent ring (HAR) area were reported. Next-generation and Sanger sequencing were performed in available members. RESULTS 12 affected members from three generations were examined. Mean (SD, range) age at onset of symptoms was 11 (4.5, 4-19) years. MS declined steadily from the third decade and EZ span and HAR area declined rapidly during the second decade. Serial microperimetry showed negligible change in MS over 2-3 years. However, mean EZ span, near-infrared and short-wavelength HAR area reduction was 203 (6.4%) µm/year, 1.8 (8.7%) mm2/year and 1.1 (8.6%) mm2/year, respectively. Genetic testing was performed on 11 affected and 10 asymptomatic members and PRPF31 c.1205 C > A (p.Ser402Ter) mutation was detected in all affected and two asymptomatic members (non-penetrant carriers). CONCLUSIONS Our findings suggest that in the studied cohort, the optimal window for therapeutic intervention is the second decade of life and residual EZ span and HAR area can be considered as efficacy outcome measures. Further studies on larger samples with different PRPF31 mutations and longer follow-up duration are recommended.
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Affiliation(s)
- Danial Roshandel
- Centre for Ophthalmology and Visual Science, The University of Western Australia , Perth, Australia.,Ocular Tissue Engineering Laboratory, Lions Eye Institute , Nedlands, Australia
| | - Jennifer A Thompson
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital , Nedlands, Australia
| | - Jason Charng
- Centre for Ophthalmology and Visual Science, The University of Western Australia , Perth, Australia.,Ocular Tissue Engineering Laboratory, Lions Eye Institute , Nedlands, Australia
| | - Dan Zhang
- Centre for Ophthalmology and Visual Science, The University of Western Australia , Perth, Australia.,Ocular Tissue Engineering Laboratory, Lions Eye Institute , Nedlands, Australia
| | - Enid Chelva
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital , Nedlands, Australia
| | - Sukanya Arunachalam
- Centre for Ophthalmology and Visual Science, The University of Western Australia , Perth, Australia.,Ocular Tissue Engineering Laboratory, Lions Eye Institute , Nedlands, Australia
| | - Mary S Attia
- Centre for Ophthalmology and Visual Science, The University of Western Australia , Perth, Australia.,Ocular Tissue Engineering Laboratory, Lions Eye Institute , Nedlands, Australia
| | - Tina M Lamey
- Centre for Ophthalmology and Visual Science, The University of Western Australia , Perth, Australia.,Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital , Nedlands, Australia
| | - Terri L McLaren
- Centre for Ophthalmology and Visual Science, The University of Western Australia , Perth, Australia.,Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital , Nedlands, Australia
| | - John N De Roach
- Centre for Ophthalmology and Visual Science, The University of Western Australia , Perth, Australia.,Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital , Nedlands, Australia
| | - David A Mackey
- Centre for Ophthalmology and Visual Science, The University of Western Australia , Perth, Australia.,Ocular Tissue Engineering Laboratory, Lions Eye Institute , Nedlands, Australia.,Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital , Nedlands, Australia
| | - Steve D Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University , Murdoch, Australia.,The Perron Institute, The University of Western Australia , Nedlands, Australia
| | - Sue Fletcher
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University , Murdoch, Australia.,The Perron Institute, The University of Western Australia , Nedlands, Australia
| | - Samuel McLenachan
- Centre for Ophthalmology and Visual Science, The University of Western Australia , Perth, Australia.,Ocular Tissue Engineering Laboratory, Lions Eye Institute , Nedlands, Australia
| | - Fred K Chen
- Centre for Ophthalmology and Visual Science, The University of Western Australia , Perth, Australia.,Ocular Tissue Engineering Laboratory, Lions Eye Institute , Nedlands, Australia.,Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital , Nedlands, Australia.,Department of Ophthalmology, Royal Perth Hospital , Perth, Australia.,Department of Ophthalmology, Perth Children's Hospital , Nedlands, Australia
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11
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Pemmasani SK, Raman R, Mohapatra R, Vidyasagar M, Acharya A. A Review on the Challenges in Indian Genomics Research for Variant Identification and Interpretation. Front Genet 2020; 11:753. [PMID: 32793285 PMCID: PMC7387655 DOI: 10.3389/fgene.2020.00753] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 06/24/2020] [Indexed: 11/13/2022] Open
Abstract
Today, genomic data holds great potential to improve healthcare strategies across various dimensions – be it disease prevention, enhanced diagnosis, or optimized treatment. The biggest hurdle faced by the medical and research community in India is the lack of genotype-phenotype correlations for Indians at a population-wide and an individual level. This leads to inefficient translation of genomic information during clinical decision making. Population-wide sequencing projects for Indian genomes help overcome hurdles and enable us to unearth and validate the genetic markers for different health conditions. Machine learning algorithms are essential to analyze huge amounts of genotype data in synergy with gene expression, demographic, clinical, and pathological data. Predictive models developed through these algorithms help in classifying the individuals into different risk groups, so that preventive measures and personalized therapies can be designed. They also help in identifying the impact of each genetic marker with the associated condition, from a clinical perspective. In India, genome sequencing technologies have now become more accessible to the general population. However, information on variants associated with several major diseases is not available in publicly-accessible databases. Creating a centralized database of variants facilitates early detection and mitigation of health risks in individuals. In this article, we discuss the challenges faced by genetic researchers and genomic testing facilities in India, in terms of dearth of public databases, people with knowledge on machine learning algorithms, computational resources and awareness in the medical community in interpreting genetic variants. Potential solutions to enhance genomic research in India, are also discussed.
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Affiliation(s)
| | - Rasika Raman
- Research and Development Division, Mapmygenome India Limited, Hyderabad, India
| | | | | | - Anuradha Acharya
- Research and Development Division, Mapmygenome India Limited, Hyderabad, India
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12
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Mutation spectrum of PRPF31, genotype-phenotype correlation in retinitis pigmentosa, and opportunities for therapy. Exp Eye Res 2020; 192:107950. [PMID: 32014492 PMCID: PMC7065041 DOI: 10.1016/j.exer.2020.107950] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 01/13/2020] [Accepted: 01/27/2020] [Indexed: 12/11/2022]
Abstract
Pathogenic variants in pre-messenger RNA (pre-mRNA) splicing factor 31, PRPF31, are the second most common genetic cause of autosomal dominant retinitis pigmentosa (adRP) in most populations. This remains a completely untreatable and incurable form of blindness, and it can be difficult to predict the clinical course of disease. In order to design appropriate targeted therapies, a thorough understanding of the genetics and molecular mechanism of this disease is required. Here, we present the structure of the PRPF31 gene and PRPF31 protein, current understanding of PRPF31 protein function and the full spectrum of all reported clinically relevant variants in PRPF31. We delineate the correlation between specific PRPF31 genotype and RP phenotype, suggesting that, except in cases of complete gene deletion or large-scale deletions, dominant negative effects contribute to phenotype as well as haploinsufficiency. This has important impacts on design of targeted therapies, particularly the feasibility of gene augmentation as a broad approach for treatment of PRPF31-associated RP. We discuss other opportunities for therapy, including antisense oligonucleotide therapy and gene-independent approaches and offer future perspectives on treatment of this form of RP. PRPF31 is the second most common cause of autosomal dominant retinitis pigmentosa and a potential target for gene therapy. We present all reported pathogenic variants in PRPF31 as a resource for clinicians, diagnostic genetics labs, and researchers. Genotype-phenotype correlations suggest that, dominant negative effects contribute to disease in addition to haploinsufficiency. This finding has important impacts on the suitability of gene augmentation approaches across all mutation types. This finding may aid prognosis of disease in PRPF31-associated RP patients.
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13
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Lin Y, Xu CL, Velez G, Yang J, Tanaka AJ, Breazzano MP, Mahajan VB, Sparrow JR, Tsang SH. Novel REEP6 gene mutation associated with autosomal recessive retinitis pigmentosa. Doc Ophthalmol 2019; 140:67-75. [PMID: 31538292 DOI: 10.1007/s10633-019-09719-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 09/04/2019] [Indexed: 01/06/2023]
Abstract
PURPOSE This study reports the ophthalmic and genetic findings of a Cameroonian patient with autosomal recessive retinitis pigmentosa (arRP) caused by a novel Receptor Expression Enhancing Protein 6 (REEP6) homozygous mutation. PATIENT AND METHODS A 33-year-old man underwent comprehensive ophthalmic examinations, including visual acuity measurements, dilated fundus imaging, electroretinography (ERG), and spectral-domain optical coherence tomography (SD-OCT). Short-wavelength fundus autofluorescence (SW-AF) and near-infrared fundus autofluorescence (NIR-AF) were also evaluated. Whole exome sequencing (WES) was used to identify potential pathogenic variants. RESULTS Fundus examination revealed typical RP findings with additional temporal ten micron yellow dots. SD-OCT imaging revealed cystoid macular edema and perifoveal outer retinal atrophy with centrally preserved inner segment ellipsoid zone (EZ) bands. Hyperreflective spots were seen in the inner retinal layers. On SW-AF images, a hypoautofluorescent area in the perifoveal area was observed. NIR-AF imaging revealed an irregularly shaped hyperautofluorescent ring. His visual acuity was mildly affected. ERG showed undetectable rod responses and intact cone responses. Genetic testing via WES revealed a novel homozygous mutation (c.295G>A, p.Glu99Lys) in the gene encoding REEP6, which is predicted to alter the charge in the transmembrane helix. CONCLUSIONS This report is not only the first description of a Cameroonian patient with arRP associated with a REEP6 mutation, but also this particular genetic alteration. Substitution of p.Glu99Lys in REEP6 likely disrupts the interactions between REEP6 and the ER membrane. NIR-AF imaging may be particularly useful for assessing functional photoreceptor cells and show an "avocado" pattern of hyperautofluorescence in patients with the REEP6 mutation.
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Affiliation(s)
- Yuchen Lin
- Jonas Children's Vision Care, and Bernard & Shirlee Brown Glaucoma Laboratory, Columbia Stem Cell Initiative, Departments of Ophthalmology, Pathology and Cell Biology, Institute of Human Nutrition, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA.,Eye Center, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Christine L Xu
- Jonas Children's Vision Care, and Bernard & Shirlee Brown Glaucoma Laboratory, Columbia Stem Cell Initiative, Departments of Ophthalmology, Pathology and Cell Biology, Institute of Human Nutrition, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA.,Edward S. Harkness Eye Institute, New York-Presbyterian Hospital, New York, NY, USA
| | - Gabriel Velez
- Omics Laboratory, Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA, USA.,Medical Scientist Training Program, University of Iowa, Iowa City, IA, USA
| | - Jing Yang
- Omics Laboratory, Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA, USA
| | - Akemi J Tanaka
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Mark P Breazzano
- Edward S. Harkness Eye Institute, New York-Presbyterian Hospital, New York, NY, USA.,Department of Ophthalmology, New York University School of Medicine, New York, NY, USA
| | - Vinit B Mahajan
- Omics Laboratory, Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA, USA.,Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA
| | - Janet R Sparrow
- Edward S. Harkness Eye Institute, New York-Presbyterian Hospital, New York, NY, USA.,Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Stephen H Tsang
- Jonas Children's Vision Care, and Bernard & Shirlee Brown Glaucoma Laboratory, Columbia Stem Cell Initiative, Departments of Ophthalmology, Pathology and Cell Biology, Institute of Human Nutrition, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA. .,Edward S. Harkness Eye Institute, New York-Presbyterian Hospital, New York, NY, USA.
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14
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Wheway G, Nazlamova L, Meshad N, Hunt S, Jackson N, Churchill A. A Combined in silico, in vitro and Clinical Approach to Characterize Novel Pathogenic Missense Variants in PRPF31 in Retinitis Pigmentosa. Front Genet 2019; 10:248. [PMID: 30967900 PMCID: PMC6438860 DOI: 10.3389/fgene.2019.00248] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 03/05/2019] [Indexed: 11/30/2022] Open
Abstract
At least six different proteins of the spliceosome, including PRPF3, PRPF4, PRPF6, PRPF8, PRPF31, and SNRNP200, are mutated in autosomal dominant retinitis pigmentosa (adRP). These proteins have recently been shown to localize to the base of the connecting cilium of the retinal photoreceptor cells, elucidating this form of RP as a retinal ciliopathy. In the case of loss-of-function variants in these genes, pathogenicity can easily be ascribed. In the case of missense variants, this is more challenging. Furthermore, the exact molecular mechanism of disease in this form of RP remains poorly understood. In this paper we take advantage of the recently published cryo EM-resolved structure of the entire human spliceosome, to predict the effect of a novel missense variant in one component of the spliceosome; PRPF31, found in a patient attending the genetics eye clinic at Bristol Eye Hospital. Monoallelic variants in PRPF31 are a common cause of autosomal dominant retinitis pigmentosa (adRP) with incomplete penetrance. We use in vitro studies to confirm pathogenicity of this novel variant PRPF31 c.341T > A, p.Ile114Asn. This work demonstrates how in silico modeling of structural effects of missense variants on cryo-EM resolved protein complexes can contribute to predicting pathogenicity of novel variants, in combination with in vitro and clinical studies. It is currently a considerable challenge to assign pathogenic status to missense variants in these proteins.
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Affiliation(s)
- Gabrielle Wheway
- Centre for Research in Biosciences, University of the West of England, Bristol, United Kingdom
| | - Liliya Nazlamova
- Centre for Research in Biosciences, University of the West of England, Bristol, United Kingdom
| | - Nervine Meshad
- Bristol Eye Hospital, University Hospitals Bristol NHS Foundation Trust, Bristol, United Kingdom
| | - Samantha Hunt
- Bristol Eye Hospital, University Hospitals Bristol NHS Foundation Trust, Bristol, United Kingdom
| | - Nicola Jackson
- Clinical Genetics Service, University Hospitals Bristol NHS Foundation Trust, Bristol, United Kingdom
| | - Amanda Churchill
- Bristol Eye Hospital, University Hospitals Bristol NHS Foundation Trust, Bristol, United Kingdom
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