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Thomson KL, Jiang C, Richardson E, Westphal DS, Burkard T, Wolf CM, Vatta M, Harrison SM, Ingles J, Bezzina CR, Kroncke BM, Vandenberg JI, Ng CA. Clinical interpretation of KCNH2 variants using a robust PS3/BS3 functional patch-clamp assay. HGG Adv 2024; 5:100270. [PMID: 38219013 PMCID: PMC10840334 DOI: 10.1016/j.xhgg.2024.100270] [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: 10/06/2023] [Revised: 01/07/2024] [Accepted: 01/08/2024] [Indexed: 01/15/2024] Open
Abstract
Long QT syndrome (LQTS), caused by the dysfunction of cardiac ion channels, increases the risk of sudden death in otherwise healthy young people. For many variants in LQTS genes, there is insufficient evidence to make a definitive genetic diagnosis. We have established a robust functional patch-clamp assay to facilitate classification of missense variants in KCNH2, one of the key LQTS genes. A curated set of 30 benign and 30 pathogenic missense variants were used to establish the range of normal and abnormal function. The extent to which variants reduced protein function was quantified using Z scores, the number of standard deviations from the mean of the normalized current density of the set of benign variant controls. A Z score of -2 defined the threshold for abnormal loss of function, which corresponds to 55% wild-type function. More extreme Z scores were observed for variants with a greater loss-of-function effect. We propose that the Z score for each variant can be used to inform the application and weighting of abnormal and normal functional evidence criteria (PS3 and BS3) within the American College of Medical Genetics and Genomics variant classification framework. The validity of this approach was demonstrated using a series of 18 KCNH2 missense variants detected in a childhood onset LQTS cohort, where the level of function assessed using our assay correlated to the Schwartz score (a scoring system used to quantify the probability of a clinical diagnosis of LQTS) and the length of the corrected QT (QTc) interval.
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Affiliation(s)
- Kate L Thomson
- Oxford Genetics Laboratories, Churchill Hospital, Oxford, UK
| | - Connie Jiang
- Faculty of Medicine and Health, UNSW Sydney, Kensington, NSW, Australia; Mark Cowley Lidwill Research Program in Cardiac Electrophysiology, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
| | - Ebony Richardson
- Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, NSW, Australia; Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Dominik S Westphal
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine and Health, Technical University of Munich, Munich, Germany; Department of Internal Medicine I, Klinikum Rechts der Isar, School of Medicine and Health, Technical University of Munich, Munich, Germany; European Reference Network for Rare, Low Prevalence and Complex Diseases of the Heart: ERN GUARD-Heart
| | - Tobias Burkard
- Department of Congenital Heart Disease and Pediatric Cardiology, German Heart Center Munich, Technical University of Munich, School of Medicine and Health, Munich, Germany
| | - Cordula M Wolf
- European Reference Network for Rare, Low Prevalence and Complex Diseases of the Heart: ERN GUARD-Heart; Department of Congenital Heart Disease and Pediatric Cardiology, German Heart Center Munich, Technical University of Munich, School of Medicine and Health, Munich, Germany; DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany
| | | | | | - Jodie Ingles
- Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, NSW, Australia; Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Connie R Bezzina
- European Reference Network for Rare, Low Prevalence and Complex Diseases of the Heart: ERN GUARD-Heart; Department of Experimental Cardiology, Amsterdam Cardiovascular Sciences, University of Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
| | - Brett M Kroncke
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jamie I Vandenberg
- Mark Cowley Lidwill Research Program in Cardiac Electrophysiology, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia; School of Clinical Medicine, UNSW Sydney, Darlinghurst, NSW, Australia.
| | - Chai-Ann Ng
- Mark Cowley Lidwill Research Program in Cardiac Electrophysiology, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia; School of Clinical Medicine, UNSW Sydney, Darlinghurst, NSW, Australia.
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Hebbar M, Al-Taweel N, Gill I, Boelman C, Dean RA, Goodchild SJ, Mezeyova J, Shuart NG, Johnson JP, Lee J, Michoulas A, Huh LL, Armstrong L, Connolly MB, Demos MK. Expanding the genotype-phenotype spectrum in SCN8A-related disorders. Res Sq 2023:rs.3.rs-3221902. [PMID: 37609289 PMCID: PMC10441468 DOI: 10.21203/rs.3.rs-3221902/v1] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Background SCN8A-related disorders are a group of variable conditions caused by pathogenic variations in SCN8A. Online Mendelian Inheritance in Man (OMIM) terms them as developmental and epileptic encephalopathy 13, benign familial infantile seizures 5 or cognitive impairment with or without cerebellar ataxia. Methods In this study, we describe clinical and genetic results on eight individuals from six families with SCN8A pathogenic variants identified via exome sequencing. Results Clinical findings ranged from normal development with well-controlled epilepsy to significant developmental delay with treatment-resistant epilepsy. Three novel and three reported variants were observed in SCN8A. Electrophysiological analysis in transfected cells revealed a loss-of-function variant in Patient 4. Conclusions This work expands the clinical and genotypic spectrum of SCN8A-related disorders and provides electrophysiological results on a novel loss-of-function SCN8A variant.
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Affiliation(s)
- Malavika Hebbar
- Division of Neurology, Department of Pediatrics, BC Children's Hospital, Faculty of Medicine, University of British Columbia, Vancouver BC
| | - Nawaf Al-Taweel
- Division of Neurology, Department of Pediatrics, BC Children's Hospital, Faculty of Medicine, University of British Columbia, Vancouver BC
| | - Inderpal Gill
- Division of Neurology, Department of Pediatrics, BC Children's Hospital, Faculty of Medicine, University of British Columbia, Vancouver BC
| | - Cyrus Boelman
- Division of Neurology, Department of Pediatrics, BC Children's Hospital, Faculty of Medicine, University of British Columbia, Vancouver BC
| | - Richard A Dean
- Xenon Pharmaceuticals, 200-3650 Gilmore Way, Burnaby, BC V5G 4W8
| | | | - Janette Mezeyova
- Xenon Pharmaceuticals, 200-3650 Gilmore Way, Burnaby, BC V5G 4W8
| | | | - J P Johnson
- Xenon Pharmaceuticals, 200-3650 Gilmore Way, Burnaby, BC V5G 4W8
| | - James Lee
- Division of Neurology, Department of Pediatrics, BC Children's Hospital, Faculty of Medicine, University of British Columbia, Vancouver BC
| | - Aspasia Michoulas
- Division of Neurology, Department of Pediatrics, BC Children's Hospital, Faculty of Medicine, University of British Columbia, Vancouver BC
| | - Linda L Huh
- Division of Neurology, Department of Pediatrics, BC Children's Hospital, Faculty of Medicine, University of British Columbia, Vancouver BC
| | - Linlea Armstrong
- Department of Medical Genetics, BC Children's Hospital, Faculty of Medicine, University of British Columbia, Vancouver BC
| | - Mary B Connolly
- Division of Neurology, Department of Pediatrics, BC Children's Hospital, Faculty of Medicine, University of British Columbia, Vancouver BC
| | - Michelle K Demos
- Division of Neurology, Department of Pediatrics, BC Children's Hospital, Faculty of Medicine, University of British Columbia, Vancouver BC
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Tam B, Sinha S, Wang SM. Combining Ramachandran plot and molecular dynamics simulation for structural-based variant classification: Using TP53 variants as model. Comput Struct Biotechnol J 2020; 18:4033-4039. [PMID: 33363700 PMCID: PMC7744649 DOI: 10.1016/j.csbj.2020.11.041] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/23/2020] [Accepted: 11/23/2020] [Indexed: 12/12/2022] Open
Abstract
The wide application of new DNA sequencing technologies is generating vast quantities of genetic variation data at unprecedented speed. Developing methodologies to decode the pathogenicity of the variants is imperatively demanding. We hypothesized that as deleterious variants may function through disturbing structural stability of their affected proteins, information from structural change caused by genetic variants can be used to identify the variants with deleterious effects. In order to measure the structural change for proteins with large size, we designed a method named RP-MDS composed of Ramachandran plot (RP) and Molecular Dynamics Simulation (MDS). Ramachandran plot captures the variant-caused secondary structural change, whereas MDS provides a quantitative measure for the variant-caused globular structural change. We tested the method using variants in TP53 DNA binding domain of 219 residues as the model. In total, RP-MDS identified 23 of 38 (60.5%) TP53 known Pathogenic variants and 17 of 42 (41%) TP53 VUS that caused significant changes of P53 structure. Our study demonstrates that RP-MDS method provides a powerful protein structure-based tool to screen deleterious genetic variants affecting large-size proteins.
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Affiliation(s)
- Benjamin Tam
- Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau
| | - Siddharth Sinha
- Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau
| | - San Ming Wang
- Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau
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