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Park KJ, Lee W, Chun S, Min WK. The Frequency of Discordant Variant Classification in the Human Gene Mutation Database: A Comparison of the American College of Medical Genetics and Genomics Guidelines and ClinVar. Lab Med 2020; 52:250-259. [PMID: 32926152 DOI: 10.1093/labmed/lmaa072] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
OBJECTIVE Discordant variant classifications among public databases is one of the well-documented limitations when interpreting the pathogenicity of variants. The aim of this study is to investigate the level of germline variant misannotation from the Human Gene Mutation Database (HGMD) and the annotation concordance between databases. METHODS We used a total of 188,106 classified variants (disease-causing mutations [n = 179,454] and polymorphisms [n = 8652]) in 6466 genes from the HGMD. All variants were reanalyzed based on the American College of Medical Genetics and Genomics (ACMG) guidelines and compared to ClinVar database variants. RESULTS When variants were classified based on the ACMG guidelines, misclassification was observed in 3.47% (2289/65,896) of variants. The overall concordance between HGMD and ClinVar was 97.62% (52,499/53,780) of variants studied. CONCLUSION Variants in databases must be used with caution when variant pathogenicity is interpreted. This study reveals the frequency of misannotation of the HGMD variants and annotation concordance between databases in depth.
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Affiliation(s)
- Kyoung-Jin Park
- Department of Laboratory Medicine, Myongji Hospital, Hanyang University College of Medicine, Goyang-Si, Gyeonggi-Do, Korea
| | - Woochang Lee
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Sail Chun
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Won-Ki Min
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
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Lin JH, Masson E, Boulling A, Hayden M, Cooper DN, Férec C, Liao Z, Chen JM. 5' splice site GC>GT and GT>GC variants differ markedly in terms of their functionality and pathogenicity. Hum Mutat 2020; 41:1358-1364. [PMID: 32369867 DOI: 10.1002/humu.24029] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 11/12/2019] [Revised: 03/27/2020] [Accepted: 04/19/2020] [Indexed: 12/11/2022]
Abstract
In the human genome, most 5' splice sites (~99%) employ the canonical GT dinucleotide whereas a small minority (~1%) use the noncanonical GC dinucleotide. The functionality and pathogenicity of 5' splice site GT>GC (+2T>C) variants have been extensively studied but we know very little about 5' splice site GC>GT (+2C>T) variants. Herein, we have addressed this deficiency by performing a meta-analysis of reported +2C>T "pathogenic" variants together with a functional analysis of engineered +2C>T substitutions using a cell culture-based full-length gene splicing assay. Our results establish proof of concept that +2C>T variants are qualitatively different from +2T>C variants in terms of their functionality and suggest that, in sharp contrast to +2T>C variants, most if not all +2C>T variants have no pathological relevance. Our findings have important implications for interpreting the clinical relevance of +2C>T variants and understanding the evolutionary switching between GT and GC 5' splice sites in mammalian genomes.
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Affiliation(s)
- Jin-Huan Lin
- EFS, Univ Brest, INSERM, UMR 1078, GGB, Brest, France.,Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai, China.,Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Emmanuelle Masson
- EFS, Univ Brest, INSERM, UMR 1078, GGB, Brest, France.,CHRU Brest, Service de Génétique Médicale et de Biologie de la Reproduction, Brest, France
| | | | - Matthew Hayden
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Claude Férec
- EFS, Univ Brest, INSERM, UMR 1078, GGB, Brest, France.,CHRU Brest, Service de Génétique Médicale et de Biologie de la Reproduction, Brest, France
| | - Zhuan Liao
- Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai, China.,Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Jian-Min Chen
- EFS, Univ Brest, INSERM, UMR 1078, GGB, Brest, France
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3
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Campuzano O, Sanchez-Molero O, Fernandez A, Mademont-Soler I, Coll M, Perez-Serra A, Mates J, Del Olmo B, Pico F, Nogue-Navarro L, Sarquella-Brugada G, Iglesias A, Cesar S, Carro E, Borondo JC, Brugada J, Castellà J, Medallo J, Brugada R. Sudden Arrhythmic Death During Exercise: A Post-Mortem Genetic Analysis. Sports Med 2018; 47:2101-2115. [PMID: 28255936 DOI: 10.1007/s40279-017-0705-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND Sudden cardiac death is a natural and unexpected death that occurs within 1 h of the first symptom. Most sudden cardiac deaths occur during exercise, mostly as a result of myocardial infarction. After autopsy, some cases, especially in the young, are diagnosed as cardiomyopathies or remain without a conclusive cause of death. In both situations, genetic alterations may explain the arrhythmia. OBJECTIVE Our aim was to identify a genetic predisposition to sudden cardiac death in a cohort of post-mortem cases of individuals who died during exercise, with a structurally normal heart, and were classified as arrhythmogenic death. METHODS We analyzed a cohort of 52 post-mortem samples from individuals <50 years old who had a negative autopsy. Next-generation sequencing technology was used to screen genes associated with sudden cardiac death. RESULTS Our cohort showed a male prevalence (12:1). Half of the deaths occurred in individuals 41-50 years of age. Running was the most common exercise activity during the fatal event, accounting for 46.15% of cases. Genetic analysis identified 83 rare variants in 37 samples (71.15% of all samples). Of all rare variants, 36.14% were classified as deleterious, being present in 53.84% of all cases. CONCLUSIONS A comprehensive analysis of sudden cardiac death-related genes in individuals who died suddenly while exercising enabled the identification of potentially causative variants. However, many genetic variants remain of indeterminate significance, thus further work is needed before clinical translation. Nonetheless, comprehensive genetic analysis of individuals who died during exercise enables the detection of potentially causative variants and helps to identify at-risk relatives.
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Affiliation(s)
- Oscar Campuzano
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica Girona (IDIBGI), University of Girona, C/Dr Castany s/n, Parc Hospitalari Martí i Julià (M-2), Salt, 17190, Girona, Spain.,Medical Science Department, School of Medicine, University of Girona, Girona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Olallo Sanchez-Molero
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica Girona (IDIBGI), University of Girona, C/Dr Castany s/n, Parc Hospitalari Martí i Julià (M-2), Salt, 17190, Girona, Spain
| | - Anna Fernandez
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica Girona (IDIBGI), University of Girona, C/Dr Castany s/n, Parc Hospitalari Martí i Julià (M-2), Salt, 17190, Girona, Spain
| | - Irene Mademont-Soler
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica Girona (IDIBGI), University of Girona, C/Dr Castany s/n, Parc Hospitalari Martí i Julià (M-2), Salt, 17190, Girona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Monica Coll
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica Girona (IDIBGI), University of Girona, C/Dr Castany s/n, Parc Hospitalari Martí i Julià (M-2), Salt, 17190, Girona, Spain
| | - Alexandra Perez-Serra
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica Girona (IDIBGI), University of Girona, C/Dr Castany s/n, Parc Hospitalari Martí i Julià (M-2), Salt, 17190, Girona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Jesus Mates
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica Girona (IDIBGI), University of Girona, C/Dr Castany s/n, Parc Hospitalari Martí i Julià (M-2), Salt, 17190, Girona, Spain
| | - Bernat Del Olmo
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica Girona (IDIBGI), University of Girona, C/Dr Castany s/n, Parc Hospitalari Martí i Julià (M-2), Salt, 17190, Girona, Spain
| | - Ferran Pico
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica Girona (IDIBGI), University of Girona, C/Dr Castany s/n, Parc Hospitalari Martí i Julià (M-2), Salt, 17190, Girona, Spain
| | - Laia Nogue-Navarro
- Medical Science Department, School of Medicine, University of Girona, Girona, Spain
| | | | - Anna Iglesias
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica Girona (IDIBGI), University of Girona, C/Dr Castany s/n, Parc Hospitalari Martí i Julià (M-2), Salt, 17190, Girona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Sergi Cesar
- Arrhythmias Unit, Hospital Sant Joan de Déu, University of Barcelona, Barcelona, Spain
| | - Esther Carro
- Arrhythmias Unit, Hospital Sant Joan de Déu, University of Barcelona, Barcelona, Spain
| | - Juan Carlos Borondo
- Histopathology Unit, Instituto Nacional Toxicología y Ciencias Forenses (INTCF), Barcelona, Spain
| | - Josep Brugada
- Arrhythmias Unit, Hospital Sant Joan de Déu, University of Barcelona, Barcelona, Spain
| | - Josep Castellà
- Forensic Pathology Service, Institut de Medicina Legal i Ciències Forenses de Catalunya (IMLCFC), Barcelona, Spain
| | - Jordi Medallo
- Forensic Pathology Service, Institut de Medicina Legal i Ciències Forenses de Catalunya (IMLCFC), Barcelona, Spain
| | - Ramon Brugada
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica Girona (IDIBGI), University of Girona, C/Dr Castany s/n, Parc Hospitalari Martí i Julià (M-2), Salt, 17190, Girona, Spain. .,Medical Science Department, School of Medicine, University of Girona, Girona, Spain. .,Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain. .,Cardiology Service, Hospital Josep Trueta, Girona, Spain.
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Ghouse J, Have CT, Weeke P, Bille Nielsen J, Ahlberg G, Balslev-Harder M, Appel EV, Skaaby T, Olesen SP, Grarup N, Linneberg A, Pedersen O, Haunsø S, Hastrup Svendsen J, Hansen T, Kanters JK, Salling Olesen M. Rare genetic variants previously associated with congenital forms of long QT syndrome have little or no effect on the QT interval. Eur Heart J 2015; 36:2523-9. [PMID: 26159999 DOI: 10.1093/eurheartj/ehv297] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [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: 01/16/2015] [Accepted: 06/04/2015] [Indexed: 11/15/2022] Open
Abstract
AIMS We studied whether variants previously associated with congenital long QT syndrome (cLQTS) have an effect on the QTc interval in a Danish population sample. Furthermore, we assessed whether carriers of variants in cLQTS-associated genes are more prone to experience syncope compared with non-carriers and whether carriers have an increased mortality compared with non-carriers. METHODS AND RESULTS All genetic variants previously associated with cLQTS were surveyed using the Human Gene Mutation Database. We screened a Danish population-based sample with available whole-exome sequencing data (n = 870) and genotype array data (n = 6161) for putative cLQTS genetic variants. In total, 33 of 1358 variants previously reported to associate with cLQTS were identified. Of these, 10 variants were found in 8 or more individuals. Electrocardiogram results showed normal mean QTc intervals in carriers compared with non-carriers. Syncope data analysis between variant and non-variant carriers showed that 4 of 227 (1.8%) and 95 of 5861 (1.6%) individuals, respectively, had experienced syncope during follow-up (P = 0.80). There was no significant difference in overall mortality rates between carriers [7/217 (3.2%)] and non-carriers [301/6453 (4.7%)] (P = 0.24). CONCLUSION We present QTc data and register data, indicating that 26 cLQTS-associated variants neither had any effect on the QTc intervals nor on syncope propensity or overall mortality. Based on the frequency of individual gene variants, we suggest that the 10 variants frequently identified, assumed to relate to cLQTS, are less likely to associate with a dominant monogenic form of the disease.
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Affiliation(s)
- Jonas Ghouse
- The Danish National Research Foundation Centre for Cardiac Arrhythmia, Copenhagen, Denmark Laboratory of Molecular Cardiology, Department of Cardiology, The Heart Centre, University Hospital of Copenhagen, Rigshospitalet, 9312, Juliane Mariesvej 20, Copenhagen OE 2100, Denmark
| | - Christian Theil Have
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Peter Weeke
- The Danish National Research Foundation Centre for Cardiac Arrhythmia, Copenhagen, Denmark Laboratory of Molecular Cardiology, Department of Cardiology, The Heart Centre, University Hospital of Copenhagen, Rigshospitalet, 9312, Juliane Mariesvej 20, Copenhagen OE 2100, Denmark
| | - Jonas Bille Nielsen
- The Danish National Research Foundation Centre for Cardiac Arrhythmia, Copenhagen, Denmark Laboratory of Molecular Cardiology, Department of Cardiology, The Heart Centre, University Hospital of Copenhagen, Rigshospitalet, 9312, Juliane Mariesvej 20, Copenhagen OE 2100, Denmark
| | - Gustav Ahlberg
- The Danish National Research Foundation Centre for Cardiac Arrhythmia, Copenhagen, Denmark Laboratory of Molecular Cardiology, Department of Cardiology, The Heart Centre, University Hospital of Copenhagen, Rigshospitalet, 9312, Juliane Mariesvej 20, Copenhagen OE 2100, Denmark
| | - Marie Balslev-Harder
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Emil Vincent Appel
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tea Skaaby
- Research Centre for Prevention and Health, The Capital Region, Copenhagen, Denmark
| | - Søren-Peter Olesen
- The Danish National Research Foundation Centre for Cardiac Arrhythmia, Copenhagen, Denmark
| | - Niels Grarup
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Allan Linneberg
- Research Centre for Prevention and Health, The Capital Region, Copenhagen, Denmark Department of Clinical Experimental Research, Glostrup University Hospital, Denmark Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Oluf Pedersen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Stig Haunsø
- The Danish National Research Foundation Centre for Cardiac Arrhythmia, Copenhagen, Denmark Laboratory of Molecular Cardiology, Department of Cardiology, The Heart Centre, University Hospital of Copenhagen, Rigshospitalet, 9312, Juliane Mariesvej 20, Copenhagen OE 2100, Denmark Department of Medicine and Surgery, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jesper Hastrup Svendsen
- The Danish National Research Foundation Centre for Cardiac Arrhythmia, Copenhagen, Denmark Laboratory of Molecular Cardiology, Department of Cardiology, The Heart Centre, University Hospital of Copenhagen, Rigshospitalet, 9312, Juliane Mariesvej 20, Copenhagen OE 2100, Denmark Department of Medicine and Surgery, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jørgen Kim Kanters
- Laboratory of Experimental Cardiology, Department of Biomedicine, University of Copenhagen, Copenhagen, Denmark Department of Cardiology, Herlev and Gentofte University Hospitals, Copenhagen, Denmark
| | - Morten Salling Olesen
- The Danish National Research Foundation Centre for Cardiac Arrhythmia, Copenhagen, Denmark Laboratory of Molecular Cardiology, Department of Cardiology, The Heart Centre, University Hospital of Copenhagen, Rigshospitalet, 9312, Juliane Mariesvej 20, Copenhagen OE 2100, Denmark
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5
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Ji X, Xing Y, Xu Y, Liu Y, Chen Y, Tao J, Xiao B. A novel mutation in MID1 in a patient with X-linked Opitz G/BBB syndrome. Gene 2014; 537:140-2. [PMID: 24374473 DOI: 10.1016/j.gene.2013.12.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [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: 08/29/2013] [Revised: 12/09/2013] [Accepted: 12/10/2013] [Indexed: 11/22/2022]
Abstract
Opitz G/BBB syndrome (OS) is a genetically heterogeneous disease. We report on an OS patient with a novel inherited mutation in MID1. Metaphase analysis showed a normal male karyotype. Array CGH revealed a maternally inherited duplication at Xp22.31 (6,467,203-7,992,261, hg18), the size was estimated to 1.5Mb. Sequence analysis of the MID1 coding region revealed a novel missense mutation in exon 8 (c.1561C>T/p. R521C) which resulted in an ammonia acid substitution (R521C) in the PRX domain of the MID1 protein. The mutation was inherited from unaffected grandmother and mildly affected mother. Prenatal diagnosis was performed for the third pregnancy after identification of the causative mutation in the family. The third fetus was found to be a female carrier. Postnatal follow-up at 2-month-old showed normal phenotype. In conclusion, we reported a familial OS patient with a novel mutation in exon 8 which provided another evidence for that mutation clustered in C-terminal domain of MID1. The newly identified mutation in our patient expands mutation spectrum in MID1 gene.
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Affiliation(s)
- Xing Ji
- Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, China; Shanghai Institute for Pediatric Research, China
| | - Ya Xing
- Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, China; Shanghai Institute for Pediatric Research, China
| | - Yan Xu
- Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, China; Shanghai Institute for Pediatric Research, China
| | - Yu Liu
- Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, China; Shanghai Institute for Pediatric Research, China
| | - Yingwei Chen
- Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, China; Shanghai Institute for Pediatric Research, China
| | - Jiong Tao
- Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, China; Shanghai Institute for Pediatric Research, China
| | - Bing Xiao
- Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, China; Shanghai Institute for Pediatric Research, China.
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6
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Zhang Z, He JW, Fu WZ, Zhang CQ, Zhang ZL. Two novel mutations in the SLCO2A1 gene in a Chinese patient with primary hypertrophic osteoarthropathy. Gene 2014; 534:421-3. [PMID: 24185079 DOI: 10.1016/j.gene.2013.10.051] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 09/19/2013] [Accepted: 10/24/2013] [Indexed: 11/23/2022]
Abstract
Primary hypertrophic osteoarthropathy (PHO) is a rare monogenetic disease characterized by digital clubbing, periostosis and pachydermia. Mutations in the 15-hydroxy-prostaglandin dehydrogenase (HPGD) gene and solute carrier organic anion transporter family member 2A1 (SLCO2A1) gene have been shown to be associated with PHO. Here, we described clinical characteristics in a Chinese patient with PHO, and identified two novel mutations in SLCO2A1: a heterozygous guanine-to-thymidine transition at the invariant -1 position of the acceptor site of intron 2 (c.235-1G>T) and a heterozygous missense mutation p.Pro219Leu (c.656C>T) in exon 5.
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7
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Yates CM, Sternberg MJE. The effects of non-synonymous single nucleotide polymorphisms (nsSNPs) on protein-protein interactions. J Mol Biol 2013; 425:3949-63. [PMID: 23867278 DOI: 10.1016/j.jmb.2013.07.012] [Citation(s) in RCA: 123] [Impact Index Per Article: 11.2] [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: 04/28/2013] [Revised: 07/02/2013] [Accepted: 07/09/2013] [Indexed: 12/23/2022]
Abstract
Non-synonymous single nucleotide polymorphisms (nsSNPs) are single base changes leading to a change to the amino acid sequence of the encoded protein. Many of these variants are associated with disease, so nsSNPs have been well studied, with studies looking at the effects of nsSNPs on individual proteins, for example, on stability and enzyme active sites. In recent years, the impact of nsSNPs upon protein-protein interactions has also been investigated, giving a greater insight into the mechanisms by which nsSNPs can lead to disease. In this review, we summarize these studies, looking at the various mechanisms by which nsSNPs can affect protein-protein interactions. We focus on structural changes that can impair interaction, changes to disorder, gain of interaction, and post-translational modifications before looking at some examples of nsSNPs at human-pathogen protein-protein interfaces and the analysis of nsSNPs from a network perspective.
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Affiliation(s)
- Christopher M Yates
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Sir Ernst Chain Building, Imperial College London, South Kensington, SW7 2AZ, UK.
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8
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Nagara M, Tiar A, Ben Halim N, Ben Rhouma F, Messaoud O, Bouyacoub Y, Kefi R, Hassayoun S, Zouari N, Ben Ammar MS, Abdelhak S, Chemli J. Mutation spectrum of primary hyperoxaluria type 1 in Tunisia: implication for diagnosis in North Africa. Gene 2013; 527:316-20. [PMID: 23810941 DOI: 10.1016/j.gene.2013.06.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Revised: 05/30/2013] [Accepted: 06/08/2013] [Indexed: 11/20/2022]
Abstract
BACKGROUND Primary hyperoxaluria type 1 (PH1) is an autosomal recessive inherited metabolic disease, characterized by progressive kidney failure due to renal deposition of calcium oxalate. Mutations in the AGXT gene, encoding the liver-specific enzyme alanine glyoxylate aminotransferase, are responsible for the disease. We aimed to determine the mutational spectrum causing PH1 and to provide an accurate tool for diagnosis as well as for prenatal diagnosis in the affected families. METHODS Direct sequencing was used to detect mutations in the AGXT gene in DNA samples from 13 patients belonging to 12 Tunisian families. RESULTS Molecular analysis revealed five mutations causing PH1 in Tunisia. The mutations were identified along exons 1, 2, 4, 5 and 7. The most predominant mutations were the Maghrebian "p.I244T" and the Arabic "p.G190R". Furthermore, three other mutations characteristic of different ethnic groups were found in our study population. These results confirm the mutational heterogeneity related to PH1 in Tunisian population. All the mutations are in a homozygous state, reflecting the high impact of endogamy in our population. CONCLUSION Mutation analysis through DNA sequencing can provide a useful first line investigation for PH1. This identification could provide an accurate tool for prenatal diagnosis, genetic counseling and screen for potential presymptomatic individuals.
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