Synonymous mutation in adenosine triphosphatase copper-transporting beta causes enhanced exon skipping in Wilson disease.
Journal
Hepatology communications
ISSN: 2471-254X
Titre abrégé: Hepatol Commun
Pays: United States
ID NLM: 101695860
Informations de publication
Date de publication:
07 2022
07 2022
Historique:
revised:
25
11
2021
received:
10
09
2021
accepted:
22
12
2021
pubmed:
11
3
2022
medline:
29
6
2022
entrez:
10
3
2022
Statut:
ppublish
Résumé
Wilson disease (WD) is caused by biallelic pathogenic variants in adenosine triphosphatase copper-transporting beta (ATP7B); however, genetic testing identifies only one or no pathogenic ATP7B variant in a number of patients with WD. Synonymous single-nucleotide sequence variants have been recognized as pathogenic in individual families. The aim of the present study was to evaluate the prevalence and disease mechanism of the synonymous variant c.2292C>T (p.Phe764=) in WD. A cohort of 280 patients with WD heterozygous for a single ATP7B variant was investigated for the presence of c.2292C>T (p.Phe764=). In this cohort of otherwise genetically unexplained WD, the allele frequency of c.2292C>T (p.Phe764=) was 2.5% (14 of 560) compared to 7.1 × 10
Identifiants
pubmed: 35271763
doi: 10.1002/hep4.1922
pmc: PMC9234614
pii: 02009842-202207000-00011
doi:
Substances chimiques
Copper
789U1901C5
Copper-Transporting ATPases
EC 7.2.2.8
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1611-1619Informations de copyright
© 2022 The Authors. Hepatology Communications published by Wiley Periodicals LLC on behalf of American Association for the Study of Liver Diseases.
Références
Członkowska A, Litwin T, Dusek P, Ferenci P, Lutsenko S, Medici V, et al. Wilson disease. Nat Rev Dis Primers. 2018;4:21.
European Association for Study of Liver . EASL Clinical Practice Guidelines: Wilson's disease. J Hepatol. 2012;56:671–85.
Roberts EA, Schilsky ML; American Association for Study of Liver Diseases . Diagnosis and treatment of Wilson disease: an update. Hepatology. 2008;47:2089–111.
Ferenci P, Stremmel W, Członkowska A, Szalay F, Viveiros A, Stättermayer AF, et al. Age and sex but not ATP7B genotype effectively influence the clinical phenotype of Wilson disease. Hepatology. 2019;69:1464–76.
Vrabelova S, Letocha O, Borsky M, Kozak L. Mutation analysis of the ATP7B gene and genotype/phenotype correlation in 227 patients with Wilson disease. Mol Genet Metab. 2005;86:277–85.
Loudianos G, Dessi V, Lovicu M, Angius A, Figus A, Lilliu F, et al. Molecular characterization of wilson disease in the Sardinian population‐evidence of a founder effect. Hum Mutat. 1999;14:294–303.
Cullen LM, Prat L, Cox DW. Genetic variation in the promoter and 5' UTR of the copper transporter, ATP7B, in patients with Wilson disease. Clin Genet. 2003;64:429–32.
Wan L, Tsai C‐H, Hsu C‐M, Huang C‐C, Yang C‐C, Liao C‐C, et al. Mutation analysis and characterization of alternative splice variants of the Wilson disease gene ATP7B. Hepatology. 2010;52:1662–70.
Richards S, Aziz N, Bale S, Bick D, Das S, Gastier‐Foster J, et al. ACMG Laboratory Quality Assurance Committee . Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015;17:405–24.
Kopanos C, Tsiolkas V, Kouris A, Chapple CE, Albarca Aguilera M, Meyer R, et al. VarSome: the human genomic variant search engine. Bioinformatics. 2019;35:1978–80.
Todorov T, Savov A, Jelev H, Panteleeva E, Konstantinova D, Krustev Z, et al. Spectrum of mutations in the Wilson disease gene (ATP7B) in the Bulgarian population. Clin Genet. 2005;68:474–6.
Landrum MJ, Lee JM, Benson M, Brown GR, Chao C, Chitipiralla S, et al. ClinVar: improving access to variant interpretations and supporting evidence. Nucleic Acids Res. 2018;46:D1062–7.
Wang C, Zhou W, Huang Y, Yin H, Jin YU, Jia Z, et al. Presumed missense and synonymous mutations in ATP7B gene cause exon skipping in Wilson disease. Liver Int. 2018;38:1504–13.
Zhou X, Zhou W, Wang C, Wang L, Jin YU, Jia Z, et al. A comprehensive analysis and splicing characterization of naturally occurring synonymous variants in the ATP7B gene. Front Genet. 2021;11:592611.
Hunt RC, Simhadri VL, Iandoli M, Sauna ZE, Kimchi‐Sarfaty C. Exposing synonymous mutations. Trends Genet. 2014;30:308–21.
Velde KJ, Kuiper J, Thompson BA, Plazzer J‐P, Valkenhoef G, Haan M, et al. InSiGHT Group . Evaluation of CADD scores in curated mismatch repair gene variants yields a model for clinical validation and prioritization. Hum Mutat. 2015;36:712–9.
Klee KMC, Janecke AR, Civan HA, Rosipal Š, Heinz‐Erian P, Huber LA, et al. AP1S1 missense mutations cause a congenital enteropathy via an epithelial barrier defect. Hum Genet. 2020;139:1247–59.
Hombach D, Schuelke M, Knierim E, Ehmke N, Schwarz JM, Fischer‐Zirnsak B, et al. MutationDistiller: user‐driven identification of pathogenic DNA variants. Nucleic Acids Res. 2019;47:W114–20.
Kamphans T, Krawitz PM. GeneTalk: an expert exchange platform for assessing rare sequence variants in personal genomes. Bioinformatics. 2012;28:2515–6.
Kircher M, Witten DM, Jain P, O'Roak BJ, Cooper GM, Shendure J. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet. 2014;46:310–5.
van Rijn JM, Ardy RC, Kuloglu Z, Harter B, van Haaften‐Visser DY, van der Doef HPJ, et al. Intestinal failure and aberrant lipid metabolism in patients with DGAT1 deficiency. Gastroenterology. 2018;155:130–43 e115.
Karczewski KJ, Francioli LC, Tiao G, Cummings BB, Alföldi J, Wang Q, et al. Genome Aggregation Database Consortium . The mutational constraint spectrum quantified from variation in 141,456 humans. Nature. 2020;581:434–43. Erratum in: Nature 2021;590:E53.
Desmet FO, Hamroun D, Lalande M, Collod‐Beroud G, Claustres M, Beroud C. Human Splicing Finder: an online bioinformatics tool to predict splicing signals. Nucleic Acids Res. 2009;37:e67.
Collins CJ, Yi F, Dayuha R, Duong P, Horslen S, Camarata M, et al. Direct measurement of ATP7B peptides is highly effective in the diagnosis of Wilson disease. Gastroenterology. 2021;160:2367–82:e1.
Ferenci P, Caca K, Loudianos G, Mieli‐Vergani G, Tanner S, Sternlieb I, et al. Diagnosis and phenotypic classification of Wilson disease. Liver Int. 2003;23:139–42.
Coffey AJ, Durkie M, Hague S, McLay K, Emmerson J, Lo C, et al. A genetic study of Wilson's disease in the United Kingdom. Brain. 2013;136:1476–87.
Bost M, Piguet‐Lacroix G, Parant F, Wilson CM. Molecular analysis of Wilson patients: direct sequencing and MLPA analysis in the ATP7B gene and Atox1 and COMMD1 gene analysis. J Trace Elem Med Biol. 2012;26:97–101.
Woimant F, Poujois A, Bloch A, Jordi T, Laplanche JL, Morel H, et al. A novel deep intronic variant in ATP7B in five unrelated families affected by Wilson disease. Mol Genet Genomic Med. 2020;8:e1428.
Sanchez‐Monteagudo A, Alvarez‐Sauco M, Sastre I, Martinez‐Torres I, Lupo V, Berenguer M, et al. Genetics of Wilson disease and Wilson‐like phenotype in a clinical series from eastern Spain. Clin Genet. 2020;97:758–63.
Sauna ZE, Kimchi‐Sarfaty C. Understanding the contribution of synonymous mutations to human disease. Nat Rev Genet. 2011;12:683–91.
Sun H, Yu G. New insights into the pathogenicity of non‐synonymous variants through multi‐level analysis. Sci Rep. 2019;9:1667.
Fanni D, Pilloni L, Orru S, Coni P, Liguori C, Serra S, et al. Expression of ATP7B in normal human liver. Eur J Histochem. 2005;49:371–8.
Girard M, Poujois A, Fabre M, Lacaille F, Debray D, Rio M, et al. CCDC115‐CDG: a new rare and misleading inherited cause of liver disease. Mol Genet Metab. 2018;124:228–35.
Jansen J, Cirak S, van Scherpenzeel M, Timal S, Reunert J, Rust S, et al. CCDC115 deficiency causes a disorder of golgi homeostasis with abnormal protein glycosylation. Am J Hum Genet. 2016;98:310–21.
Espinos C, Ferenci P. Are the new genetic tools for diagnosis of Wilson disease helpful in clinical practice? JHEP Rep. 2020;2:100114.
Marchi G, Busti F, Lira Zidanes A, Castagna A, Girelli D. Aceruloplasminemia: a severe neurodegenerative disorder deserving an early diagnosis. Front Neurosci. 2019;13:325.
Yang Y, Muzny DM, Reid JG, Bainbridge MN, Willis A, Ward PA, et al. Clinical whole‐exome sequencing for the diagnosis of mendelian disorders. N Engl J Med. 2013;369:1502–11.
Liu WL, Li F, Liu L, Chen W, He ZX, Gu H, et al. A novel gross deletion and breakpoint junction sequence analysis of ATP7B in a Chinese family with Wilson disease using next‐generation sequencing and Sanger sequencing. Mol Med Rep. 2020;21:517–23.
Todorov T, Balakrishnan P, Savov A, Socha P, Schmidt HH. Intragenic deletions in ATP7B as an unusual molecular genetics mechanism of Wilson's disease pathogenesis. PLoS One. 2016;11:e0168372.