Research Article: Genetic analysis of ATP7B in 102 south Indian families with Wilson disease

Date Published: May 6, 2019

Publisher: Public Library of Science

Author(s): Nivedita Singh, Pradeep Kallollimath, Mohd Hussain Shah, Saketh Kapoor, Vishwanath Kumble Bhat, Lakshminarayanapuram Gopal Viswanathan, Madhu Nagappa, Parayil S. Bindu, Arun B. Taly, Sanjib Sinha, Arun Kumar, Andreas R. Janecke.

http://doi.org/10.1371/journal.pone.0215779

Abstract

Wilson disease (WD) is an autosomal recessive disorder, characterized by excessive deposition of copper in various parts of the body, mainly in the liver and brain. It is caused by mutations in ATP7B. We report here the genetic analysis of 102 WD families from a south Indian population. Thirty-six different ATP7B mutations, including 13 novel ones [p.Ala58fs*19, p.Lys74fs*9, p.Gln281*, p.Pro350fs*12, p.Ser481*, p.Leu735Arg, p.Val752Gly, p.Asn812fs*2, p.Val845Ala, p.His889Pro, p.Ile1184fs*1, p.Val1307Glu and p.Ala1339Pro], were identified in 76/102 families. Interestingly, the mutation analysis of affected individuals in two families identified two different homozygous mutations in each family, and thus each affected individual from these families harbored two mutations in each ATP7B allele. Of 36 mutations, 28 were missense, thus making them the most prevalent mutations identified in the present study. Nonsense, insertion and deletion represented 3/36, 2/36 and 3/36 mutations, respectively. The haplotype analysis suggested founder effects for all the 14 recurrent mutations. Our study thus expands the mutational landscape of ATP7B with a total number of 758 mutations. The mutations identified during the present study will facilitate carrier and pre-symptomatic detection, and prenatal genetic diagnosis in affected families.

Partial Text

Wilson disease (WD, MIM #277900) is an autosomal recessive disorder, characterized by the excessive deposition of copper in the body, mainly in the liver and brain. The worldwide disease incidence of WD is 1/5,000–1/30,000 live births. The disease presentation varies from as early as 2 years to as old as 72 years of age [1–3]. WD patients commonly manifest with hepatic and neuropsychiatric problems. The hepatic manifestations are acute hepatitis, chronic active hepatitis, cirrhosis and acute fulminant hepatic failure. Patients with neuropsychiatric manifestations have dysarthria, dystonia, tremor, ataxia, parkinsonian features, behavioral problems and cognitive disturbances. ATP7B (MIM #606882; ATPase copper transporting beta), the causative gene of WD, is located on the chromosome 13q14.3-q21 [4–6]. It has 21 coding exons and codes for a 1,465 amino acid long protein of 165 kDa, which contains following domains: six copper binding domains (CBD1-6), eight transmembrane domains (TMS1-8), A-domain and ATP binding domain. It shows granular cytoplasmic expression in most tissues (https://www.proteinatlas.org/ENSG00000123191-ATP7B/tissue), and resides mainly in the trans-Golgi network (TGN). Under normal physiological conditions, ATP7B delivers copper to apoceruloplasmin. As the copper level increases inside the cells, ATP7B traffics to the vesicular compartments and lysosomes to remove excess of copper into the bile [7].

Sanger Sequencing of the entire coding region of ATP7B in 102 WD families identified a total of 36 different mutations in 76/102 (74.51%) families, with a frequency ranging from 0.4% to 8.4% (Table 1). These mutations were missense, nonsense, insertions and deletions (Table 1). Of these, 13 were novel mutations [p.Ala58fs*19, p.Lys74fs*9, p.Gln281*, p.Pro350fs*12, p.Ser481*, p.Leu735Arg, p.Val752Gly, p.Asn812fs*2, p.Val845Ala, p.His889Pro, p.Ile1184fs*1, p.Val1307Glu and p.Ala1339Pro] (Table 1; Figs 1–7). Further, 28/36 (77.8%) mutations were missense, thus making them the most prevalent mutations identified in the present study. Based on this analysis, a mutational landscape was constructed, which depicts the spread of mutations across different exons (Fig 8A) and domains (Fig 8B) of ATP7B. Of 76 families with mutations, 20 families had a single mutation in a heterozygous condition, and thus the second mutation was not identified (Table 1). We used the following criteria to name a novel variant as a mutation. 1) The novel variant was segregating in the family. 2) The novel variant was not observed in 50 normal controls. 3) The novel variant was absent in the 1000 Genomes and ExAC databases. 4) The affected amino acid residue was conserved across species (Fig 9). 5) At least two of the following three mutation prediction programs, PolyPhen-2, Mutation Taster and SIFT, predicted a novel missense variant to be disease causing (Table F in S1 File). Interestingly, the mutation analysis of affected individuals in family-90 (Fig 1) and family-72 (Fig 10) identified two different homozygous mutations in each family, and thus each affected individual from these families harbored 2 mutations in each ATP7B allele.

 

Source:

http://doi.org/10.1371/journal.pone.0215779

 

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