Exon duplications in the ATP7A gene: Frequency and Transcriptional Behaviour

Abstract

BackgroundMenkes disease (MD) is an X-linked, fatal neurodegenerative disorder of copper metabolism, caused by mutations in the ATP7A gene. Thirty-three Menkes patients in whom no mutation had been detected with standard diagnostic tools were screened for exon duplications in the ATP7A gene.MethodsThe ATP7A gene was screened for exon duplications using multiplex ligation-dependent probe amplification (MLPA). The expression level of ATP7A was investigated by real-time PCR and detailed analysis of the ATP7A mRNA was performed by RT-PCR followed by sequencing. In order to investigate whether the identified duplicated fragments originated from a single or from two different X-chromosomes, polymorphic markers located in the duplicated fragments were analyzed.ResultsPartial ATP7A gene duplication was identified in 20 unrelated patients including one patient with Occipital Horn Syndrome (OHS). Duplications in the ATP7A gene are estimated from our material to be the disease causing mutation in 4% of the Menkes disease patients. The duplicated regions consist of between 2 and 15 exons. In at least one of the cases, the duplication was due to an intra-chromosomal event. Characterization of the ATP7A mRNA transcripts in 11 patients revealed that the duplications were organized in tandem, in a head to tail direction. The reading frame was disrupted in all 11 cases. Small amounts of wild-type transcript were found in all patients as a result of exon-skipping events occurring in the duplicated regions. In the OHS patient with a duplication of exon 3 and 4, the duplicated out-of-frame transcript coexists with an almost equally represented wild-type transcript, presumably leading to the milder phenotype.ConclusionsIn general, patients with duplication of only 2 exons exhibit a milder phenotype as compared to patients with duplication of more than 2 exons. This study provides insight into exon duplications in the ATP7A gene.

New insights into genetic variant spectrum and genotype–phenotype correlations of Rubinstein‐Taybi syndrome in 39 CREBBP‐positive patients

“…Two patients from our cohort harbored the same pathogenic nonsense variant in exon 5 (#172 and #37), which was also previously described (Coupry et al, 2002;Roelfsema et al, 2005;Schorry et al, 2008). Twelve of the 25 point Ex1del HGMD (Breuning et al, 1993;Udaka et al, 2005) #76 Ex2del HGMD (Breuning et al, 1993;López et al, 2018;Mogensen et al, 2011;Negri et al, 2019) #196 Ex1-2del HGMD (Breuning et al, 1993) #256 Ex1-31del HGMD (Bentivegna et al, 2006;Mogensen et T A B L E 2 (Continued)…”

“…Roelfsema et al (2005) described exon 1 duplication, although it was not clear how this leaded to the inactivation of the allele. Partial gene duplication has been related to disease in several syndromes as Duchenne, Menkes, Optiz, Johansson-Blizzard or Mowat-Wilson syndromes (Baxter et al, 2017;Mogensen et al, 2011;Schwaibold et al, 2014;Sukalo et al, 2017), although with minor weight in the global variant spectrum. The specific role of the missense variant in exon 4 and duplication of CREBBP exons 14-19 as causative of the clinical manifestations in #118 needs to be further elucidated.…”

Tandem Duplication of Exons 1–7 Neither Impairs ATP7A Expression Nor Causes a Menkes Disease Phenotype

“…All prior reported ATP7A duplications (n ¼ 24) involved intragenic tandem duplications predicted to disrupt the normal translational reading frame and produce nonfunctional ATP7A proteins (Moizard et al 2011;Mogensen et al 2011;T€ umer 2013). In contrast, the exon 1-7 duplication occurred at the 5 0 end of ATP7A rather than within the gene.…”

“…On a molecular basis, the spectrum of ATP7A mutations causing the Menkes disease clinical and biochemical phenotype includes gene deletions and duplications, as well as missense and splice junction alterations (Moizard et al 2011;Mogensen et al 2011;T€ umer 2013). While ATP7A genotype is generally predictive of response to early copper replacement therapy (Kaler 1996;Kaler et al 2008), ambiguous situations involving novel molecular alterations in this gene may occur, as we recently reported (Schoonveld et al 2013).…”

Prenatal diagnostic conundrum involving a novel ATP7A duplication

“…ATP7A duplications are estimated to represent the molecular cause of Menkes disease in 4–10% of affected patients (4, 5). All prior reported examples ( n =24) involved intragenic ATP7A tandem duplications, predicted to disrupt the normal translational reading frame and produce nonfunctional ATP7A proteins.…”