ClinVar Miner

Submissions for variant NM_000053.4(ATP7B):c.3053C>T (p.Ala1018Val) (rs371840514)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000169019 SCV000220164 likely pathogenic Wilson disease 2014-03-17 criteria provided, single submitter literature only
Invitae RCV000169019 SCV000948175 pathogenic Wilson disease 2020-09-25 criteria provided, single submitter clinical testing This sequence change replaces alanine with valine at codon 1018 of the ATP7B protein (p.Ala1018Val). The alanine residue is highly conserved and there is a small physicochemical difference between alanine and valine. This variant is present in population databases (rs371840514, ExAC 0.01%). This variant has been observed in individual(s) with Wilson disease (PMID: 17154398, 30884209, 31059521, Invitae). In at least one individual the data is consistent with the variant being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 188722). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: Tolerated; PolyPhen-2: Probably Damaging; Align-GVGD: Class C0). For these reasons, this variant has been classified as Pathogenic.
GeneDx RCV001558241 SCV001780147 likely pathogenic not provided 2021-01-04 criteria provided, single submitter clinical testing Reported in multiple individuals with Wilson disease with no information provided regarding the presence of a second ATP7B variant (Loudianos et al., 1998; Loudianos et al., 1999; Vrabelova et al., 2005; Lepori et al., 2007; Zappu et al., 2008; Mak et al., 2008; Chen et al., 2019); Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 30275481, 31246682, 30655162, 17949296, 22692182, 17154398, 18034201, 23486543, 18728530, 15967699, 10502776, 9671269, 30556376, 30884209)

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