ClinVar Miner

Submissions for variant NM_000053.4(ATP7B):c.2512A>G (p.Lys838Glu)

gnomAD frequency: 0.00001  dbSNP: rs748113748
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Total submissions: 1
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001067105 SCV001232141 pathogenic Wilson disease 2024-01-05 criteria provided, single submitter clinical testing This sequence change replaces lysine, which is basic and polar, with glutamic acid, which is acidic and polar, at codon 838 of the ATP7B protein (p.Lys838Glu). This variant is present in population databases (rs748113748, gnomAD 0.02%). This missense change has been observed in individual(s) with clinical features of Wilson disease (PMID: 34400371; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 860738). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on ATP7B protein function. For these reasons, this variant has been classified as Pathogenic.

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