ClinVar Miner

Submissions for variant NM_004320.6(ATP2A1):c.118G>A (p.Glu40Lys)

gnomAD frequency: 0.00001  dbSNP: rs762501478
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Total submissions: 1
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV002025720 SCV002297189 uncertain significance Brody myopathy 2022-09-07 criteria provided, single submitter clinical testing 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: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). ClinVar contains an entry for this variant (Variation ID: 1503806). This variant has not been reported in the literature in individuals affected with ATP2A1-related conditions. This variant is present in population databases (rs762501478, gnomAD 0.002%). This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 40 of the ATP2A1 protein (p.Glu40Lys). This variant also falls at the last nucleotide of exon 1, which is part of the consensus splice site for this exon. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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