ClinVar Miner

Submissions for variant NM_004320.6(ATP2A1):c.521G>A (p.Arg174Gln)

gnomAD frequency: 0.00006  dbSNP: rs149506518
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000688052 SCV000815649 uncertain significance Brody myopathy 2021-08-30 criteria provided, single submitter clinical testing This sequence change replaces arginine with glutamine at codon 174 of the ATP2A1 protein (p.Arg174Gln). The arginine residue is moderately conserved and there is a small physicochemical difference between arginine and glutamine. This variant is present in population databases (rs149506518, ExAC 0.002%). This variant has not been reported in the literature in individuals affected with ATP2A1-related conditions. 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: "Possibly Damaging"; Align-GVGD: "Class C0"). 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.
GeneDx RCV001766470 SCV001999287 uncertain significance not provided 2019-11-18 criteria provided, single submitter clinical testing Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Has not been previously published as pathogenic or benign to our knowledge
Ambry Genetics RCV003258921 SCV003946250 uncertain significance Inborn genetic diseases 2023-05-05 criteria provided, single submitter clinical testing The c.521G>A (p.R174Q) alteration is located in exon 6 (coding exon 6) of the ATP2A1 gene. This alteration results from a G to A substitution at nucleotide position 521, causing the arginine (R) at amino acid position 174 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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