ClinVar Miner

Submissions for variant NM_004320.5(ATP2A1):c.2464del (p.Arg822fs) (rs751365374)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000529448 SCV000638290 pathogenic Brody myopathy 2017-03-26 criteria provided, single submitter clinical testing This sequence change deletes 1 nucleotide from exon 17 of the ATP2A1 mRNA (c.2464delC), causing a frameshift at codon 822. This creates a premature translational stop signal (p.Arg822Glyfs*49) and is expected to result in an absent or disrupted protein product. While this particular variant has not been reported in the literature, loss-of-function variants in ATP2A1 are known to be pathogenic (PMID: 8841193). For these reasons, this variant has been classified as Pathogenic.
GeneDx RCV000598570 SCV000710210 likely pathogenic not provided 2017-12-14 criteria provided, single submitter clinical testing The c.2464delC variant in the ATP2A1 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The c.2464delC variant causes a frameshift starting with codon Arginine 822, changes this amino acid to a Glycine residue, and creates a premature Stop codon at position 49 of the new reading frame, denoted p.Arg822GlyfsX49. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.2464delC variant is not observed at a significant frequency in large population cohorts (Lek et al., 2016). We interpret c.2464delC as a likely pathogenic variant.

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