ClinVar Miner

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

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000544224 SCV000638291 pathogenic Brody myopathy 2020-01-08 criteria provided, single submitter clinical testing This sequence change inserts 1 nucleotide in exon 17 of the ATP2A1 mRNA (c.2464dupC), causing a frameshift at codon 822. This creates a premature translational stop signal (p.Arg822Profs*39) 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 RCV000598958 SCV000710022 pathogenic not provided 2017-12-27 criteria provided, single submitter clinical testing The c.2464dupC pathogenic variant in the ATP2A1 gene causes a frameshift starting with codon Arginine 822, changes this amino acid to a Proline residue and creates a premature Stop codon at position 39 of the new reading frame, denoted p.Arg822ProfsX39. This pathogenic variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.2464dupC variant is not observed at a significant frequency in large population cohorts (Lek et al., 2016). Although this pathogenic variant has not been previously reported to our knowledge, its is classified as a pathogenic variant.
Athena Diagnostics Inc RCV000598958 SCV001143087 likely pathogenic not provided 2018-11-29 criteria provided, single submitter clinical testing The variant results in a shift of the reading frame, and is therefore predicted to result in the loss of a functional protein. The best available variant frequency is uninformative because it is below the disease allele frequency.

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