ClinVar Miner

Submissions for variant NM_004320.5(ATP2A1):c.1740_1741CT[1] (p.Ser581fs) (rs1421005631)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Athena Diagnostics Inc RCV000517623 SCV000612455 pathogenic not provided 2017-01-20 criteria provided, single submitter clinical testing
Invitae RCV000550407 SCV000638277 pathogenic Brody myopathy 2017-06-07 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Ser581Cysfs*7) in the ATP2A1 gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has been reported in an individual affected with Brody disease (PMID: 26248958). Loss-of-function variants in ATP2A1 are known to be pathogenic (PMID: 26248958). For these reasons, this variant has been classified as Pathogenic.
GeneDx RCV000517623 SCV001169112 pathogenic not provided 2019-03-19 criteria provided, single submitter clinical testing The c.1742_1743delCT variant in the ATP2A1 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The c.1742_1743delCT variant causes a frameshift starting with codon Serine 581, changes this amino acid to a Cysteine residue, and creates a premature Stop codon at position 7 of the new reading frame, denoted p.Ser581CysfsX7. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.1742_1743delCT variant is not observed in large population cohorts (Lek et al., 2016). We interpret c.1742_1743delCT as a pathogenic variant.

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