ClinVar Miner

Submissions for variant NM_004320.5(ATP2A1):c.2595del (p.Asn866fs) (rs398124554)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000082697 SCV000114741 pathogenic not provided 2014-04-02 criteria provided, single submitter clinical testing
GeneDx RCV000082697 SCV000567263 pathogenic not provided 2015-08-07 criteria provided, single submitter clinical testing The c.2595delC deletion in the ATP2A1 gene has not been reported previously as a pathogenic variant nor as a benign polymorphism, to our knowledge. The c.2595delC deletion causes a frameshiftstarting with codon Asparagine 866, changes this amino acid to a Threonine residue, and creates apremature Stop codon at position 5 of the new reading frame, denoted p.Asn866ThrfsX5. This variant ispredicted to cause loss of normal protein function either through protein truncation or nonsense-mediatedmRNA decay. The c.2595delC deletion was not observed in approximately 6,500 individuals of Europeanand African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a commonbenign variant in these populations. We interpret c.2595delC as a pathogenic variant.
Illumina Clinical Services Laboratory,Illumina RCV000326788 SCV000396406 uncertain significance Brody myopathy 2018-05-03 criteria provided, single submitter clinical testing The ATP2A1 c.2595delC (Asn866ThrfsTer5) variant results in a frameshift and is predicted to result in premature termination of the protein. A literature search was performed for the gene, cDNA change, and amino acid change. No publications were found based on this search. This variant is not found in the 1000 Genomes Project, the Exome Sequencing Project, the Exome Aggregation Consortium, or the Genome Aggregation Database. Due to the potential impact of frameshift variants and the lack of clarifying evidence, this variant is classified as a variant of unknown significance but suspicious for pathogenicity for Brody myopathy. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.

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