ClinVar Miner

Submissions for variant NM_000702.4(ATP1A2):c.1234C>T (p.Arg412Ter)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Department Of Biochemistry, Hamamatsu University School Of Medicine RCV003238158 SCV003935998 likely pathogenic Fetal akinesia, respiratory insufficiency, microcephaly, polymicrogyria, and dysmorphic facies 2023-06-30 criteria provided, single submitter research The c.1234C>T, p.(Arg412X) variant in ATP1A2 was observed in one African individual with heterozygous state (Allele Frequency 6.57x10-6) in the gnomAD but not registered in either HGMD or ClinVar databases. Based on American College of Medical Genetics and Genomics standards and guidelines, p.(Arg412X) variant was classified as Likely pathogenic (PVS1, PM2).
GeneDx RCV003443190 SCV004168071 likely pathogenic not provided 2023-10-18 criteria provided, single submitter clinical testing Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed at a significant frequency in large population cohorts (gnomAD); Has not been previously published as pathogenic or benign to our knowledge
Labcorp Genetics (formerly Invitae), Labcorp RCV003746665 SCV004453539 pathogenic Familial hemiplegic migraine 2023-11-28 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg412*) in the ATP1A2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in ATP1A2 are known to be pathogenic (PMID: 30690204). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with ATP1A2-related conditions. ClinVar contains an entry for this variant (Variation ID: 2507016). For these reasons, this variant has been classified as Pathogenic.
Dr.Nikuei Genetic Center RCV003238158 SCV005068181 pathogenic Fetal akinesia, respiratory insufficiency, microcephaly, polymicrogyria, and dysmorphic facies no assertion criteria provided clinical testing

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