ClinVar Miner

Submissions for variant NM_000053.4(ATP7B):c.3598C>T (p.Gln1200Ter)

dbSNP: rs786204658
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000169453 SCV000220874 likely pathogenic Wilson disease 2014-11-11 criteria provided, single submitter literature only
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000169453 SCV001774457 likely pathogenic Wilson disease 2021-07-13 criteria provided, single submitter clinical testing Variant summary: ATP7B c.3598C>T (p.Gln1200X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic by our laboratory. The variant was absent in 249532 control chromosomes (gnomAD). c.3598C>T has been reported in the literature in a compound heterozygous individual affected with Wilson Disease (Chappuis_2007). To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as likely pathogenic.
Invitae RCV000169453 SCV003442168 pathogenic Wilson disease 2022-02-04 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Gln1200*) in the ATP7B gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in ATP7B are known to be pathogenic (PMID: 10441329, 16283883). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with Wilson disease (PMID: 17317524). ClinVar contains an entry for this variant (Variation ID: 189056). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. For these reasons, this variant has been classified as Pathogenic.

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