ClinVar Miner

Submissions for variant NM_000053.4(ATP7B):c.1716del (p.Gly572_Met573insTer) (rs1057516893)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000410735 SCV000486394 likely pathogenic Wilson disease 2016-05-25 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000410735 SCV000916616 pathogenic Wilson disease 2018-02-05 criteria provided, single submitter clinical testing Variant summary: ATP7B c.1716delG (p.Met573X) 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 (e.g., p.Ile582fsX25 and p.Tyr670fsX1). The variant was absent in 246180 control chromosomes in gnomAD. The c.1716delG variant has been reported in the literature in two individuals affected with Wilson Disease, both of whom were described as early-onset of symptoms and a higher burden of disease (Aggarwal_2013). These data indicate that the variant is likely to be associated with disease. One publication reports experimental evidence evaluating several different aspects of protein function; the most pronounced variant effect results in <10% of normal activity (Chandhok_2016). One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. One laboratory classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.
Invitae RCV000410735 SCV001584177 pathogenic Wilson disease 2020-08-26 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Met573*) in the ATP7B 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 observed in individual(s) with Wilson disease (PMID: 23551039). ClinVar contains an entry for this variant (Variation ID: 370955). Loss-of-function variants in ATP7B are known to be pathogenic (PMID: 10441329, 16283883). For these reasons, this variant has been classified as Pathogenic.
Natera, Inc. RCV000410735 SCV001463845 pathogenic Wilson disease 2020-09-16 no assertion criteria provided clinical testing

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