ClinVar Miner

Submissions for variant NM_000053.4(ATP7B):c.3990_3993del (p.Tyr1331fs) (rs1566441447)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000755841 SCV000883443 pathogenic not provided 2017-05-10 criteria provided, single submitter clinical testing To our knowledge, the ATP7B c.3990_3993delTTAT; p.Tyr1331fs variant has not been previously reported in the literature, gene-specific variant databases, or general population databases (Exome Variant Server, Genome Aggregation Database). This variant creates a frameshift and is predicted to result in a truncated protein or absent transcript, and is considered pathogenic.
Integrated Genetics/Laboratory Corporation of America RCV001175559 SCV001339185 likely pathogenic Wilson disease 2020-03-26 criteria provided, single submitter clinical testing Variant summary: ATP7B c.3990_3993delTTAT (p.Tyr1331ThrfsX61) 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 249548 control chromosomes (gnomAD). c.3990_3993delTTAT has been reported in the literature in individuals affected with Wilson Disease (Jung_2017). These data do not allow any conclusion about variant significance. At least one publication reports experimental evidence evaluating an impact on protein function, however, does not allow convincing conclusions about the variant effect (Jung_2017). 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.

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