ClinVar Miner

Submissions for variant NM_000053.4(ATP7B):c.1760C>T (p.Thr587Met)

gnomAD frequency: 0.00003  dbSNP: rs757716093
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000423231 SCV000526127 likely benign not specified 2016-04-12 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Labcorp Genetics (formerly Invitae), Labcorp RCV001861551 SCV002191872 uncertain significance Wilson disease 2021-08-27 criteria provided, single submitter clinical testing This sequence change replaces threonine with methionine at codon 587 of the ATP7B protein (p.Thr587Met). The threonine residue is moderately conserved and there is a moderate physicochemical difference between threonine and methionine. This variant is present in population databases (rs757716093, ExAC 0.004%). This variant has not been reported in the literature in individuals affected with ATP7B-related conditions. ClinVar contains an entry for this variant (Variation ID: 385010). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The methionine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
All of Us Research Program, National Institutes of Health RCV001861551 SCV004815970 uncertain significance Wilson disease 2024-01-11 criteria provided, single submitter clinical testing This missense variant replaces threonine with methionine at codon 587 of the ATP7B protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has been reported in an individual affected with Wilson disease (PMID: 27022412). This variant has been identified in 7/249564 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.
Fulgent Genetics, Fulgent Genetics RCV001861551 SCV005636237 uncertain significance Wilson disease 2024-04-26 criteria provided, single submitter clinical testing

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