ClinVar Miner

Submissions for variant NM_000053.4(ATP7B):c.3863C>G (p.Thr1288Arg)

dbSNP: rs373748155
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000672804 SCV000797948 uncertain significance Wilson disease 2018-02-26 criteria provided, single submitter clinical testing
Invitae RCV000672804 SCV001586746 pathogenic Wilson disease 2020-06-30 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. This variant disrupts the p.Thr1288 amino acid residue in ATP7B. Other variant(s) that disrupt this residue have been observed in individuals with ATP7B-related conditions (PMID: 20967755, Invitae), which suggests that this may be a clinically significant amino acid residue. This sequence change replaces threonine with arginine at codon 1288 of the ATP7B protein (p.Thr1288Arg). The threonine residue is highly conserved and there is a moderate physicochemical difference between threonine and arginine. This variant is not present in population databases (ExAC no frequency). This variant has been observed in individual(s) with Wilson disease (PMID: 16416207, 17410460). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 556754). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies.
Genome-Nilou Lab RCV000672804 SCV001977536 likely pathogenic Wilson disease 2021-08-10 criteria provided, single submitter clinical testing

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