ClinVar Miner

Submissions for variant NM_000053.4(ATP7B):c.2145C>T (p.Tyr715=)

gnomAD frequency: 0.00001  dbSNP: rs751202110
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001001455 SCV001079183 pathogenic Wilson disease 2023-12-28 criteria provided, single submitter clinical testing This sequence change affects codon 715 of the ATP7B mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the ATP7B protein. This variant is present in population databases (rs751202110, gnomAD 0.07%). This variant has been observed in individual(s) with Wilson disease (PMID: 23235335, 23333878, 23551039, 34324271). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 756012). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant is not likely to affect RNA splicing. For these reasons, this variant has been classified as Pathogenic.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV001001455 SCV001158703 likely benign Wilson disease 2018-08-07 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV001172064 SCV001334999 uncertain significance not provided 2020-04-01 criteria provided, single submitter clinical testing
Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics RCV001001455 SCV001571482 uncertain significance Wilson disease 2021-01-07 criteria provided, single submitter clinical testing A heterozygous missense variation in exon 8 of the ATP7B gene that results in the amino acid substitution of Cysteine for Arginine at codon 715 was detected. The c. 2145C>T (p.Tyr715(=)) variant has not been reported in the 1000 genomes database and has a minor allele frequency of 0.01% in the gnomAD database. The in silico prediction of the variant is damaging by MutationTaster2. The variant is found in trans of a known pathogenic variant c.3182G>A. The reference codon is conserved across species. In summary, the variant meets our criteria to be classified as a variant of uncertain significance.
Genome-Nilou Lab RCV001001455 SCV001977168 likely benign Wilson disease 2021-08-10 criteria provided, single submitter clinical testing

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