ClinVar Miner

Submissions for variant NM_000053.4(ATP7B):c.2575+1G>C (rs766149114)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000169063 SCV000220227 likely pathogenic Wilson disease 2014-04-09 criteria provided, single submitter literature only
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000169063 SCV000694425 likely pathogenic Wilson disease 2021-02-28 criteria provided, single submitter clinical testing Variant summary: ATP7B c.2575+1G>C is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: Four predict the variant abolishes the canonical 5' splicing donor site. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 8e-06 in 249552 control chromosomes. c.2575+1G>C has been reported in the literature in individuals affected with Wilson Disease and subsequently cited by others (example, Thomas_1995, Coffey_2013, Singh_2019). These data indicate that the variant may be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. No other 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.
GeneDx RCV001582664 SCV001813009 pathogenic not provided 2020-06-04 criteria provided, single submitter clinical testing Not observed at a significant frequency in large population cohorts (Lek et al., 2016); Canonical splice site variant in a gene for which loss-of-function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 25525159, 7626145, 23518715)

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