ClinVar Miner

Submissions for variant NM_000053.4(ATP7B):c.3556+1G>A (rs184388696)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000169452 SCV000220873 likely pathogenic Wilson disease 2014-11-11 criteria provided, single submitter literature only
Integrated Genetics/Laboratory Corporation of America RCV000169452 SCV000694449 likely pathogenic Wilson disease 2019-04-01 criteria provided, single submitter clinical testing Variant summary: ATP7B c.3556+1G>A 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: Three predict the variant abolishes a 5' splicing donor site. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 8.1e-06 in 246256 control chromosomes (gnomAD). c.3556+1G>A has been reported in the literature in two unrelated individuals affected with Wilson Disease (Thomas 1995, Ljubic 2016). 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.

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