ClinVar Miner

Submissions for variant NM_000053.4(ATP7B):c.1829C>T (p.Pro610Leu)

gnomAD frequency: 0.00009  dbSNP: rs368381292
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000508427 SCV000602610 uncertain significance not specified 2016-12-06 criteria provided, single submitter clinical testing
Invitae RCV000691710 SCV000819500 uncertain significance Wilson disease 2022-08-14 criteria provided, single submitter clinical testing This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 610 of the ATP7B protein (p.Pro610Leu). This variant is present in population databases (rs368381292, gnomAD 0.03%). 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: 439430). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. 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.
Illumina Laboratory Services, Illumina RCV000691710 SCV001268680 uncertain significance Wilson disease 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Genome-Nilou Lab RCV000691710 SCV002027171 uncertain significance Wilson disease 2021-09-05 criteria provided, single submitter clinical testing
GeneDx RCV001840619 SCV002099652 uncertain significance not provided 2022-02-24 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 31217899)
Fulgent Genetics, Fulgent Genetics RCV000691710 SCV002794449 uncertain significance Wilson disease 2021-09-08 criteria provided, single submitter clinical testing
Revvity Omics, Revvity RCV000691710 SCV004234586 uncertain significance Wilson disease 2023-04-04 criteria provided, single submitter clinical testing
Natera, Inc. RCV000691710 SCV001463844 uncertain significance Wilson disease 2020-09-16 no assertion criteria provided clinical testing

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