ClinVar Miner

Submissions for variant NM_007078.3(LDB3):c.11G>A (p.Ser4Asn)

gnomAD frequency: 0.00001  dbSNP: rs766405051
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001536972 SCV001753794 likely benign not provided 2020-03-05 criteria provided, single submitter clinical testing Has not been previously published as pathogenic or benign to our knowledge; Not observed in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function
Invitae RCV001873806 SCV002219089 uncertain significance Myofibrillar myopathy 4 2023-06-20 criteria provided, single submitter clinical testing This variant has not been reported in the literature in individuals affected with LDB3-related conditions. 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. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. ClinVar contains an entry for this variant (Variation ID: 1179890). This variant is present in population databases (rs766405051, gnomAD 0.009%). This sequence change replaces serine, which is neutral and polar, with asparagine, which is neutral and polar, at codon 4 of the LDB3 protein (p.Ser4Asn).
Ambry Genetics RCV004039241 SCV005025577 likely benign Cardiovascular phenotype 2024-01-09 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

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