ClinVar Miner

Submissions for variant NM_007078.3(LDB3):c.13G>A (p.Val5Met)

gnomAD frequency: 0.00001  dbSNP: rs773170985
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001774003 SCV001994475 uncertain significance not provided 2019-08-20 criteria provided, single submitter clinical testing Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Has not been previously published as pathogenic or benign to our knowledge
Invitae RCV002034481 SCV002305337 uncertain significance Myofibrillar myopathy 4 2022-12-23 criteria provided, single submitter clinical testing ClinVar contains an entry for this variant (Variation ID: 1308092). This variant has not been reported in the literature in individuals affected with LDB3-related conditions. This variant is present in population databases (rs773170985, gnomAD 0.006%). This sequence change replaces valine, which is neutral and non-polar, with methionine, which is neutral and non-polar, at codon 5 of the LDB3 protein (p.Val5Met). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). 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.
Fulgent Genetics, Fulgent Genetics RCV002506770 SCV002815892 uncertain significance Dilated cardiomyopathy 1C; Myofibrillar myopathy 4 2021-07-29 criteria provided, single submitter clinical testing
Ambry Genetics RCV003298969 SCV003999256 uncertain significance Cardiovascular phenotype 2023-03-18 criteria provided, single submitter clinical testing The p.V5M variant (also known as c.13G>A), located in coding exon 1 of the LDB3 gene, results from a G to A substitution at nucleotide position 13. The valine at codon 5 is replaced by methionine, an amino acid with highly similar properties. This amino acid position is conserved. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

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