ClinVar Miner

Submissions for variant NM_007078.3(LDB3):c.1696A>G (p.Met566Val)

gnomAD frequency: 0.00002  dbSNP: rs775232208
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000801372 SCV000941146 uncertain significance Myofibrillar myopathy 4 2024-10-15 criteria provided, single submitter clinical testing The LDB3 gene has multiple clinically relevant transcripts. This variant occurs in alternate transcript NM_007078.3, and corresponds to NM_001080116.1:c.*18609A>G in the primary transcript. This sequence change replaces methionine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 566 of the LDB3 protein (p.Met566Val). This variant is present in population databases (rs775232208, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with LDB3-related conditions. ClinVar contains an entry for this variant (Variation ID: 646981). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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.
Molecular Diagnostic Laboratory for Inherited Cardiovascular Disease, Montreal Heart Institute RCV000845315 SCV000987357 uncertain significance Primary familial dilated cardiomyopathy criteria provided, single submitter clinical testing
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine RCV001449770 SCV001653045 uncertain significance not specified 2020-06-15 criteria provided, single submitter clinical testing The p.Met566Val variant in LDB3 has not been previously reported in individuals with cardiomyopathy but has been identified in 0.01% (5/34590) of Latino and 0.004% (5/113736) of European chromosomes by gnomAD (http://gnomad.broadinstitute.org). Computational prediction tools and conservation analyses do not provide strong support for or against an impact to the protein. In summary, the clinical significance of this variant is uncertain. ACMG/AMP Criteria applied: none.
Baylor Genetics RCV003147552 SCV003836243 uncertain significance Dilated cardiomyopathy 1C 2022-02-10 criteria provided, single submitter clinical testing
Ambry Genetics RCV003372857 SCV004095148 uncertain significance Cardiovascular phenotype 2023-06-19 criteria provided, single submitter clinical testing The p.M566V variant (also known as c.1696A>G), located in coding exon 10 of the LDB3 gene, results from an A to G substitution at nucleotide position 1696. The methionine at codon 566 is replaced by valine, an amino acid with highly similar properties. This amino acid position is conserved. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
GeneDx RCV004723206 SCV005332726 uncertain significance not provided 2023-07-05 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge

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