ClinVar Miner

Submissions for variant NM_007078.3(LDB3):c.646A>T (p.Met216Leu)

gnomAD frequency: 0.00002  dbSNP: rs765199175
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001720007 SCV000515802 likely benign not provided 2020-02-06 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000867148 SCV001008344 uncertain significance Myofibrillar myopathy 4 2025-01-27 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.321+1603A>T in the primary transcript. This sequence change replaces methionine, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 216 of the LDB3 protein (p.Met216Leu). This variant is present in population databases (rs765199175, gnomAD 0.02%). This missense change has been observed in individual(s) with clinical features of myofibrillar myopathy (internal data). ClinVar contains an entry for this variant (Variation ID: 379172). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant is not likely to affect RNA splicing. 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.
Ambry Genetics RCV002365486 SCV002660725 likely benign Cardiovascular phenotype 2024-05-13 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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