ClinVar Miner

Submissions for variant NM_007078.3(LDB3):c.415A>G (p.Arg139Gly)

gnomAD frequency: 0.00001  dbSNP: rs199801766
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV001812528 SCV002049019 uncertain significance not provided 2020-12-14 criteria provided, single submitter clinical testing The LDB3 c.415A>G; p.Arg139Gly variant (rs199801766), to our knowledge, is not reported in the medical literature or gene-specific databases. This variant is found on only three chromosomes (3/247834 alleles) in the Genome Aggregation Database. The arginine at codon 139 is weakly conserved, and computational analyses predict that this variant is neutral (REVEL: 0.069). However, given the lack of clinical and functional data, the significance of the p.Arg139Gly variant is uncertain at this time.
Invitae RCV002074167 SCV002467765 uncertain significance Myofibrillar myopathy 4 2024-01-22 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+1372A>G in the primary transcript. This sequence change replaces arginine, which is basic and polar, with glycine, which is neutral and non-polar, at codon 139 of the LDB3 protein (p.Arg139Gly). This variant is present in population databases (rs199801766, gnomAD 0.003%). 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: 1330942). 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.

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