ClinVar Miner

Submissions for variant NM_007078.3(LDB3):c.321+1G>A

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Revvity Omics, Revvity RCV003131466 SCV003816502 uncertain significance not provided 2019-05-04 criteria provided, single submitter clinical testing
Invitae RCV003778727 SCV004622888 likely pathogenic Myofibrillar myopathy 4 2023-10-05 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 the same sequence change NM_001080116.1:c.321+1G>A in the primary transcript. This sequence change affects a donor splice site in intron 4 of the LDB3 gene. It is expected to disrupt RNA splicing on both transcripts. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547); however, loss-of-function variants in LDB3 are only known to be pathogenic in the alternate transcript (PMID: 36253531). This variant is present in population databases (rs763970235, 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: 2433419). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

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