ClinVar Miner

Submissions for variant NM_007078.3(LDB3):c.548del (p.Pro183fs)

dbSNP: rs1285270306
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000617200 SCV000736224 uncertain significance Cardiovascular phenotype 2023-03-30 criteria provided, single submitter clinical testing The c.548delC variant, located in coding exon 4 of the LDB3 gene, results from a deletion of one nucleotide at nucleotide position 548, causing a translational frameshift with a predicted alternate stop codon (p.P183Qfs*25). This alteration is expected to result in protein truncation or nonsense-mediated mRNA decay. However, loss of function of LDB3 has not been established as a mechanism of disease. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Invitae RCV001242444 SCV001415531 pathogenic Myofibrillar myopathy 4 2023-05-05 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant is not likely to affect RNA splicing. ClinVar contains an entry for this variant (Variation ID: 518778). This variant has not been reported in the literature in individuals affected with LDB3-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.0009%). This sequence change creates a premature translational stop signal (p.Pro183Glnfs*25) in the LDB3 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in LDB3 are known to be pathogenic (PMID: 36253531). 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+1505del (Intronic) in the primary transcript.
Fulgent Genetics, Fulgent Genetics RCV002506495 SCV002816252 uncertain significance Dilated cardiomyopathy 1C; Myofibrillar myopathy 4 2021-09-17 criteria provided, single submitter clinical testing

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