ClinVar Miner

Submissions for variant NM_007078.3(LDB3):c.1633A>G (p.Ser545Gly)

gnomAD frequency: 0.00001  dbSNP: rs1370639524
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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 RCV000793729 SCV000933096 uncertain significance Myofibrillar myopathy 4 2023-12-13 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.*17354A>G in the primary transcript. This sequence change replaces serine, which is neutral and polar, with glycine, which is neutral and non-polar, at codon 545 of the LDB3 protein (p.Ser545Gly). This variant is present in population databases (no rsID available, gnomAD 0.0009%). 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: 640656). 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.
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute RCV002470983 SCV002769436 uncertain significance Familial isolated dilated cardiomyopathy 2021-05-06 criteria provided, single submitter clinical testing Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as VUS-3B. Following criteria are met: 0102 - Loss of function is the proposed mechanism of disease in this gene associated with missense variants and is associated with dilated cardiomyopathy, 1C, with or without LVNC (MIM#601493), hypertrophic cardiomyopathy, 24 (MIM#601493), left ventricular noncompaction 3 (MIM#601493) and myofibrillar myopathy, 4 (MIM#609452) (PMID: 19377068). (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0200 - Variant is predicted to result in a missense amino acid change from serine to glycine. (I) 0251 - This variant is heterozygous. (I) 0302 - Variant is present in gnomAD (v2) <0.001 for a dominant condition (2 heterozygotes, 0 homozygotes). (SP) 0502 - Missense variant with conflicting in silico predictions and uninformative conservation. (I) 0604 - Variant is not located in an established domain, motif, hotspot or informative constraint region. (I) 0705 - No comparable missense variants have previous evidence for pathogenicity. (I) 0807 - This variant has no previous evidence of pathogenicity. (I) 0905 - No published segregation evidence has been identified for this variant. (I) 1007 - No published functional evidence has been identified for this variant. (I) 1206 - This variant has been shown to be paternally inherited. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign
Fulgent Genetics, Fulgent Genetics RCV002493446 SCV002782383 uncertain significance Dilated cardiomyopathy 1C; Myofibrillar myopathy 4 2021-08-12 criteria provided, single submitter clinical testing
Mayo Clinic Laboratories, Mayo Clinic RCV003480824 SCV004225285 uncertain significance not provided 2022-10-19 criteria provided, single submitter clinical testing BP4
Ambry Genetics RCV004994009 SCV005612243 uncertain significance Cardiovascular phenotype 2024-08-04 criteria provided, single submitter clinical testing The c.1633A>G (p.S545G) alteration is located in exon 9 (coding exon 9) of the LDB3 gene. This alteration results from a A to G substitution at nucleotide position 1633, causing the serine (S) at amino acid position 545 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
GeneDx RCV003480824 SCV005628372 uncertain significance not provided 2024-07-18 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis indicates that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge; Reported using an alternate transcript of the gene

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