ClinVar Miner

Submissions for variant NM_007078.3(LDB3):c.236C>T (p.Thr79Ile)

gnomAD frequency: 0.00001  dbSNP: rs397517221
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000507721 SCV000604095 uncertain significance not provided 2017-05-17 criteria provided, single submitter clinical testing The p.Thr79Ile variant (rs397517221) has not been reported in the medical literature nor has it been previously identified in our laboratory; however, it is listed in the ClinVar database as a variant of uncertain significance (Variation ID: 45541). It is listed in the Genome Aggregation Database (gnomAD) browser with an overall frequency of 0.0004% (identified in 1 out of 245,870 chromosomes). The threonine at codon 79 is highly conserved considering 11 species up to Cow (Alamut software v2.9), and computational analyses suggest this variant has a significant effect on LDB3 protein structure/function (SIFT: damaging, PolyPhen2: probably damaging, and Mutation Taster: disease causing). However, based on the available information, the clinical significance of the p.Thr79Ile variant cannot be determined with certainty.
Fulgent Genetics, Fulgent Genetics RCV002481640 SCV002777149 uncertain significance Dilated cardiomyopathy 1C; Myofibrillar myopathy 4 2021-08-11 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV002527360 SCV003451323 uncertain significance Myofibrillar myopathy 4 2023-01-26 criteria provided, single submitter clinical testing This variant has not been reported in the literature in individuals affected with LDB3-related conditions. 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. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). ClinVar contains an entry for this variant (Variation ID: 439858). This variant is present in population databases (rs397517221, gnomAD 0.0009%). This sequence change replaces threonine, which is neutral and polar, with isoleucine, which is neutral and non-polar, at codon 79 of the LDB3 protein (p.Thr79Ile).

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