ClinVar Miner

Submissions for variant NM_000234.3(LIG1):c.2014C>T (p.Arg672Cys)

gnomAD frequency: 0.00026  dbSNP: rs55950593
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV002046305 SCV002317111 uncertain significance not provided 2022-08-21 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 672 of the LIG1 protein (p.Arg672Cys). This variant is present in population databases (rs55950593, gnomAD 0.03%). This missense change has been observed in individual(s) with primary immunodeficiency (PMID: 32888943). ClinVar contains an entry for this variant (Variation ID: 1521453). 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 C15"). 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.
Fulgent Genetics, Fulgent Genetics RCV002486766 SCV002793244 uncertain significance Immunodeficiency 96 2022-04-08 criteria provided, single submitter clinical testing
GeneDx RCV002046305 SCV003927655 uncertain significance not provided 2022-11-25 criteria provided, single submitter clinical testing Observed in the apparent homozygous state in a patient with likely primary immunodeficiency, but detailed clinical information was not provided and this individual was also reported to have a potentially causative variant in another gene (Platt et al., 2021); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 32888943)

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