ClinVar Miner

Submissions for variant NM_001364905.1(LRBA):c.8528G>A (p.Arg2843Gln)

gnomAD frequency: 0.00002  dbSNP: rs200336029
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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 RCV001063255 SCV001228093 uncertain significance Combined immunodeficiency due to LRBA deficiency 2022-05-25 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 2854 of the LRBA protein (p.Arg2854Gln). This variant is present in population databases (rs200336029, gnomAD 0.004%). This variant has not been reported in the literature in individuals affected with LRBA-related conditions. ClinVar contains an entry for this variant (Variation ID: 857551). 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: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. 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.
Neuberg Centre For Genomic Medicine, NCGM RCV001063255 SCV004047923 uncertain significance Combined immunodeficiency due to LRBA deficiency criteria provided, single submitter clinical testing The missense variant c.8528G>A (p.Arg2843Gln) has been submitted to ClinVar as a Variant of Uncertain Significance, but no details are available for independent assessment. The p.Arg2843Gln variant has allele frequency of 0.002850% in the gnomAD and novel (not in any individuals) in 1000 genome database. The amino acid Arg at position 2843 is changed to a Gln changing protein sequence and it might alter its composition and physico-chemical properties. The amino acid change p.Arg2843Gln in LRBA is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Uncertain Significance. In the absence of another variant , the molecular diagnosis can not be confirmed.
PreventionGenetics, part of Exact Sciences RCV004751870 SCV005348776 uncertain significance LRBA-related disorder 2024-05-10 no assertion criteria provided clinical testing The LRBA c.8561G>A variant is predicted to result in the amino acid substitution p.Arg2854Gln. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0040% of alleles in individuals of African descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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