ClinVar Miner

Submissions for variant NM_001364905.1(LRBA):c.5899G>A (p.Ala1967Thr)

gnomAD frequency: 0.00010  dbSNP: rs141395658
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000813647 SCV000954015 uncertain significance Combined immunodeficiency due to LRBA deficiency 2022-08-09 criteria provided, single submitter clinical testing This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 1967 of the LRBA protein (p.Ala1967Thr). This variant is present in population databases (rs141395658, gnomAD 0.01%). 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: 657092). 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"). 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.
Baylor Genetics RCV000813647 SCV001528612 uncertain significance Combined immunodeficiency due to LRBA deficiency 2018-06-15 criteria provided, single submitter clinical testing This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].
Ambry Genetics RCV002538171 SCV003714282 uncertain significance Inborn genetic diseases 2022-12-19 criteria provided, single submitter clinical testing The c.5899G>A (p.A1967T) alteration is located in exon 37 (coding exon 36) of the LRBA gene. This alteration results from a G to A substitution at nucleotide position 5899, causing the alanine (A) at amino acid position 1967 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Revvity Omics, Revvity RCV000813647 SCV003817058 uncertain significance Combined immunodeficiency due to LRBA deficiency 2020-09-21 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV003396425 SCV004119570 uncertain significance LRBA-related disorder 2023-01-24 criteria provided, single submitter clinical testing The LRBA c.5899G>A variant is predicted to result in the amino acid substitution p.Ala1967Thr. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.014% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/4-151604725-C-T). 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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