ClinVar Miner

Submissions for variant NM_001364905.1(LRBA):c.4947T>A (p.Asn1649Lys)

gnomAD frequency: 0.00011  dbSNP: rs200578734
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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 RCV000793282 SCV000932630 uncertain significance Combined immunodeficiency due to LRBA deficiency 2021-12-19 criteria provided, single submitter clinical testing This sequence change replaces asparagine, which is neutral and polar, with lysine, which is basic and polar, at codon 1649 of the LRBA protein (p.Asn1649Lys). This variant is present in population databases (rs200578734, 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: 640287). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. 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 RCV000793282 SCV002815292 uncertain significance Combined immunodeficiency due to LRBA deficiency 2021-10-14 criteria provided, single submitter clinical testing
Ambry Genetics RCV004027439 SCV004898424 uncertain significance Inborn genetic diseases 2022-12-13 criteria provided, single submitter clinical testing The c.4947T>A (p.N1649K) alteration is located in exon 30 (coding exon 29) of the LRBA gene. This alteration results from a T to A substitution at nucleotide position 4947, causing the asparagine (N) at amino acid position 1649 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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