ClinVar Miner

Submissions for variant NM_006904.7(PRKDC):c.2966T>A (p.Met989Lys)

dbSNP: rs749565098
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001059495 SCV001224119 uncertain significance Severe combined immunodeficiency due to DNA-PKcs deficiency 2022-12-02 criteria provided, single submitter clinical testing 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. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on PRKDC protein function. ClinVar contains an entry for this variant (Variation ID: 854437). This variant has not been reported in the literature in individuals affected with PRKDC-related conditions. This variant is present in population databases (rs749565098, gnomAD 0.003%). This sequence change replaces methionine, which is neutral and non-polar, with lysine, which is basic and polar, at codon 989 of the PRKDC protein (p.Met989Lys).
Ambry Genetics RCV003160478 SCV003912921 uncertain significance Inborn genetic diseases 2022-11-26 criteria provided, single submitter clinical testing The p.M989K variant (also known as c.2966T>A), located in coding exon 26 of the PRKDC gene, results from a T to A substitution at nucleotide position 2966. The methionine at codon 989 is replaced by lysine, an amino acid with similar properties. This amino acid position is conserved. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

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