ClinVar Miner

Submissions for variant NM_005228.5(EGFR):c.2648T>C (p.Leu883Ser)

gnomAD frequency: 0.00001  dbSNP: rs1787457693
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001358850 SCV001554703 uncertain significance EGFR-related lung cancer 2024-06-17 criteria provided, single submitter clinical testing This sequence change replaces leucine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 883 of the EGFR protein (p.Leu883Ser). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with EGFR-related conditions. ClinVar contains an entry for this variant (Variation ID: 1050891). 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) performed at Invitae indicates that this missense variant is expected to disrupt EGFR protein function with a positive predictive value of 80%. 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.
Quest Diagnostics Nichols Institute San Juan Capistrano RCV004998848 SCV005625033 uncertain significance not provided 2023-11-09 criteria provided, single submitter clinical testing The EGFR c.2648T>C (p.Leu883Ser) variant has not been reported in individuals with EGFR-related conditions in the published literature. The frequency of this variant in the general population, 0.0000066 (1/152186 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is uninformative in the assessment of its pathogenicity. Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded predictions that this variant is damaging. Based on the available information, we are unable to determine the clinical significance of this variant.

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