ClinVar Miner

Submissions for variant NM_005228.5(EGFR):c.1690C>T (p.Pro564Ser)

gnomAD frequency: 0.00001  dbSNP: rs773651001
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Baylor Genetics RCV001292731 SCV001481362 uncertain significance Inflammatory skin and bowel disease, neonatal, 2 2020-08-27 criteria provided, single submitter clinical testing This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].
Labcorp Genetics (formerly Invitae), Labcorp RCV001863172 SCV002206517 uncertain significance EGFR-related lung cancer 2024-02-05 criteria provided, single submitter clinical testing This sequence change replaces proline, which is neutral and non-polar, with serine, which is neutral and polar, at codon 564 of the EGFR protein (p.Pro564Ser). This variant is present in population databases (rs773651001, gnomAD 0.003%). 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: 997522). 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 not expected to disrupt EGFR protein function with a negative 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.
Ambry Genetics RCV004035595 SCV003587996 uncertain significance Hereditary cancer-predisposing syndrome 2022-01-07 criteria provided, single submitter clinical testing The c.1690C>T (p.P564S) alteration is located in exon 14 (coding exon 14) of the EGFR gene. This alteration results from a C to T substitution at nucleotide position 1690, causing the proline (P) at amino acid position 564 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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