ClinVar Miner

Submissions for variant NM_004360.5(CDH1):c.1687G>T (p.Ala563Ser)

gnomAD frequency: 0.00004  dbSNP: rs587782044
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000130507 SCV000185376 uncertain significance Hereditary cancer-predisposing syndrome 2021-02-25 criteria provided, single submitter clinical testing The p.A563S variant (also known as c.1687G>T), located in coding exon 11 of the CDH1 gene, results from a G to T substitution at nucleotide position 1687. The alanine at codon 563 is replaced by serine, an amino acid with similar properties. This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
GeneDx RCV000212374 SCV000210919 uncertain significance not provided 2024-03-25 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; Observed in individual(s) with a family history of breast cancer (PMID: 36436516); This variant is associated with the following publications: (PMID: 15235021, 22850631, 36436516)
Labcorp Genetics (formerly Invitae), Labcorp RCV000473796 SCV000545407 uncertain significance Hereditary diffuse gastric adenocarcinoma 2023-11-02 criteria provided, single submitter clinical testing This sequence change replaces alanine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 563 of the CDH1 protein (p.Ala563Ser). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with CDH1-related conditions (PMID: 36436516). ClinVar contains an entry for this variant (Variation ID: 141834). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. 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.
Color Diagnostics, LLC DBA Color Health RCV000130507 SCV000684375 uncertain significance Hereditary cancer-predisposing syndrome 2019-04-05 criteria provided, single submitter clinical testing
European Reference Network on Genetic Tumour Risk Syndromes (ERN-GENTURIS), i3s - Instituto de Investigação e Inovação em Saúde, University of Porto RCV000473796 SCV003926830 uncertain significance Hereditary diffuse gastric adenocarcinoma 2022-08-01 criteria provided, single submitter clinical testing PM2 (PMID: 30311375)

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