ClinVar Miner

Submissions for variant NM_004360.5(CDH1):c.257A>G (p.Lys86Arg)

gnomAD frequency: 0.00001  dbSNP: rs1160169015
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Color Diagnostics, LLC DBA Color Health RCV000584323 SCV000689519 uncertain significance Hereditary cancer-predisposing syndrome 2019-04-19 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 RCV003229595 SCV003927010 uncertain significance Hereditary diffuse gastric adenocarcinoma 2022-08-01 criteria provided, single submitter clinical testing PM2 (PMID: 30311375)
Ambry Genetics RCV000584323 SCV005022279 uncertain significance Hereditary cancer-predisposing syndrome 2022-11-30 criteria provided, single submitter clinical testing The p.K86R variant (also known as c.257A>G), located in coding exon 3 of the CDH1 gene, results from an A to G substitution at nucleotide position 257. The lysine at codon 86 is replaced by arginine, an amino acid with highly similar properties. This amino acid position is conserved. 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.
Labcorp Genetics (formerly Invitae), Labcorp RCV003229595 SCV005718055 uncertain significance Hereditary diffuse gastric adenocarcinoma 2024-05-28 criteria provided, single submitter clinical testing This sequence change replaces lysine, which is basic and polar, with arginine, which is basic and polar, at codon 86 of the CDH1 protein (p.Lys86Arg). This variant is present in population databases (no rsID available, gnomAD 0.002%). This missense change has been observed in individual(s) with breast cancer (PMID: 36436516). ClinVar contains an entry for this variant (Variation ID: 491531). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The arginine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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.

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