ClinVar Miner

Submissions for variant NM_000038.6(APC):c.3866G>A (p.Cys1289Tyr)

dbSNP: rs1765540901
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV003538623 SCV001399640 uncertain significance Familial adenomatous polyposis 1 2023-09-22 criteria provided, single submitter clinical testing ClinVar contains an entry for this variant (Variation ID: 954769). This sequence change replaces cysteine, which is neutral and slightly polar, with tyrosine, which is neutral and polar, at codon 1289 of the APC protein (p.Cys1289Tyr). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with APC-related conditions. 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 APC 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.
Ambry Genetics RCV002356964 SCV002620009 uncertain significance Hereditary cancer-predisposing syndrome 2022-03-10 criteria provided, single submitter clinical testing The p.C1289Y variant (also known as c.3866G>A), located in coding exon 15 of the APC gene, results from a G to A substitution at nucleotide position 3866. The cysteine at codon 1289 is replaced by tyrosine, an amino acid with highly dissimilar properties. This amino acid position is not 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.

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