ClinVar Miner

Submissions for variant NM_000038.6(APC):c.7204A>T (p.Asn2402Tyr)

dbSNP: rs587780550
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV003764828 SCV000153944 uncertain significance Familial adenomatous polyposis 1 2023-12-01 criteria provided, single submitter clinical testing This sequence change replaces asparagine, which is neutral and polar, with tyrosine, which is neutral and polar, at codon 2402 of the APC protein (p.Asn2402Tyr). This variant is present in population databases (rs587780550, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with APC-related conditions. ClinVar contains an entry for this variant (Variation ID: 132747). 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 with a negative predictive value of 95%. 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 RCV002371952 SCV002673428 uncertain significance Hereditary cancer-predisposing syndrome 2019-09-26 criteria provided, single submitter clinical testing The p.N2402Y variant (also known as c.7204A>T), located in coding exon 15 of the APC gene, results from an A to T substitution at nucleotide position 7204. The asparagine at codon 2402 is replaced by tyrosine, an amino acid with dissimilar 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.

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