ClinVar Miner

Submissions for variant NM_000038.6(APC):c.6539A>C (p.Lys2180Thr)

dbSNP: rs762955111
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000575863 SCV000676336 uncertain significance Hereditary cancer-predisposing syndrome 2020-03-12 criteria provided, single submitter clinical testing The p.K2180T variant (also known as c.6539A>C), located in coding exon 15 of the APC gene, results from an A to C substitution at nucleotide position 6539. The lysine at codon 2180 is replaced by threonine, an amino acid with similar properties. This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Invitae RCV003537209 SCV000834268 uncertain significance Familial adenomatous polyposis 1 2022-12-11 criteria provided, single submitter clinical testing This variant has not been reported in the literature in individuals affected with APC-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces lysine, which is basic and polar, with threonine, which is neutral and polar, at codon 2180 of the APC protein (p.Lys2180Thr). 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. 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. ClinVar contains an entry for this variant (Variation ID: 487029).

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