ClinVar Miner

Submissions for variant NM_000038.6(APC):c.8060C>T (p.Ser2687Leu)

gnomAD frequency: 0.00001  dbSNP: rs144746572
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV003537090 SCV000647750 uncertain significance Familial adenomatous polyposis 1 2023-08-04 criteria provided, single submitter clinical testing This sequence change replaces serine, which is neutral and polar, with leucine, which is neutral and non-polar, at codon 2687 of the APC protein (p.Ser2687Leu). This variant is present in population databases (rs144746572, gnomAD 0.0009%). 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: 470127). 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 RCV000576128 SCV000672548 uncertain significance Hereditary cancer-predisposing syndrome 2021-10-04 criteria provided, single submitter clinical testing The p.S2687L variant (also known as c.8060C>T), located in coding exon 15 of the APC gene, results from a C to T substitution at nucleotide position 8060. The serine at codon 2687 is replaced by leucine, an amino acid with dissimilar properties. 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.
Color Diagnostics, LLC DBA Color Health RCV000576128 SCV001359487 uncertain significance Hereditary cancer-predisposing syndrome 2019-11-14 criteria provided, single submitter clinical testing This missense variant replaces serine with leucine at codon 2687 of the APC protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, PMID: 27666373). Splice site prediction tools suggest that this variant may not impact RNA splicing. To our knowledge, functional studies have not been performed for this variant. This variant has not been reported in individuals affected with hereditary cancer in the literature. This variant has been identified in 1/251220 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

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