ClinVar Miner

Submissions for variant NM_000038.6(APC):c.7397C>T (p.Ser2466Phe)

gnomAD frequency: 0.00001  dbSNP: rs765669629
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Color Diagnostics, LLC DBA Color Health RCV000775348 SCV000909628 uncertain significance Hereditary cancer-predisposing syndrome 2019-01-24 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV001284369 SCV001470119 uncertain significance not provided 2020-03-17 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV004569463 SCV002191995 uncertain significance Familial adenomatous polyposis 1 2024-01-07 criteria provided, single submitter clinical testing This sequence change replaces serine, which is neutral and polar, with phenylalanine, which is neutral and non-polar, at codon 2466 of the APC protein (p.Ser2466Phe). This variant is present in population databases (rs765669629, gnomAD 0.006%). 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: 630200). 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 RCV000775348 SCV002673604 uncertain significance Hereditary cancer-predisposing syndrome 2021-11-23 criteria provided, single submitter clinical testing The p.S2466F variant (also known as c.7397C>T), located in coding exon 15 of the APC gene, results from a C to T substitution at nucleotide position 7397. The serine at codon 2466 is replaced by phenylalanine, an amino acid with highly dissimilar properties. This amino acid position is highly conserved in available vertebrate species. In addition, in silico predictors for this gene do not accurately predict pathogenicity. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Fulgent Genetics, Fulgent Genetics RCV005036095 SCV005667890 uncertain significance Desmoid disease, hereditary; Familial adenomatous polyposis 1; Hepatocellular carcinoma; Gastric cancer; Colorectal cancer; Gastric adenocarcinoma and proximal polyposis of the stomach 2024-06-08 criteria provided, single submitter clinical testing

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