ClinVar Miner

Submissions for variant NM_000038.6(APC):c.5125A>T (p.Thr1709Ser)

dbSNP: rs1554086463
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV003742727 SCV000647560 benign Familial adenomatous polyposis 1 2023-04-20 criteria provided, single submitter clinical testing
Color Diagnostics, LLC DBA Color Health RCV001189874 SCV001357240 uncertain significance Hereditary cancer-predisposing syndrome 2023-12-05 criteria provided, single submitter clinical testing This missense variant replaces threonine with serine at codon 1709 of the APC protein. Computational prediction tools and conservation analyses suggest that this variant may not impact the protein function. Computational splicing tools suggest that this variant may not impact RNA splicing. To our knowledge, functional assays have not been performed for this variant nor has this variant been reported in individuals affected with hereditary cancer in the literature. This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). 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.
GeneDx RCV001775866 SCV002013010 uncertain significance not provided 2020-05-14 criteria provided, single submitter clinical testing Not observed in large population cohorts (Lek 2016); In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Ambry Genetics RCV001189874 SCV002642244 uncertain significance Hereditary cancer-predisposing syndrome 2022-10-21 criteria provided, single submitter clinical testing The p.T1709S variant (also known as c.5125A>T), located in coding exon 15 of the APC gene, results from an A to T substitution at nucleotide position 5125. The threonine at codon 1709 is replaced by serine, an amino acid with similar 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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