ClinVar Miner

Submissions for variant NM_000038.6(APC):c.6560G>A (p.Gly2187Glu)

gnomAD frequency: 0.00001  dbSNP: rs146695342
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000576010 SCV000667487 uncertain significance Hereditary cancer-predisposing syndrome 2023-02-24 criteria provided, single submitter clinical testing The p.G2187E variant (also known as c.6560G>A), located in coding exon 15 of the APC gene, results from a G to A substitution at nucleotide position 6560. The glycine at codon 2187 is replaced by glutamic acid, an amino acid with similar properties. This amino acid position is well 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.
Color Diagnostics, LLC DBA Color Health RCV000576010 SCV000908554 uncertain significance Hereditary cancer-predisposing syndrome 2023-06-15 criteria provided, single submitter clinical testing This missense variant replaces glycine with glutamic acid at codon 2187 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). To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with APC-related disorders in the literature. This variant has been identified in 2/280494 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.
Invitae RCV003537121 SCV001235261 uncertain significance Familial adenomatous polyposis 1 2023-12-21 criteria provided, single submitter clinical testing This sequence change replaces glycine, which is neutral and non-polar, with glutamic acid, which is acidic and polar, at codon 2187 of the APC protein (p.Gly2187Glu). This variant is present in population databases (rs146695342, gnomAD 0.008%). 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: 482296). 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.

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