ClinVar Miner

Submissions for variant NM_000038.6(APC):c.7679G>A (p.Arg2560Gln)

gnomAD frequency: 0.00001  dbSNP: rs759069096
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Color Diagnostics, LLC DBA Color Health RCV001190913 SCV001358549 uncertain significance Hereditary cancer-predisposing syndrome 2021-09-21 criteria provided, single submitter clinical testing This missense variant replaces arginine with glutamine at codon 2560 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 hereditary cancer in the literature. This variant has been identified in 4/282166 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 RCV003538595 SCV001376384 uncertain significance Familial adenomatous polyposis 1 2024-01-30 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 2560 of the APC protein (p.Arg2560Gln). This variant is present in population databases (rs759069096, gnomAD 0.01%). 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: 927546). 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 RCV001190913 SCV002672251 likely benign Hereditary cancer-predisposing syndrome 2022-02-22 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Baylor Genetics RCV002560964 SCV004205872 uncertain significance Familial adenomatous polyposis 1 2023-05-22 criteria provided, single submitter clinical testing

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