ClinVar Miner

Submissions for variant NM_000038.6(APC):c.7588C>T (p.Arg2530Trp)

gnomAD frequency: 0.00001  dbSNP: rs730881265
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000656751 SCV000209552 uncertain significance not provided 2023-09-10 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 23085758, 27997549, 25583476)
Ambry Genetics RCV000159576 SCV000217928 likely benign Hereditary cancer-predisposing syndrome 2021-07-22 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, 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.
Labcorp Genetics (formerly Invitae), Labcorp RCV002516419 SCV000552720 uncertain significance Familial adenomatous polyposis 1 2025-01-29 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 2530 of the APC protein (p.Arg2530Trp). This variant is present in population databases (rs730881265, gnomAD 0.007%). 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: 181824). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) 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.
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000211935 SCV000600154 uncertain significance not specified 2017-06-13 criteria provided, single submitter clinical testing
Color Diagnostics, LLC DBA Color Health RCV000159576 SCV000681879 uncertain significance Hereditary cancer-predisposing syndrome 2023-03-16 criteria provided, single submitter clinical testing This missense variant replaces arginine with tryptophan at codon 2530 of the APC protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, 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 8/250688 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.
Baylor Genetics RCV002516419 SCV004201435 uncertain significance Familial adenomatous polyposis 1 2023-07-19 criteria provided, single submitter clinical testing
All of Us Research Program, National Institutes of Health RCV003998423 SCV004835698 uncertain significance Classic or attenuated familial adenomatous polyposis 2023-08-15 criteria provided, single submitter clinical testing This missense variant replaces arginine with tryptophan at codon 2530 of the APC protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, 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 8/250688 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.
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital RCV000211935 SCV005873279 uncertain significance not specified 2025-03-04 criteria provided, single submitter clinical testing Classification criteria: BP1

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