ClinVar Miner

Submissions for variant NM_000038.6(APC):c.1139G>C (p.Arg380Pro)

dbSNP: rs587782886
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Color Diagnostics, LLC DBA Color Health RCV000580846 SCV000681445 uncertain significance Hereditary cancer-predisposing syndrome 2020-01-28 criteria provided, single submitter clinical testing This missense variant replaces arginine with proline at codon 380 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). Splice site prediction tools suggest that this variant may not impact RNA splicing. To our knowledge, functional studies have not been performed for this variant. This variant has not 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). 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.
Labcorp Genetics (formerly Invitae), Labcorp RCV002526940 SCV002294556 uncertain significance Familial adenomatous polyposis 1 2021-02-02 criteria provided, single submitter clinical testing This variant has not been reported in the literature in individuals with APC-related conditions. ClinVar contains an entry for this variant (Variation ID: 489410). 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. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C15"). This variant is not present in population databases (ExAC no frequency). This sequence change replaces arginine with proline at codon 380 of the APC protein (p.Arg380Pro). The arginine residue is highly conserved and there is a moderate physicochemical difference between arginine and proline.

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