ClinVar Miner

Submissions for variant NM_000038.6(APC):c.6355G>T (p.Ala2119Ser)

dbSNP: rs1561606713
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Color Diagnostics, LLC DBA Color Health RCV000776736 SCV000912377 uncertain significance Hereditary cancer-predisposing syndrome 2023-12-04 criteria provided, single submitter clinical testing This missense variant replaces alanine with serine at codon 2119 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 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.
Invitae RCV003768407 SCV001515469 uncertain significance Familial adenomatous polyposis 1 2020-03-18 criteria provided, single submitter clinical testing 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 C0"). This variant has not been reported in the literature in individuals with APC-related conditions. ClinVar contains an entry for this variant (Variation ID: 630743). This variant is not present in population databases (ExAC no frequency). This sequence change replaces alanine with serine at codon 2119 of the APC protein (p.Ala2119Ser). The alanine residue is highly conserved and there is a moderate physicochemical difference between alanine and serine.
Ambry Genetics RCV000776736 SCV002661411 uncertain significance Hereditary cancer-predisposing syndrome 2022-04-19 criteria provided, single submitter clinical testing The p.A2119S variant (also known as c.6355G>T), located in coding exon 15 of the APC gene, results from a G to T substitution at nucleotide position 6355. The alanine at codon 2119 is replaced by serine, an amino acid with similar properties. This amino acid position is conserved. In addition, in silico predictors for this gene do not accurately predict pathogenicity. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

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