ClinVar Miner

Submissions for variant NM_000038.6(APC):c.1219C>G (p.Leu407Val)

dbSNP: rs1554080075
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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 RCV000575850 SCV000667739 uncertain significance Hereditary cancer-predisposing syndrome 2022-12-09 criteria provided, single submitter clinical testing The p.L407V variant (also known as c.1219C>G), located in coding exon 9 of the APC gene, results from a C to G substitution at nucleotide position 1219. The leucine at codon 407 is replaced by valine, an amino acid with highly similar properties. This amino acid position is highly conserved in available vertebrate species. 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.
Color Diagnostics, LLC DBA Color Health RCV000575850 SCV000686810 uncertain significance Hereditary cancer-predisposing syndrome 2023-12-04 criteria provided, single submitter clinical testing This missense variant replaces leucine with valine at codon 407 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 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 RCV004562437 SCV001421844 uncertain significance Familial adenomatous polyposis 1 2019-10-08 criteria provided, single submitter clinical testing This variant is not present in population databases (ExAC no frequency). 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: 482471). This sequence change replaces leucine with valine at codon 407 of the APC protein (p.Leu407Val). The leucine residue is highly conserved and there is a small physicochemical difference between leucine and valine.

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