ClinVar Miner

Submissions for variant NM_000038.6(APC):c.1168A>G (p.Ile390Val)

gnomAD frequency: 0.00001  dbSNP: rs1060503345
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV002526458 SCV000552704 uncertain significance Familial adenomatous polyposis 1 2022-09-19 criteria provided, single submitter clinical testing This sequence change replaces isoleucine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 390 of the APC protein (p.Ile390Val). This variant is not present in population databases (gnomAD no frequency). 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: 411512). 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. 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 RCV000573761 SCV000667232 uncertain significance Hereditary cancer-predisposing syndrome 2021-12-02 criteria provided, single submitter clinical testing The p.I390V variant (also known as c.1168A>G), located in coding exon 9 of the APC gene, results from an A to G substitution at nucleotide position 1168. The isoleucine at codon 390 is replaced by valine, an amino acid with highly similar properties. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Baylor Genetics RCV002526458 SCV004195694 uncertain significance Familial adenomatous polyposis 1 2023-10-19 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV003477987 SCV004222493 uncertain significance not provided 2023-04-12 criteria provided, single submitter clinical testing To the best of our knowledge, the variant has not been reported in the published literature. The frequency of this variant in the general population, 0.0000066 (1/152190 chromosomes, http://gnomad.broadinstitute.org), is uninformative in assessment of its pathogenicity. Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded predictions that this variant is benign. Based on the available information, we are unable to determine the clinical significance of this variant.
Color Diagnostics, LLC DBA Color Health RCV000573761 SCV004361839 uncertain significance Hereditary cancer-predisposing syndrome 2022-11-21 criteria provided, single submitter clinical testing This missense variant replaces isoleucine with valine at codon 390 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.

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