ClinVar Miner

Submissions for variant NM_000038.6(APC):c.989T>C (p.Met330Thr)

gnomAD frequency: 0.00001  dbSNP: rs1554079959
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV003535953 SCV000944905 uncertain significance Familial adenomatous polyposis 1 2018-11-10 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: "Benign"; Align-GVGD: "Class C65"). This variant has not been reported in the literature in individuals with APC-related disease. This variant is not present in population databases (ExAC no frequency). This sequence change replaces methionine with threonine at codon 330 of the APC protein (p.Met330Thr). The methionine residue is highly conserved and there is a moderate physicochemical difference between methionine and threonine.
Ambry Genetics RCV001019870 SCV001181281 uncertain significance Hereditary cancer-predisposing syndrome 2021-11-03 criteria provided, single submitter clinical testing The p.M330T variant (also known as c.989T>C), located in coding exon 9 of the APC gene, results from a T to C substitution at nucleotide position 989. The methionine at codon 330 is replaced by threonine, an amino acid with similar properties. This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Color Diagnostics, LLC DBA Color Health RCV001019870 SCV001349745 uncertain significance Hereditary cancer-predisposing syndrome 2019-12-31 criteria provided, single submitter clinical testing This missense variant replaces methionine with threonine at codon 330 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.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV002298779 SCV002599059 uncertain significance not specified 2022-09-04 criteria provided, single submitter clinical testing

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