ClinVar Miner

Submissions for variant NM_000314.8(PTEN):c.7G>A (p.Ala3Thr)

dbSNP: rs1589596120
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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 RCV001027042 SCV001189541 uncertain significance Hereditary cancer-predisposing syndrome 2019-07-09 criteria provided, single submitter clinical testing The p.A3T variant (also known as c.7G>A), located in coding exon 1 of the PTEN gene, results from a G to A substitution at nucleotide position 7. The alanine at codon 3 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.
Invitae RCV001862394 SCV002188312 uncertain significance PTEN hamartoma tumor syndrome 2021-02-17 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: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available"). This variant has not been reported in the literature in individuals with PTEN-related conditions. ClinVar contains an entry for this variant (Variation ID: 827381). This variant is not present in population databases (ExAC no frequency). This sequence change replaces alanine with threonine at codon 3 of the PTEN protein (p.Ala3Thr). The alanine residue is moderately conserved and there is a small physicochemical difference between alanine and threonine.
Color Diagnostics, LLC DBA Color Health RCV001027042 SCV004359778 uncertain significance Hereditary cancer-predisposing syndrome 2023-12-11 criteria provided, single submitter clinical testing This missense variant replaces alanine with threonine at codon 3 of the PTEN protein. To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with PTEN-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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