ClinVar Miner

Submissions for variant NM_000314.8(PTEN):c.476G>A (p.Arg159Lys)

dbSNP: rs1114167673
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000800205 SCV000939905 likely pathogenic PTEN hamartoma tumor syndrome 2023-08-10 criteria provided, single submitter clinical testing In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. This variant disrupts the p.Arg159 amino acid residue in PTEN. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 17942903, 21194675, 31594918; Invitae). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. Experimental studies have shown that this missense change affects PTEN function (PMID: 30886105). Advanced modeling performed at Invitae incorporating data from internal and/or published experimental studies (Invitae) indicates that this missense variant is expected to disrupt PTEN function. ClinVar contains an entry for this variant (Variation ID: 646006). This missense change has been observed in individual(s) with clinical features of PTEN hamartoma tumor syndrome (PMID: 34184188). This variant is not present in population databases (gnomAD no frequency). This sequence change replaces arginine, which is basic and polar, with lysine, which is basic and polar, at codon 159 of the PTEN protein (p.Arg159Lys).
GeneDx RCV001766656 SCV002008417 pathogenic not provided 2021-08-20 criteria provided, single submitter clinical testing Published functional studies demonstrate a damaging effect: significantly reduced phosphatase activity, increased expression of pAKT (Mighell 2018, Feng 2019); Not observed in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 24475377, 15492994, 30886105, 29706350)
Laboratory of Virology, Oncology, Biosciences and Environment, Faculty of Sciences and Techniques, Mohammedia- University Hassan II of Casablanca RCV003483732 SCV004231923 uncertain significance Prostate cancer, hereditary, 1 2024-01-01 no assertion criteria provided clinical testing

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