ClinVar Miner

Submissions for variant NM_001304718.2(PTEN):c.-420T>C (rs398123321)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen PTEN Variant Curation Expert Panel RCV000758231 SCV000886868 likely pathogenic PTEN hamartoma tumor syndrome 2018-11-28 reviewed by expert panel curation PTEN c.331T>C (p.W111R) meets criteria to be classified as likely pathogenic for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (PMID 30311380). Please see a summary of the rules and criteria codes in the "PTEN ACMG Specifications Summary" document (assertion method column). PS3: Phosphatase activity <50% of wild type (PMID 29785012, 29706350) PM2: Absent in large sequenced populations (PMID 27535533). PP2: PTEN is defined by the PTEN Expert Panel as a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease.
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000078613 SCV000110469 likely pathogenic not provided 2012-07-25 criteria provided, single submitter clinical testing
Invitae RCV000758231 SCV001225621 uncertain significance PTEN hamartoma tumor syndrome 2020-10-28 criteria provided, single submitter clinical testing This sequence change replaces tryptophan with arginine at codon 111 of the PTEN protein (p.Trp111Arg). The tryptophan residue is highly conserved and there is a moderate physicochemical difference between tryptophan and arginine. This variant is not present in population databases (ExAC no frequency). This variant has been observed in an individual affected with Proteus syndrome (PMID: 11476841). ClinVar contains an entry for this variant (Variation ID: 92820). This variant has been reported to affect PTEN protein function (PMID: 29706350, 29785012). 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.

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