ClinVar Miner

Submissions for variant NM_000314.7(PTEN):c.1061C>T (p.Pro354Leu) (rs375709098)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen PTEN Variant Curation Expert Panel RCV000469633 SCV000930118 uncertain significance PTEN hamartoma tumor syndrome 2019-06-25 reviewed by expert panel curation PTEN c.1061C>T (p.Pro354Leu) is currently classified as a variant of uncertain significance 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). PM2: Present at extremely low (<0.00001, 0.001%) allele frequency in the gnomAD cohort. (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. BS3_P: In vitro or in vivo functional study or studies showing no damaging effect on protein function but BS3 not met. (PMID 29706350)
Ambry Genetics RCV000131204 SCV000186154 uncertain significance Hereditary cancer-predisposing syndrome 2013-03-20 criteria provided, single submitter clinical testing Lines of evidence used in support of classification: Insufficient or conflicting evidence
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000180490 SCV000232944 uncertain significance not provided 2015-04-18 criteria provided, single submitter clinical testing
Invitae RCV000469633 SCV000541591 uncertain significance PTEN hamartoma tumor syndrome 2018-03-06 criteria provided, single submitter clinical testing This sequence change replaces proline with leucine at codon 354 of the PTEN protein (p.Pro354Leu). The proline residue is moderately conserved and there is a moderate physicochemical difference between proline and leucine. This variant is present in population databases (rs375709098, ExAC 0.01%). This variant has been reported in an individual affected with glioblastoma (PMID: 21869887). ClinVar contains an entry for this variant (Variation ID: 142212). Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). 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.
Color RCV000131204 SCV000691139 uncertain significance Hereditary cancer-predisposing syndrome 2018-07-25 criteria provided, single submitter clinical testing
Counsyl RCV000662697 SCV000785430 uncertain significance Cowden syndrome 1 2017-08-04 criteria provided, single submitter clinical testing

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