ClinVar Miner

Submissions for variant NM_000314.7(PTEN):c.1A>G (p.Met1Val) (rs1554890324)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000572416 SCV000671706 uncertain significance Hereditary cancer-predisposing syndrome 2017-06-08 criteria provided, single submitter clinical testing Lines of evidence used in support of classification: Insufficient evidence
Invitae RCV000706088 SCV000835120 likely pathogenic PTEN hamartoma tumor syndrome 2018-06-22 criteria provided, single submitter clinical testing This sequence change affects the initiator methionine of the PTEN mRNA. The next in-frame methionine is located at codon 35. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with PTEN-related disease. ClinVar contains an entry for this variant (Variation ID: 484600). A different substitution at this codon (c.3G>T) has been reported in individuals affected with PTEN-related disease (PMID: 23695273, 25669429). A missense variant (p.Asp24Gly) located upstream of the next in-frame methionine has been determined to be pathogenic (PMID: 21194675, 22503188, 24498881, Invitae). This indicates that the N-terminal region is critical for PTEN protein function. 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.

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