ClinVar Miner

Submissions for variant NM_000314.7(PTEN):c.165-1G>A (rs786203847)

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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 RCV000710306 SCV000840484 likely pathogenic PTEN hamartoma tumor syndrome 2020-03-23 reviewed by expert panel curation PTEN c.165-1G>A (IVS2-1G>A) 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). PVS1: Null variant predicted to result in nonsense-mediated decay or causing truncation/frameshift at or 5' to c.1121 (NM_000314.4). PM2: Absent in large sequenced populations
Ambry Genetics RCV000167333 SCV000218184 pathogenic Hereditary cancer-predisposing syndrome 2018-01-25 criteria provided, single submitter clinical testing Detected in individual satisfying established diagnostic critera for classic disease without a clear mutation;Alterations at the canonical donor/acceptor sites (+/- 1, 2) without other strong (b-level) evidence supporting pathogenicity
GeneDx RCV000212879 SCV000222180 pathogenic not provided 2014-09-15 criteria provided, single submitter clinical testing This pathogenic variant is denoted PTEN c.165-1 G>A or IVS2-1 G>A and consists of a G>A nucleotide substitution at the -1 position of intron 2 of the PTEN gene. The variant destroys a canonical splice acceptor site and is predicted to cause abnormal gene splicing, leading to either an abnormal message that is subject to nonsense-mediated mRNA decay or to an abnormal protein product. This variant has been reported in a case meeting relaxed International Cowden Consortium operational criteria (Tan 2011). Thus, we consider this variant to be pathogenic.

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