ClinVar Miner

Submissions for variant NM_001304717.5(PTEN):c.1012+1del (rs1564830522)

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Total submissions: 1
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000700203 SCV000828950 pathogenic PTEN hamartoma tumor syndrome 2018-11-08 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 5 of the PTEN gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has been observed in a family affected with Cowden syndrome (PMID: 11918710). This variant is also known as c.492delG or IVS5+1delG in the literature. ClinVar contains an entry for this variant (Variation ID: 577445). Donor and acceptor splice site variants typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in PTEN are known to be pathogenic (PMID: 9467011, 21194675). Different variants affecting this donor splice site (c.492+1G>T, c.492+2T>C, c.492+2delT) have also been reported in individuals affected with Cowden syndrome, juvenile polyposis, and PTEN hamartoma tumor syndrome, and determined to be pathogenic (PMID: 28677221, 9425889, 24345843, 21659347). This suggests that other variants affecting this splice site may also be pathogenic. For these reasons, this variant has been classified as Pathogenic.

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