ClinVar Miner

Submissions for variant NM_000314.8(PTEN):c.80-1_80del (rs1554893747)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000595358 SCV000700901 pathogenic not provided 2015-07-13 criteria provided, single submitter clinical testing
Mendelics RCV000988412 SCV001138123 pathogenic PTEN hamartoma tumor syndrome 2019-05-28 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV001260300 SCV001437222 uncertain significance not specified 2020-09-29 criteria provided, single submitter clinical testing Variant summary: PTEN c.80-1_80delGA is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Though computational tools were not able to predict an impact on splicing for this variant, it is still possible that the variant can abolish the canonical splice acceptor site. However, this has yet to be confirmed by functional studies. The variant was absent in 250762 control chromosomes (gnomAD). To our knowledge, no occurrence of c.80-1_80delGA in individuals affected with Cowden Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. However, other variants affecting the same splice site were reported in affected individuals (in HGMD and ClinVar). Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic.

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