ClinVar Miner

Submissions for variant NM_000314.8(PTEN):c.289C>T (p.Gln97Ter)

gnomAD frequency: 0.00001  dbSNP: rs786204928
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000169873 SCV000222202 pathogenic not provided 2016-08-09 criteria provided, single submitter clinical testing This pathogenic variant is denoted PTEN c.289C>T at the cDNA level and p.Gln97Ter (Q97X) at the protein level. The substitution creates a nonsense variant, which changes a Glutamine to a premature stop codon (CAG>TAG), and is predicted to cause loss of normal protein function through either protein truncation or nonsense-mediated mRNA decay. This variant has been reported in association with Cowden syndrome (Nelen 1999) and is considered pathogenic.
Labcorp Genetics (formerly Invitae), Labcorp RCV000645061 SCV000766801 pathogenic PTEN hamartoma tumor syndrome 2022-12-07 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Gln97*) in the PTEN gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PTEN are known to be pathogenic (PMID: 9467011, 21194675). For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 189483). This premature translational stop signal has been observed in individual(s) with Cowden syndrome (PMID: 10234502). This variant is present in population databases (rs786204928, gnomAD 0.01%).
Ambry Genetics RCV002433728 SCV002746795 pathogenic Hereditary cancer-predisposing syndrome 2022-10-13 criteria provided, single submitter clinical testing The p.Q97* variant (also known as c.289C>T), located in coding exon 5 of the PTEN gene, results from a C to T substitution at nucleotide position 289. This changes the amino acid from a glutamine to a stop codon within coding exon 5. In a massively parallel functional assay using a humanized yeast model, lipid phosphatase activity for this variant was functionally deficient (Mighell TL et al. Am J Hum Genet, 2018 05;102:943-955). This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation.

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