ClinVar Miner

Submissions for variant NM_000314.4(PTEN):c.-1242G>A (rs587779985)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000588504 SCV000149470 uncertain significance not provided 2018-02-15 criteria provided, single submitter clinical testing This variant is denoted PTEN c.-1243G>A, and describes a nucleotide substitution 1243 base pairs upstream of the ATG translational start site in the PTEN promoter region. The surrounding sequence, with the base that is substituted in brackets, is CTGG[G/A]CAGA. This variant, also called c.-1242G>A using alternate numbering, and other variants within the PTEN promoter have been observed in individuals with features of Cowden syndrome (Zhou 2003, Nizialek 2015). Based on currently available information, it is unclear whether PTEN c.-1243G>A is pathogenic or benign. We consider it to be a variant of uncertain significance.
Integrated Genetics/Laboratory Corporation of America RCV000588504 SCV000696529 uncertain significance not provided 2017-04-20 criteria provided, single submitter clinical testing Variant summary: The PTEN variant c.-1242G>A (also known as c.-1243G>A) is located in the 5' UTR at a non-conserved position, which one in silico tool predicts the variant to be a "polymorphism." However, this prediction has yet to be functionally assessed. The location of this variant is not evaluated in the large, broad control population, ExAC, therefore, it cannot be established as to whether this variant is observed in controls or not. In addition, the variant of interest has not, to our knowledge, been reported in publications. One reputable clinical lab has classified this variant as a VUS. Therefore, due to the limited available information (ie, lack of clinical and functional studies), the variant of interest has been classified as a "Variant of Uncertain Significance (VUS)."
Mendelics RCV000988407 SCV001138114 uncertain significance PTEN hamartoma tumor syndrome 2019-05-28 criteria provided, single submitter clinical testing

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