ClinVar Miner

Submissions for variant NM_000314.4(PTEN):c.-920G>A (rs786204937)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000590720 SCV000222211 uncertain significance not provided 2018-06-07 criteria provided, single submitter clinical testing This variant is denoted PTEN c.-921G>A, and describes a nucleotide substitution 921 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 GCCG[G/A]CGGG. This variant, also called c.-920G>A using alternate numbering, has not been published in the literature to our knowledge; however, a different variant at the same position, published as c.-920G>T, was observed in a patient with features of Cowden syndrome and was reported to alter a putative Sp1 transcription factor–binding site (Zhou 2003). Based on currently available information, it is unclear whether PTEN c.-921G>A is a pathogenic or benign variant. We consider it to be a variant of uncertain significance.
Integrated Genetics/Laboratory Corporation of America RCV000590720 SCV000696550 uncertain significance not provided 2016-10-28 criteria provided, single submitter clinical testing Variant summary: The PTEN variant c.-920G>A (also known as c.-921G>A) involves the alteration of a conserved nucleotide located in the 5' UTR. One in silico tool predicts a damaging outcome for this variant. The frequency of the variant in the general population cannot be assessed as ExAC does not have coverage for 5' UTR variants. The variant of interest has not, to our knowledge, been reported in affected individuals via publications nor evaluated for functional impact by in vivo/vitro studies. One reputable clinical lab has classified the variant as a VUS. Because of the absence of clinical information and the lack of functional studies, the variant was classified as a variant of uncertain significance (VUS) until additional information becomes available.
Mendelics RCV000709127 SCV000838412 uncertain significance PTEN hamartoma tumor syndrome 2018-07-02 criteria provided, single submitter clinical testing

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