ClinVar Miner

Submissions for variant NM_000314.8(PTEN):c.235G>A (p.Ala79Thr) (rs202004587)

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Total submissions: 15
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen PTEN Variant Curation Expert Panel RCV000123046 SCV000840467 likely benign PTEN hamartoma tumor syndrome 2018-04-06 reviewed by expert panel curation PTEN c.235G>A (p.A79T) meets criteria to be classified as likely benign for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (Mester et al. 2018; manuscript in preparation). Please see a summary of the rules and criteria codes in the 'PTEN ACMG Specifications Summary' document (assertion method column). BS1: Allele frequency of 0.0045 (0.45%, 9/1984 alleles) in the GME variome. (PMID 27428751) BS2_P: Meets criteria for BS2 (observed in the homozygous state in at least one healthy or PHTS-unaffected individual) but BS1 is also applied. (Internal laboratory contributor(s) SCV000222198.12) PP2: PTEN is defined by the PTEN Expert Panel as a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease.
Invitae RCV000123046 SCV000166341 benign PTEN hamartoma tumor syndrome 2019-12-20 criteria provided, single submitter clinical testing
Ambry Genetics RCV000129085 SCV000183790 likely benign Hereditary cancer-predisposing syndrome 2019-01-11 criteria provided, single submitter clinical testing In silico models in agreement (benign);Other data supporting benign classification
GeneDx RCV000034594 SCV000222198 likely benign not provided 2018-07-18 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Division of Genomic Diagnostics,The Children's Hospital of Philadelphia RCV000123046 SCV000257666 uncertain significance PTEN hamartoma tumor syndrome 2015-07-10 criteria provided, single submitter clinical testing
Counsyl RCV000409443 SCV000487786 uncertain significance Cowden syndrome 1 2015-11-17 criteria provided, single submitter clinical testing
Fulgent Genetics,Fulgent Genetics RCV000515193 SCV000611427 uncertain significance Endometrial carcinoma; Macrocephaly/autism syndrome; Meningioma, familial; Squamous cell carcinoma of the head and neck; Bannayan-Riley-Ruvalcaba syndrome; Malignant tumor of prostate; Follicular thyroid carcinoma; VACTERL association with hydrocephalus; Glioma susceptibility 2; Cowden syndrome 1; Cutaneous malignant melanoma 1 2017-05-23 criteria provided, single submitter clinical testing
Genomic Research Center, Shahid Beheshti University of Medical Sciences RCV000626250 SCV000746903 uncertain significance Macrocephaly/autism syndrome 2017-12-18 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000034594 SCV000806056 uncertain significance not provided 2014-09-18 criteria provided, single submitter clinical testing
GeneKor MSA RCV000129085 SCV000822140 uncertain significance Hereditary cancer-predisposing syndrome 2018-08-01 criteria provided, single submitter clinical testing
Mendelics RCV000123046 SCV000838417 uncertain significance PTEN hamartoma tumor syndrome 2018-07-02 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000034594 SCV000888591 likely benign not provided 2019-04-16 criteria provided, single submitter clinical testing
Color RCV000129085 SCV000902713 likely benign Hereditary cancer-predisposing syndrome 2016-04-11 criteria provided, single submitter clinical testing
Biesecker Lab/Clinical Genomics Section,National Institutes of Health RCV000034594 SCV000043462 variant of unknown significance not provided 2012-07-13 no assertion criteria provided research Converted during submission to Uncertain significance.
AlTemaimi Lab, Faculty of Medicine,Kuwait University RCV000409443 SCV000577862 pathogenic Cowden syndrome 1 2017-05-19 no assertion criteria provided clinical testing CMT panel and gene duplication assays were negative and investigative exome sequencing was conducted. Clinical presentation is 80% match with Cowden Syndrome (exception unilateral pes cavus).

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