ClinVar Miner

Submissions for variant NM_000314.7(PTEN):c.132C>T (p.Gly44=) (rs150651961)

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Total submissions: 14
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000078606 SCV000604970 benign not specified 2016-09-22 criteria provided, single submitter clinical testing
Ambry Genetics RCV000162387 SCV000212700 likely benign Hereditary cancer-predisposing syndrome 2014-06-12 criteria provided, single submitter clinical testing
CeGaT Praxis fuer Humangenetik Tuebingen RCV000512721 SCV000608560 likely benign not provided 2017-05-31 criteria provided, single submitter clinical testing
ClinGen PTEN Variant Curation Expert Panel RCV000123045 SCV000840470 likely benign PTEN hamartoma tumor syndrome 2016-11-09 reviewed by expert panel curation PTEN c.132C>T (p.G44=) 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 0.167 (1.67%, 463/276,792 alleles) in the gnomAD cohort. (PMID 27535533) 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) SCV000212700.3) BP5: Variant found in multiple cases with alternate molecular basis for disease. (Internal laboratory contributor(s) SCV000212700.3) BP7: Variant is synonymous (silent), nucleotide is not conserved, and no splicing impact is predicted.
Color RCV000162387 SCV000686277 likely benign Hereditary cancer-predisposing syndrome 2015-04-27 criteria provided, single submitter clinical testing
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000078606 SCV000110462 benign not specified 2013-10-21 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000123045 SCV000365736 likely benign PTEN hamartoma tumor syndrome 2016-06-14 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000512721 SCV000696530 benign not provided 2016-01-25 criteria provided, single submitter clinical testing Variant summary: The c.132C>T variant affects a non-conserved nucleotide, resulting in no amino acid change. One in-silico tool predicts damaging outcome for this variant. 3/5 programs in Alamut predict that this variant may create a novel 5' splicing donnor site. ESE finder predicts that this variant may affect ESE site of SRp55. However, these predictions are not confirmed by experimental studies. This variant is found in 190/121096 control chromosomes (1 homozygote) at a frequency of 0.001569. These alleles are unlikely from the PTEN pseudogene based on the sequence homology analysis and homozygous occurrences. This frequency is about 282 times of maximal expected frequency of a pathogenic allele (0.0000056), suggesting this variant is benign. In addition, multiple clinical laboratories classified this variant as benign/likely benign. Taken together, this variant was classified as benign.
Invitae RCV000123045 SCV000166340 benign PTEN hamartoma tumor syndrome 2018-01-15 criteria provided, single submitter clinical testing
Mayo Clinic Genetic Testing Laboratories,Mayo Clinic RCV000078606 SCV000692003 likely benign not specified no assertion criteria provided clinical testing
PreventionGenetics RCV000078606 SCV000806055 benign not specified 2016-05-25 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000078606 SCV000602114 likely benign not specified 2017-01-04 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000512721 SCV000888588 benign not provided 2018-03-02 criteria provided, single submitter clinical testing
True Health Diagnostics RCV000162387 SCV000788197 likely benign Hereditary cancer-predisposing syndrome 2017-09-29 no assertion criteria provided clinical testing

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