ClinVar Miner

Submissions for variant NM_000152.3(GAA):c.2065G>A (p.Glu689Lys) (rs1800309)

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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000078165 SCV000110003 benign not specified 2012-09-10 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000078165 SCV000302673 benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000383641 SCV000407290 benign Glycogen storage disease, type II 2018-03-06 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Phosphorus, Inc. RCV000383641 SCV000679831 benign Glycogen storage disease, type II 2017-08-01 criteria provided, single submitter clinical testing
Invitae RCV000383641 SCV000752099 other Glycogen storage disease, type II 2019-01-07 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000383641 SCV001158934 benign Glycogen storage disease, type II 2018-09-20 criteria provided, single submitter clinical testing
OMIM RCV000004245 SCV000024411 pathogenic Acid alpha-glucosidase, allele 4 1996-09-01 no assertion criteria provided literature only
Genetic Services Laboratory, University of Chicago RCV000078165 SCV000151253 likely benign not specified no assertion criteria provided clinical testing Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed.
Mayo Clinic Genetic Testing Laboratories,Mayo Clinic RCV000675237 SCV000800883 benign not provided 2015-12-16 no assertion criteria provided clinical testing
Broad Institute Rare Disease Group,Broad Institute RCV000383641 SCV001422940 benign Glycogen storage disease, type II 2020-01-22 no assertion criteria provided curation The p.Glu689Lys variant in GAA has been reported as a benign and likely benign variant for Glycogen Storage Disease II in ClinVar (Variation ID: 4030). This variant has been identified in 5.490% (13805/251476) of chromosomes, including 757 homozygotes, by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs1800309). This variant has been seen in the general population at a frequency high enough to rule out a pathogenic role. It is a known pseudodeficiency allele that causes false-positive results in GAA deficiency enzyme assays (PMID: 20080426, 18301443). In summary, this variant meets criteria to be classified as benign for Glycogen Storage Disease II in an autosomal recessive manner based on its frequency in the general population. ACMG/AMP Criteria applied: BA1 (Richards 2015).

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