ClinVar Miner

Submissions for variant NM_000152.5(GAA):c.1920T>G (p.Pro640=) (rs144090460)

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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
PreventionGenetics,PreventionGenetics RCV000243841 SCV000302671 likely benign not specified criteria provided, single submitter clinical testing
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000675235 SCV000337540 uncertain significance not provided 2015-11-11 criteria provided, single submitter clinical testing
GeneDx RCV000243841 SCV000721670 likely benign not specified 2017-08-18 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.
Invitae RCV001079385 SCV000752097 likely benign Glycogen storage disease, type II 2020-11-17 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV001079385 SCV001287879 uncertain significance Glycogen storage disease, type II 2017-04-28 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
CeGaT Praxis fuer Humangenetik Tuebingen RCV000675235 SCV001502247 likely benign not provided 2021-01-01 criteria provided, single submitter clinical testing
Mayo Clinic Laboratories, Mayo Clinic RCV000675235 SCV000800881 likely benign not provided 2017-05-10 no assertion criteria provided clinical testing
Broad Institute Rare Disease Group, Broad Institute RCV001079385 SCV001423081 uncertain significance Glycogen storage disease, type II 2020-01-22 no assertion criteria provided curation The c.1920T>G (p.Pro640=) variant in GAA has not been reported in individuals with Glycogen Storage Disease II but has been reported in 2 European individuals with unexplained limb-girdle muscle weakness (PMID: 29149851). This variant has also been reported likely benign (by GeneDx, PreventionGenetics, Mayo Clinic Genetic Testing Laboratories, and Invitae) and as a VUS by EGL in ClinVar (Variation ID: 255358). This variant has been identified in 0.09150% (18/19672) of East Asian chromosomes, 0.04553% (11/24162) of European (Finnish) chromosomes, and 0.01683% (21/124752) of European (non-Finnish) chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs144090460). Although this variant has been seen in the general population, its frequency is low enough to be consistent with a recessive carrier frequency. Computational prediction tools and conservation analyses suggest that this variant may not impact the protein, though this information is not predictive enough to rule out pathogenicity. However, novel synonymous variants supported by computational evidence without raised suspicion for an impact are likely benign (Richards 2015). In summary, although additional studies are required to fully establish its clinical significance, this variant is likely benign. ACMG/AMP Criteria applied: PM2, BP4, BP7 (Richards 2015).

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