ClinVar Miner

Submissions for variant NM_000642.3(AGL):c.100C>T (p.Arg34Ter) (rs781580050)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000169056 SCV000220217 likely pathogenic Glycogen storage disease type III 2014-04-04 criteria provided, single submitter literature only
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000169056 SCV000918403 pathogenic Glycogen storage disease type III 2018-06-15 criteria provided, single submitter clinical testing Variant summary: AGL c.100C>T (p.Arg34X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. The variant allele was found at a frequency of 2.8e-05 in 246030 control chromosomes (gnomAD). The variant, c.100C>T, has been reported in the literature in multiple compound heterozygote and homozygote individuals affected with Glycogen Storage Disease Type III (Goldstein_2010, Horinishi_2002, Lu_2016, Lucchiari_2002, Wu_2013). These individuals also showed no AGL activity (Goldstein_2010, Lucchiari_2002). These data indicate that the variant is very likely to be associated with disease. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as pathogenic.
Invitae RCV000169056 SCV000951932 pathogenic Glycogen storage disease type III 2018-10-16 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg34*) in the AGL gene. It is expected to result in an absent or disrupted protein product. This variant is present in population databases (rs781580050, ExAC 0.006%). This variant has been observed in several individuals affected with glycogen storage disease type III (PMID: 11977176, 24495762, 11924557). ClinVar contains an entry for this variant (Variation ID: 188743). Loss-of-function variants in AGL are known to be pathogenic (PMID: 19299494). For these reasons, this variant has been classified as Pathogenic.
Centogene AG - the Rare Disease Company RCV000169056 SCV001424353 pathogenic Glycogen storage disease type III criteria provided, single submitter clinical testing

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