ClinVar Miner

Submissions for variant NM_000642.3(AGL):c.1783C>T (p.Arg595Ter)

gnomAD frequency: 0.00001  dbSNP: rs765367405
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000805441 SCV000945397 pathogenic Glycogen storage disease type III 2022-09-03 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg595*) in the AGL gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in AGL are known to be pathogenic (PMID: 19299494). This variant is present in population databases (rs765367405, gnomAD 0.002%). This premature translational stop signal has been observed in individuals with glycogen storage disease (PMID: 19834502, 25388549). ClinVar contains an entry for this variant (Variation ID: 650313). For these reasons, this variant has been classified as Pathogenic.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000805441 SCV001426804 pathogenic Glycogen storage disease type III 2020-07-20 criteria provided, single submitter clinical testing Variant summary: AGL c.1783C>T (p.Arg595X) 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. Truncations downstream of this position have been classified as pathogenic by our laboratory. The variant allele was found at a frequency of 8e-06 in 251218 control chromosomes (gnomAD). c.1783C>T has been reported in the literature in compound heterozygous or homozygous state in individuals affected with Glycogen Storage Disease Type III (Aoyama_2009, Goldstein_2010, Decostre_2017). These data indicate that the variant is likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. One ClinVar submitter (evaluation after 2014) cites the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.
Genome-Nilou Lab RCV000805441 SCV002055482 pathogenic Glycogen storage disease type III 2021-07-15 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV000805441 SCV002813259 pathogenic Glycogen storage disease type III 2021-10-15 criteria provided, single submitter clinical testing
Baylor Genetics RCV000805441 SCV004190895 pathogenic Glycogen storage disease type III 2023-02-08 criteria provided, single submitter clinical testing
Natera, Inc. RCV000805441 SCV002091513 pathogenic Glycogen storage disease type III 2020-08-12 no assertion criteria provided clinical testing

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