ClinVar Miner

Submissions for variant NM_000642.3(AGL):c.3554del (p.Thr1185fs)

gnomAD frequency: 0.00001  dbSNP: rs764318570
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000409329 SCV000486321 likely pathogenic Glycogen storage disease type III 2016-05-11 criteria provided, single submitter clinical testing
Invitae RCV000409329 SCV000835741 pathogenic Glycogen storage disease type III 2023-09-17 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 370894). This premature translational stop signal has been observed in individual(s) with AGL-related conditions (PMID: 20648714). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Thr1185Lysfs*42) 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).
Genome-Nilou Lab RCV000409329 SCV002055499 pathogenic Glycogen storage disease type III 2021-07-15 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000409329 SCV002511558 pathogenic Glycogen storage disease type III 2022-04-06 criteria provided, single submitter clinical testing Variant summary: AGL c.3554delC (p.Thr1185LysfsX42) 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 was absent in 251464 control chromosomes (gnomAD). c.3554delC has been reported in the literature in individuals affected with Glycogen Storage Disease Type III (Goldstein_2010, Sentner_2016, Decostre_2016), including one verified occurrence in trans with a pathogenic nonsense variant (Decostre_2016). 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. Three ClinVar submitters have assessed the variant since 2014: one classified the variant as likely pathogenic and two as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

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