ClinVar Miner

Submissions for variant NM_000642.3(AGL):c.4422del (p.Ala1475fs)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV001193899 SCV001363065 likely pathogenic Glycogen storage disease type III 2019-09-16 criteria provided, single submitter clinical testing Variant summary: AGL c.4422delT (p.Ala1475GlnfsX4) 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. A truncation downstream of this position has been classified as pathogenic by our laboratory. The variant allele was found at a frequency of 4e-06 in 250766 control chromosomes (gnomAD). c.4422delT has been reported in the literature in an individual affected with Glycogen Storage Disease Type III (Goldstein_2010). To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. 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 likely pathogenic.
Invitae RCV001193899 SCV001392685 pathogenic Glycogen storage disease type III 2020-10-08 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Ala1475Glnfs*4) in the AGL gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has been observed in individual(s) with clinical features of glycogen storage disease type III (PMID: 20648714). ClinVar contains an entry for this variant (Variation ID: 929046). Loss-of-function variants in AGL are known to be pathogenic (PMID: 19299494). For these reasons, this variant has been classified as Pathogenic.

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