ClinVar Miner

Submissions for variant NM_000642.3(AGL):c.3965del (p.Val1322fs) (rs113994132)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000723821 SCV000229304 pathogenic not provided 2014-06-13 criteria provided, single submitter clinical testing
Invitae RCV000020378 SCV000752138 pathogenic Glycogen storage disease type III 2020-08-07 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Val1322Alafs*27) in the AGL gene. It is expected to result in an absent or disrupted protein product. This variant is present in population databases (rs113994132, ExAC 0.002%). This variant has been reported as homozygous in an individual affected with glycogen storage disease type III (PMID: 10655153). ClinVar contains an entry for this variant (Variation ID: 1103). Loss-of-function variants in AGL are known to be pathogenic (PMID: 19299494). For these reasons, this variant has been classified as Pathogenic.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000020378 SCV001363061 pathogenic Glycogen storage disease type III 2019-09-23 criteria provided, single submitter clinical testing Variant summary: AGL c.3965delT (p.Val1322AlafsX27, also known as c.3964delT) 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 250742 control chromosomes (gnomAD). c.3965delT has been reported in the literature in multiple individuals affected with Glycogen Storage Disease Type III (Shaiu_2000). These data indicate that the variant is very likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. A ClinVar submission (evaluation after 2014) cite the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.
OMIM RCV000001162 SCV000021312 pathogenic Glycogen storage disease IIIa 2000-01-01 no assertion criteria provided literature only
GeneReviews RCV000020378 SCV000040766 pathologic Glycogen storage disease type III 2012-09-06 no assertion criteria provided curation Converted during submission to Pathogenic.
Natera, Inc. RCV000020378 SCV001456553 pathogenic Glycogen storage disease type III 2020-09-16 no assertion criteria provided clinical testing

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