ClinVar Miner

Submissions for variant NM_000642.3(AGL):c.3216_3217del (p.Glu1072fs) (rs771069887)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000497957 SCV000589664 pathogenic not provided 2019-12-16 criteria provided, single submitter clinical testing Not observed at a significant frequency in large population cohorts (Lek et al., 2016); Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 27460348, 19754354, 20648714, 26885414, 23649758, 29809327, 22035446, 23507172, 25602008, 28888851, 31589614)
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000590818 SCV000697532 pathogenic Glycogen storage disease IIIa 2016-12-30 criteria provided, single submitter clinical testing Variant summary: The AGL c.3216_3217delGA (p.Glu1072Aspfs) variant results in a premature termination codon, predicted to cause a truncated or absent AGL protein due to nonsense mediated decay, which are commonly known mechanisms for disease. This variant was found in 1/121086 control chromosomes at a frequency of 0.0000083, which does not exceed the estimated maximal expected allele frequency of a pathogenic AGL variant (0.0022822). The variant was reported in numerous affected individuals and was shown to result in no AGL activity in peripheral leukocytes. Taken together, this variant is classified as pathogenic.
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000497957 SCV000701400 pathogenic not provided 2016-09-28 criteria provided, single submitter clinical testing
Invitae RCV000596959 SCV000834601 pathogenic Glycogen storage disease type III 2020-05-20 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Glu1072Aspfs*36) in the AGL gene. It is expected to result in an absent or disrupted protein product. This variant is present in population databases (rs771069887, ExAC 0.009%). This variant has been reported in several individuals affected with glycogen storage disease type III (PMID: 20648714, 22035446, 28888851). ClinVar contains an entry for this variant (Variation ID: 432008). Loss-of-function variants in AGL are known to be pathogenic (PMID: 19299494). For these reasons, this variant has been classified as Pathogenic.
Counsyl RCV000596959 SCV001132329 likely pathogenic Glycogen storage disease type III 2015-07-11 no assertion criteria provided clinical testing
Natera, Inc. RCV000596959 SCV001456540 pathogenic Glycogen storage disease type III 2020-09-16 no assertion criteria provided clinical testing

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