ClinVar Miner

Submissions for variant NM_000642.3(AGL):c.4529dup (p.Tyr1510Ter) (rs387906244)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000169573 SCV000221073 likely pathogenic Glycogen storage disease type III 2015-01-23 criteria provided, single submitter literature only
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000001152 SCV000697534 pathogenic Glycogen storage disease IIIa 2017-01-06 criteria provided, single submitter clinical testing Variant summary: The AGL c.4529dupA (p.Tyr1510X) 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. The variant of interest was observed in the large, broad control population, ExAC, with an allele frequency of 2/121034 (1/60517), which does not exceed the estimated maximal expected allele frequency for a pathogenic AGL variant of 1/438. Multiple publications have cited the variant in affected individuals, who were homozygous and compound heterozygous. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as likely pathogenic/pathogenic. Taken together, this variant is classified as pathogenic.
Invitae RCV000169573 SCV000752145 pathogenic Glycogen storage disease type III 2018-10-08 criteria provided, single submitter clinical testing This sequence change results in a premature translational stop signal in the AGL gene (p.Tyr1510*). While this is not anticipated to result in nonsense mediated decay, it is expected to delete the last 23 amino acids of the AGL protein. This variant is present in population databases (rs756759628, ExAC 0.003%). This variant has been reported in the homozygous and compound heterozygous state in several individuals affected with glycogen storage disease type III (PMID: 8990006, 23430490, 20071996, 20490926). ClinVar contains an entry for this variant (Variation ID: 1094). For these reasons, this variant has been classified as Pathogenic.
Ambry Genetics RCV001265666 SCV001443833 pathogenic Inborn genetic diseases 2016-03-01 criteria provided, single submitter clinical testing
OMIM RCV000001152 SCV000021302 pathogenic Glycogen storage disease IIIa 1997-01-01 no assertion criteria provided literature only
Natera, Inc. RCV000169573 SCV001460668 pathogenic Glycogen storage disease type III 2020-09-16 no assertion criteria provided clinical testing

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