ClinVar Miner

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

gnomAD frequency: 0.00003  dbSNP: rs387906244
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Total submissions: 11
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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.
Labcorp Genetics (formerly Invitae), Labcorp RCV000169573 SCV000752145 pathogenic Glycogen storage disease type III 2024-12-18 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Tyr1510*) in the AGL gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 23 amino acid(s) of the AGL protein. This variant is present in population databases (rs756759628, gnomAD 0.004%). This premature translational stop signal has been observed in individuals with glycogen storage disease type III (PMID: 8990006, 20071996, 20490926, 23430490). ClinVar contains an entry for this variant (Variation ID: 1094). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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
Genome-Nilou Lab RCV000169573 SCV002055514 pathogenic Glycogen storage disease type III 2021-07-15 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV000169573 SCV002811460 likely pathogenic Glycogen storage disease type III 2021-07-12 criteria provided, single submitter clinical testing
Revvity Omics, Revvity RCV000169573 SCV003816708 pathogenic Glycogen storage disease type III 2022-01-13 criteria provided, single submitter clinical testing
Baylor Genetics RCV000169573 SCV004212970 pathogenic Glycogen storage disease type III 2024-01-24 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
GeneReviews RCV000169573 SCV002072438 not provided Glycogen storage disease type III no assertion provided literature only Associated with more severe phenotype

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