Submissions for variant NM_000642.3(AGL):c.1437C>A (p.Tyr479Ter)

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Minimum conflict level: Report conflict between different conditions
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Total submissions: 4

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Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Labcorp Genetics (formerly Invitae), Labcorp	RCV000631125	SCV000752120	pathogenic	Glycogen storage disease type III	2024-04-08	criteria provided, single submitter	clinical testing	This sequence change creates a premature translational stop signal (p.Tyr479*) in the AGL gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in AGL are known to be pathogenic (PMID: 19299494). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with AGL-related conditions. ClinVar contains an entry for this variant (Variation ID: 526564). For these reasons, this variant has been classified as Pathogenic.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000631125	SCV002572354	likely pathogenic	Glycogen storage disease type III	2022-08-26	criteria provided, single submitter	clinical testing	Variant summary: AGL c.1437C>A (p.Tyr479X) 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 was absent in 251230 control chromosomes. To our knowledge, no occurrence of c.1437C>A in individuals affected with Glycogen Storage Disease Type III and no experimental evidence demonstrating its impact on protein function have been reported. One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar and classified it as pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic.
Genome-Nilou Lab	RCV000631125	SCV004049963	likely pathogenic	Glycogen storage disease type III	2023-04-11	criteria provided, single submitter	clinical testing
Baylor Genetics	RCV000631125	SCV004193334	pathogenic	Glycogen storage disease type III	2022-11-24	criteria provided, single submitter	clinical testing

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