ClinVar Miner

Submissions for variant NM_000642.3(AGL):c.256C>T (p.Gln86Ter)

gnomAD frequency: 0.00014  dbSNP: rs193186112
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Total submissions: 11
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000724625 SCV000228908 pathogenic not provided 2015-03-11 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000177086 SCV000626700 pathogenic Glycogen storage disease type III 2024-11-23 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Gln86*) 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 present in population databases (rs193186112, gnomAD 0.07%). This premature translational stop signal has been observed in individuals with glycogen storage disease (PMID: 10655153, 20648714, 22899091). ClinVar contains an entry for this variant (Variation ID: 196286). For these reasons, this variant has been classified as Pathogenic.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000588509 SCV000697531 pathogenic Glycogen storage disease IIIa 2017-08-25 criteria provided, single submitter clinical testing Variant summary: The AGL c.256C>T (p.Gln86X) 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. Truncations downstream of this position have been classified as pathogenic by our laboratory (e.g. c.3216_3217delGA (p.Glu1072fsX36) and c.4529dupA (p.Tyr1510X)). This variant was found in 3/121018 control chromosomes at a frequency of 0.0000248, which does not exceed the estimated maximal expected allele frequency of a pathogenic AGL variant (0.0022822). Multiple publications have cited the variant in affected individuals. In addition, a clinical diagnostic laboratory classified this variant as pathogenic. Taken together, this variant is classified as pathogenic.
GeneDx RCV000724625 SCV000890327 likely pathogenic not provided 2020-02-02 criteria provided, single submitter clinical testing Nonsense 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: 25525159, 20648714, 22899091, 10655153, 31589614)
Fulgent Genetics, Fulgent Genetics RCV000177086 SCV000893164 pathogenic Glycogen storage disease type III 2022-04-06 criteria provided, single submitter clinical testing
Baylor Genetics RCV000177086 SCV001483008 pathogenic Glycogen storage disease type III 2024-02-21 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000177086 SCV002055465 pathogenic Glycogen storage disease type III 2021-07-15 criteria provided, single submitter clinical testing
AiLife Diagnostics, AiLife Diagnostics RCV000724625 SCV002501776 pathogenic not provided 2021-07-23 criteria provided, single submitter clinical testing
3billion, Medical Genetics RCV000177086 SCV002572519 pathogenic Glycogen storage disease type III 2022-09-01 criteria provided, single submitter clinical testing The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.007%). This stop-gained (nonsense) variant is predicted to result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant. The variant has been reported at least twice as pathogenic with clinical assertions and evidence for the classification (ClinVar ID: VCV000196286 / PMID: 10655153). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline.
Revvity Omics, Revvity RCV000177086 SCV003832506 likely pathogenic Glycogen storage disease type III 2022-05-20 criteria provided, single submitter clinical testing
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center RCV000177086 SCV004013290 likely pathogenic Glycogen storage disease type III 2023-06-13 criteria provided, single submitter clinical testing PVS1, PM2

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