ClinVar Miner

Submissions for variant NM_000642.3(AGL):c.3816_3817del (p.Gly1273fs)

dbSNP: rs867341758
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000410186 SCV000486462 likely pathogenic Glycogen storage disease type III 2016-06-03 criteria provided, single submitter clinical testing
Invitae RCV000410186 SCV000834220 pathogenic Glycogen storage disease type III 2023-10-11 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Gly1273Asnfs*18) 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 premature translational stop signal has been observed in individual(s) with glycogen storage disease type III (PMID: 10982190, 31028654). This variant is also known as 4216-4217delAG or 3814_3815delAG. ClinVar contains an entry for this variant (Variation ID: 371009). For these reasons, this variant has been classified as Pathogenic.
Genome-Nilou Lab RCV000410186 SCV002055549 likely pathogenic Glycogen storage disease type III 2021-07-15 criteria provided, single submitter clinical testing
Genetics and Molecular Pathology, SA Pathology RCV000410186 SCV004175272 pathogenic Glycogen storage disease type III 2022-10-27 criteria provided, single submitter clinical testing The AGL c.3816_3817del variant is classified as Pathogenic (PVS1, PS4_Moderate, PM2, PM3) The AGL c.3816_3817del variant is located in exon 28/34 and is predicted to cause a shift in the reading frame at codon 1273, resulting in the introduction of a premature stop codon 18bp downstream (PVS1). The variant has been reported in at least 3 probands with a clinical presentation of Glycogen Storage Disease III (PS4_Moderate). The variant is rare in population databases (PM2). This variant has been previously reported in trans with pathogenic variants for this recessive condition (Okubo et al, 2000 PubMed: 10982190; Laforet et al, 2019 PubMed: 31661040) (PM3). The variant has been reported in dbSNP (rs867341758) and in the HGMD database: CD000242. It has been reported as Pathogenic/Likely pathogenic by other diagnostic laboratories (ClinVar Variation ID: 371009).
Natera, Inc. RCV000410186 SCV001456549 pathogenic Glycogen storage disease type III 2020-09-16 no assertion criteria provided clinical testing

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