ClinVar Miner

Submissions for variant NM_000642.3(AGL):c.3816_3817del (p.Gly1273fs) (rs867341758)

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Total submissions: 4
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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 2018-07-06 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. This variant is not present in population databases (ExAC no frequency). This variant has been observed in combination with another AGL variant in an individual affected with glycogen storage disease type IIIa (PMID: 10982190). This variant is also known as 4216-4217delAG in the literature. ClinVar contains an entry for this variant (Variation ID: 371009). Loss-of-function variants in AGL are known to be pathogenic (PMID: 19299494). For these reasons, this variant has been classified as Pathogenic.
Illumina Clinical Services Laboratory,Illumina RCV000410186 SCV000914337 uncertain significance Glycogen storage disease type III 2019-01-09 criteria provided, single submitter clinical testing The AGL c.3816_3817delAG (p.Gly1273AsnfsTer18) variant results in a frameshift and is predicted to result in premature termination of the protein. The p.Gly1273AsnfsTer18 variant, which is also known as c.4216_4217delAG in the literature, is reported in one study in which it is identified in two individuals with glycogen storage disease type III, in one in a compound heterozygous state in trans with a splice donor variant and in another in a heterozygous state with no second variant identified (Okubo et al. 2000). Control data are unavailable for this variant which is reported at a frequency of 0.000121 in the European American population of the Exome Sequencing Project but this is based on one allele in a region of good sequence coverage so the variant is presumed to be rare. Based on the limited evidence and the potential impact of frameshift variants, the p.Gly1273AsnfsTer18 variant is classified as a variant of unknown significance but suspicious for pathogenicity for glycogen storage disease type III. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.
Natera, Inc. RCV000410186 SCV001456549 pathogenic Glycogen storage disease type III 2020-09-16 no assertion criteria provided clinical testing

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