ClinVar Miner

Submissions for variant NM_000642.3(AGL):c.3652C>T (p.Arg1218Ter)

gnomAD frequency: 0.00003  dbSNP: rs771853367
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000553978 SCV000626733 pathogenic Glycogen storage disease type III 2023-08-29 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg1218*) 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 (rs771853367, gnomAD 0.003%). This premature translational stop signal has been observed in individual(s) with glycogen storage disease type III (PMID: 11977176). ClinVar contains an entry for this variant (Variation ID: 456492). 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.
Eurofins Ntd Llc (ga) RCV000730413 SCV000858146 pathogenic not provided 2017-11-20 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000553978 SCV002055501 pathogenic Glycogen storage disease type III 2021-07-15 criteria provided, single submitter clinical testing
Neuberg Supratech Reference Laboratories Pvt Ltd, Neuberg Centre for Genomic Medicine RCV000553978 SCV004047136 pathogenic Glycogen storage disease type III criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal at codon 1218 (p.Arg1218*) of 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. This particular variant has been reported in individuals affected with glycogen storage disease type III (Lucchiari S et al). This variant has been reported to the ClinVar database as Pathogenic. The nucleotide change in AGL is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. The variant is reported in gnomAD with the allele frequency of 0.00001064 and is novel (not in any individuals) in 1000 Genomes. For these reasons, this variant has been classified as Pathogenic.
Counsyl RCV000553978 SCV000794122 pathogenic Glycogen storage disease type III 2017-09-14 no assertion criteria provided clinical testing
Natera, Inc. RCV000553978 SCV002094550 pathogenic Glycogen storage disease type III 2020-08-10 no assertion criteria provided clinical testing

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