ClinVar Miner

Submissions for variant NM_000642.3(AGL):c.4353G>T (p.Trp1451Cys)

gnomAD frequency: 0.00001  dbSNP: rs775685508
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Neuberg Centre For Genomic Medicine, NCGM RCV000415279 SCV004048055 likely pathogenic Glycogen storage disease type III criteria provided, single submitter clinical testing The missense variant c.4353G>T (p.Trp1451Cys) in AGL gene has been reported in individuals affected with Glycogen storage disease type III (Perveen et al., 2020) and IEM (Alfadhel et al., 2016). This variant is reported with the allele frequency (0.001%) in the gnomAD and novel in 1000 genome database. It has been submitted to ClinVar with varying interpretations: Pathogenic/ Likely Pathogenic. The amino acid Trp at position 1451 is changed to a Cys changing protein sequence and it might alter its composition and physico-chemical properties. The amino acid change p.Trp1451Cys in AGL is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Likely Pathogenic.
Labcorp Genetics (formerly Invitae), Labcorp RCV000415279 SCV004291955 pathogenic Glycogen storage disease type III 2023-10-23 criteria provided, single submitter clinical testing This sequence change replaces tryptophan, which is neutral and slightly polar, with cysteine, which is neutral and slightly polar, at codon 1451 of the AGL protein (p.Trp1451Cys). This variant is present in population databases (rs775685508, gnomAD 0.01%). This missense change has been observed in individual(s) with glycogen storage disease (PMID: 27629047, 32222031). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 374339). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt AGL protein function with a positive predictive value of 80%. For these reasons, this variant has been classified as Pathogenic.
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center RCV000415279 SCV004806020 likely pathogenic Glycogen storage disease type III 2024-03-25 criteria provided, single submitter clinical testing
Baylor Genetics RCV000415279 SCV000328819 likely pathogenic Glycogen storage disease type III 2014-08-19 no assertion criteria provided clinical testing Our laboratory has reported dual molecular diagnoses in AGL (NM_000028.2, c.4353G>T) and PCCA (NM_000282.3, c.425G>A) in this individual who has reported features of delayed motor milestones, delayed speech, hypotonia, short stature, failure to thrive, hepatomegaly, and elevated liver enzymes.
Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City RCV000415279 SCV001190751 pathogenic Glycogen storage disease type III 2020-02-05 no assertion criteria provided clinical testing

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