ClinVar Miner

Submissions for variant NM_000642.3(AGL):c.4259+5G>A

dbSNP: rs780504025
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Molecular Diagnostics Laboratory, M Health Fairview: University of Minnesota RCV000991301 SCV001142703 likely pathogenic Glycogen storage disease type III 2019-07-09 criteria provided, single submitter clinical testing
GeneDx RCV001558704 SCV001780708 likely pathogenic not provided 2019-11-08 criteria provided, single submitter clinical testing Intronic +5 splice site variant in a gene for which loss-of-function is a known mechanism of disease, and both in silico predictors and evolutionary conservation support a deleterious effect; Not observed at a significant frequency in large population cohorts (Lek et al., 2016); Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 10925384)
Invitae RCV000991301 SCV002131034 uncertain significance Glycogen storage disease type III 2021-04-27 criteria provided, single submitter clinical testing This sequence change falls in intron 31 of the AGL gene. It does not directly change the encoded amino acid sequence of the AGL protein. It affects a nucleotide within the consensus splice site of the intron. This variant is present in population databases (rs780504025, ExAC 0.002%). This variant has not been reported in the literature in individuals with AGL-related conditions. ClinVar contains an entry for this variant (Variation ID: 1105). Nucleotide substitutions within the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site, but this prediction has not been confirmed by published transcriptional studies. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Baylor Genetics RCV000991301 SCV004211090 likely pathogenic Glycogen storage disease type III 2023-09-02 criteria provided, single submitter clinical testing
OMIM RCV000001164 SCV000021314 pathogenic Glycogen storage disease IIIb 2000-07-31 no assertion criteria provided literature only
Natera, Inc. RCV000991301 SCV002094576 likely pathogenic Glycogen storage disease type III 2021-03-17 no assertion criteria provided clinical testing

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