ClinVar Miner

Submissions for variant NM_000158.4(GBE1):c.993-1G>T

gnomAD frequency: 0.00001  dbSNP: rs763016962
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Baylor Genetics RCV000560920 SCV004198718 likely pathogenic Glycogen storage disease, type IV 2023-04-14 criteria provided, single submitter clinical testing
Invitae RCV003767090 SCV004580635 likely pathogenic Glycogen storage disease, type IV; Glycogen storage disease IV, classic hepatic 2023-12-18 criteria provided, single submitter clinical testing This sequence change affects an acceptor splice site in intron 7 of the GBE1 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in GBE1 are known to be pathogenic (PMID: 15452297, 20058079). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. Disruption of this splice site has been observed in individual(s) with clinical features of glycogen storage disease (PMID: 32617483). ClinVar contains an entry for this variant (Variation ID: 478912). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.
Jacobi Internal Medicine Residency Program, Jacobi Medical Center RCV000560920 SCV000612162 pathogenic Glycogen storage disease, type IV no assertion criteria provided clinical testing

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