ClinVar Miner

Submissions for variant NM_002863.5(PYGL):c.1768+1G>A

gnomAD frequency: 0.00002  dbSNP: rs113993982
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000012772 SCV000819606 pathogenic Glycogen storage disease, type VI 2023-01-04 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. Studies have shown that disruption of this splice site results in 3 aberrantly spliced mRNAs and introduces a premature termination codon (PMID: 9529348). The resulting mRNA is expected to undergo nonsense-mediated decay. ClinVar contains an entry for this variant (Variation ID: 11992). Disruption of this splice site has been observed in individuals with glycogen storage disease type VI (PMID: 9529348, 32892177). This variant is present in population databases (rs113993982, gnomAD 0.006%). This sequence change affects a donor splice site in intron 14 of the PYGL gene. RNA analysis indicates that disruption of this splice site induces altered splicing and may result in an absent or disrupted protein product.
Pathology and Clinical Laboratory Medicine, King Fahad Medical City RCV000012772 SCV000996283 pathogenic Glycogen storage disease, type VI criteria provided, single submitter clinical testing
Baylor Genetics RCV000012772 SCV001522876 pathogenic Glycogen storage disease, type VI 2020-07-27 criteria provided, single submitter clinical testing This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868].
3billion RCV000012772 SCV002573001 pathogenic Glycogen storage disease, type VI 2022-09-01 criteria provided, single submitter clinical testing The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.004%). Canonical splice site is predicted to alter splicing and result in a loss or disruption of normal protein function. Multiple pathogenic loss-of-function variants are reported downstream of the variant. The variant has been reported at least twice as pathogenic with clinical assertions and evidence for the classification (ClinVar ID: VCV000011992). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline.
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center RCV000012772 SCV004804946 pathogenic Glycogen storage disease, type VI 2024-03-17 criteria provided, single submitter research
OMIM RCV000012772 SCV000033007 pathogenic Glycogen storage disease, type VI 1998-04-01 no assertion criteria provided literature only
GeneReviews RCV000012772 SCV000040944 not provided Glycogen storage disease, type VI no assertion provided literature only

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