ClinVar Miner

Submissions for variant NM_005609.4(PYGM):c.1193C>T (p.Pro398Leu)

gnomAD frequency: 0.00001  dbSNP: rs773204705
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000667688 SCV000792177 uncertain significance Glycogen storage disease, type V 2017-06-09 criteria provided, single submitter clinical testing
Invitae RCV000667688 SCV001418233 likely pathogenic Glycogen storage disease, type V 2023-11-20 criteria provided, single submitter clinical testing This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 398 of the PYGM protein (p.Pro398Leu). 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. This missense change has been observed in individual(s) with glycogen storage disease (PMID: 21880526; Invitae). ClinVar contains an entry for this variant (Variation ID: 552430). 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 PYGM protein function with a positive predictive value of 95%. 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.
Revvity Omics, Revvity RCV000667688 SCV003810408 uncertain significance Glycogen storage disease, type V 2020-10-05 criteria provided, single submitter clinical testing
Baylor Genetics RCV000667688 SCV004207211 likely pathogenic Glycogen storage disease, type V 2023-10-25 criteria provided, single submitter clinical testing
Natera, Inc. RCV000667688 SCV002092326 uncertain significance Glycogen storage disease, type V 2020-01-22 no assertion criteria provided clinical testing

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