ClinVar Miner

Submissions for variant NM_005609.4(PYGM):c.13_14del (p.Leu5fs)

dbSNP: rs772194378
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000409435 SCV000486533 pathogenic Glycogen storage disease, type V 2016-06-21 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000409435 SCV003439886 pathogenic Glycogen storage disease, type V 2023-07-29 criteria provided, single submitter clinical testing This premature translational stop signal has been observed in individual(s) with glycogen storage disease (PMID: 17172620). For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 371064). This variant is present in population databases (rs772194378, gnomAD 0.0009%). This sequence change creates a premature translational stop signal (p.Leu5Valfs*22) in the PYGM gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PYGM are known to be pathogenic (PMID: 8316268, 16786513).
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000409435 SCV005726960 pathogenic Glycogen storage disease, type V 2024-11-07 criteria provided, single submitter clinical testing Variant summary: PYGM c.13_14delCT (p.Leu5ValfsX22) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. The variant allele was found at a frequency of 4e-06 in 251176 control chromosomes. c.13_14delCT has been reported in the literature in compound heterozygous and homozygous individuals affected with Glycogen Storage Disease, Type V (Rubio_2006, Snchez-Tejerina_2021). These data indicate that the variant is likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 17172620, 33837115). ClinVar contains an entry for this variant (Variation ID: 371064). Based on the evidence outlined above, the variant was classified as pathogenic.

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