ClinVar Miner

Submissions for variant NM_005609.4(PYGM):c.21_28dup (p.Lys10fs)

dbSNP: rs770037766
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000706083 SCV000835114 pathogenic Glycogen storage disease, type V 2022-10-24 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 582100). This premature translational stop signal has been observed in individual(s) with recurrent rhabdomyolysis (PMID: 22899091). This variant is present in population databases (rs770037766, gnomAD 0.002%). This sequence change creates a premature translational stop signal (p.Lys10Thrfs*19) 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 RCV000706083 SCV003922970 likely pathogenic Glycogen storage disease, type V 2023-03-10 criteria provided, single submitter clinical testing Variant summary: PYGM c.21_28dupCCAAGAGA (p.Lys10ThrfsX19) 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. Truncations downstream of this position have been classified as pathogenic by our laboratory. The variant allele was found at a frequency of 4e-06 in 251390 control chromosomes. c.21_28dupCCAAGAGA has been reported in the literature in the heterozygous state in an individual affected with recurrent rhabdomyolysis which was explained by CPTII deficiency (Wang_2013). To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. One laboratory classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic.
Baylor Genetics RCV000706083 SCV004207257 pathogenic Glycogen storage disease, type V 2023-07-05 criteria provided, single submitter clinical testing

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