ClinVar Miner

Submissions for variant NM_000152.5(GAA):c.2499_2500CA[1] (p.Thr834fs) (rs886043343)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000725814 SCV000339572 pathogenic not provided 2016-02-23 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000285320 SCV000917399 pathogenic Glycogen storage disease, type II 2018-11-30 criteria provided, single submitter clinical testing Variant summary: GAA c.2501_2502delCA (p.Thr834ArgfsX49) 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 (eg. c.2544delC, p.Lys849fsX38 and c.2560C>T, p.Arg854X). The variant allele was found at a frequency of 8.1e-06 in 245500 control chromosomes (gnomAD). The variant, c.2501_2502delCA, has been reported in the literature in individuals affected with Glycogen Storage Disease, Type 2 (Pompe Disease)(Kroos_2008, Palermo_2012, Musumeci_2012). These data indicate that the variant is likely to be associated with disease. One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation and classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.
Tehran Medical Genetics Laboratory RCV000285320 SCV000692564 likely pathogenic Glycogen storage disease, type II criteria provided, single submitter clinical testing

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