ClinVar Miner

Submissions for variant NM_000152.5(GAA):c.853C>T (p.Pro285Ser) (rs886042086)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000383868 SCV000791139 uncertain significance Glycogen storage disease, type II 2017-05-01 criteria provided, single submitter clinical testing
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000723486 SCV000331150 pathogenic not provided 2018-06-13 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000383868 SCV000917401 pathogenic Glycogen storage disease, type II 2018-12-13 criteria provided, single submitter clinical testing Variant summary: GAA c.853C>T (p.Pro285Ser) results in a non-conservative amino acid change located in the Glycoside hydrolase family 31, N-terminal domain of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 3.7e-05 in 27092 control chromosomes. c.853C>T has been reported in the literature in individuals affected with Late Onset Pompe Disease (Bali_2011, Carlier_2011, Kroos_2008, Nallamilli_2018, Orlikowski_2011), and in one reported case the GAA activity in the patients fibroblasts was <1% (Bali_2011). These data indicate that the variant is likely to be associated with disease. Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. One laboratory classified the variant as likely pathogenic, and one laboratory classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as pathogenic.

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