ClinVar Miner

Submissions for variant NM_005476.7(GNE):c.1556A>G (p.Asn519Ser)

dbSNP: rs1554658910
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000672708 SCV000797842 likely pathogenic GNE myopathy 2018-02-13 criteria provided, single submitter clinical testing
Revvity Omics, Revvity RCV003140071 SCV003826494 pathogenic not provided 2022-06-27 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000672708 SCV005204370 likely pathogenic GNE myopathy 2024-06-12 criteria provided, single submitter clinical testing Variant summary: GNE c.1649A>G (p.Asn550Ser) results in a conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant was absent in 251494 control chromosomes. c.1649A>G has been reported in the literature in two homozygous individuals affected with Inclusion Body Myopathy 2 (Broccolini_2006, Tasca_2012) and in 1 compound heterozygous individual with autosomal recessive macrothrombocytopenia without associated muscle wasting at an young age (Revel-Vilk_2018). These data indicate that the variant is likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in 40% of normal UDP-GlcNAc 2-epimerase activity activity and 20% of normal ManNAc kinase activity using purified protein (Penner_2006). The following publications have been ascertained in the context of this evaluation (PMID: 30171045, 15146476, 16503651, 22231866). ClinVar contains an entry for this variant (Variation ID: 556674). Based on the evidence outlined above, the variant was classified as likely pathogenic.
Fulgent Genetics, Fulgent Genetics RCV005046900 SCV005682215 likely pathogenic GNE myopathy; Sialuria; Thrombocytopenia 12 with or without myopathy 2024-06-13 criteria provided, single submitter clinical testing

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