ClinVar Miner

Submissions for variant NM_005476.7(GNE):c.1523T>C (p.Leu508Ser)

gnomAD frequency: 0.00001  dbSNP: rs1057516798
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000411466 SCV000486237 likely pathogenic GNE myopathy 2016-04-22 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001861380 SCV002282100 likely pathogenic GNE myopathy; Sialuria 2024-01-13 criteria provided, single submitter clinical testing This sequence change replaces leucine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 539 of the GNE protein (p.Leu539Ser). This variant is present in population databases (no rsID available, gnomAD 0.007%). This missense change has been observed in individuals with distal myopathy (PMID: 21307865, 30390020). This variant is also known as p.L508S. ClinVar contains an entry for this variant (Variation ID: 370826). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on GNE protein function. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.
Mayo Clinic Laboratories, Mayo Clinic RCV003480623 SCV004226608 pathogenic not provided 2022-05-18 criteria provided, single submitter clinical testing PP3, PM2, PM3_strong, PS4

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