ClinVar Miner

Submissions for variant NM_005476.7(GNE):c.1525C>T (p.His509Tyr)

gnomAD frequency: 0.00001  dbSNP: rs754892377
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000669521 SCV000794280 likely pathogenic GNE myopathy 2017-10-06 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001861778 SCV002127778 likely pathogenic GNE myopathy; Sialuria 2023-11-14 criteria provided, single submitter clinical testing This sequence change replaces histidine, which is basic and polar, with tyrosine, which is neutral and polar, at codon 540 of the GNE protein (p.His540Tyr). This variant is present in population databases (rs754892377, gnomAD 0.006%). This missense change has been observed in individuals with autosomal recessive GNE-related myopathy (PMID: 21307865, 22196754, 25986339). This variant is also known as c.1525C >T (p.H509Y). ClinVar contains an entry for this variant (Variation ID: 553974). 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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. 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.
Baylor Genetics RCV000669521 SCV004191658 pathogenic GNE myopathy 2024-01-23 criteria provided, single submitter clinical testing

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