ClinVar Miner

Submissions for variant NM_003896.4(ST3GAL5):c.601G>A (p.Gly201Arg)

gnomAD frequency: 0.00001  dbSNP: rs771732955
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000240856 SCV001228015 pathogenic GM3 synthase deficiency 2023-12-18 criteria provided, single submitter clinical testing This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 201 of the ST3GAL5 protein (p.Gly201Arg). This variant is present in population databases (rs771732955, gnomAD 0.003%). This missense change has been observed in individual(s) with reduced gangliosides in serum but atypical clinical features for GM3 synthase deficiency (PMID: 27232954). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 254246). 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) performed at Invitae indicates that this missense variant is expected to disrupt ST3GAL5 protein function with a positive predictive value of 80%. For these reasons, this variant has been classified as Pathogenic.
OMIM RCV000240856 SCV000299339 pathogenic GM3 synthase deficiency 2016-09-16 no assertion criteria provided literature only

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