ClinVar Miner

Submissions for variant NM_000170.3(GLDC):c.2489C>T (p.Thr830Met)

gnomAD frequency: 0.00004  dbSNP: rs386833560
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Centre for Translational Omics - GOSgene, University College London RCV000049488 SCV000778572 likely pathogenic Glycine encephalopathy 2018-03-16 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000049488 SCV000958225 pathogenic Glycine encephalopathy 2024-01-09 criteria provided, single submitter clinical testing This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 830 of the GLDC protein (p.Thr830Met). This variant is present in population databases (rs386833560, gnomAD 0.03%). This missense change has been observed in individual(s) with non-ketotic hyperglycinemia (PMID: 27362913). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 56079). 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 GLDC protein function with a positive predictive value of 80%. For these reasons, this variant has been classified as Pathogenic.
Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM) RCV000049488 SCV000081922 probable-pathogenic Glycine encephalopathy no assertion criteria provided not provided Converted during submission to Likely pathogenic.
Natera, Inc. RCV000049488 SCV001457114 pathogenic Glycine encephalopathy 2020-09-16 no assertion criteria provided clinical testing

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