ClinVar Miner

Submissions for variant NM_000170.2(GLDC):c.2489C>T (p.Thr830Met) (rs386833560)

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Total submissions: 3
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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 Non-ketotic hyperglycinemia 2018-03-16 criteria provided, single submitter clinical testing
Invitae RCV000049488 SCV000958225 pathogenic Non-ketotic hyperglycinemia 2019-11-15 criteria provided, single submitter clinical testing This sequence change replaces threonine with methionine at codon 830 of the GLDC protein (p.Thr830Met). The threonine residue is moderately conserved and there is a moderate physicochemical difference between threonine and methionine. This variant is present in population databases (rs386833560, ExAC 0.01%). This variant has been observed in individuals with non-ketotic hyperglycinemia (PMID: 27362913). In at least one individual the data is consistent with the variant being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 56079). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). For these reasons, this variant has been classified as Pathogenic.
Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM) RCV000049488 SCV000081922 probable-pathogenic Non-ketotic hyperglycinemia no assertion criteria provided not provided Converted during submission to Likely pathogenic.

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