ClinVar Miner

Submissions for variant NM_000170.3(GLDC):c.1819G>A (p.Gly607Ser)

dbSNP: rs1554646517
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000672824 SCV000797969 uncertain significance Glycine encephalopathy 2018-02-20 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000672824 SCV005835703 pathogenic Glycine encephalopathy 2024-03-14 criteria provided, single submitter clinical testing This sequence change replaces glycine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 607 of the GLDC protein (p.Gly607Ser). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with Glycine encephalopathy (PMID: 26179960, 27896094). 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: 556772). 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.

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