ClinVar Miner

Submissions for variant NM_000170.2(GLDC):c.2368C>T (p.Arg790Trp) (rs386833556)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genomic Research Center, Shahid Beheshti University of Medical Sciences RCV000049484 SCV000845322 uncertain significance Non-ketotic hyperglycinemia 2018-08-07 criteria provided, single submitter clinical testing
Invitae RCV000049484 SCV000963027 pathogenic Non-ketotic hyperglycinemia 2018-08-28 criteria provided, single submitter clinical testing This sequence change replaces arginine with tryptophan at codon 790 of the GLDC protein (p.Arg790Trp). The arginine residue is weakly conserved and there is a moderate physicochemical difference between arginine and tryptophan. This variant is present in population databases (rs386833556, ExAC 0.001%). This variant has been observed as homozygous, as heterozygous in combination with a second allele, or on the opposite chromosome (in trans) from a pathogenic variant in individuals affected with glycine encephalopathy (nonketotic hyperglycinemia) (PMID: 28244183, 15192636, 27362913, 16450403). This finding is consistent with autosomal recessive inheritance, and suggests that this variant contributes to disease. ClinVar contains an entry for this variant (Variation ID: 56075). Experimental studies have shown that this missense change resulted in reduced enzyme activity (PMID: 15192636, 28244183). For these reasons, this variant has been classified as Pathogenic.
Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM) RCV000049484 SCV000081918 probable-pathogenic Non-ketotic hyperglycinemia no assertion criteria provided not provided Converted during submission to Likely pathogenic.

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