ClinVar Miner

Submissions for variant NM_000170.2(GLDC):c.1545G>A (p.Arg515=) (rs121964976)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
PreventionGenetics,PreventionGenetics RCV000248102 SCV000302841 benign not specified criteria provided, single submitter clinical testing
Athena Diagnostics Inc RCV000248102 SCV000613526 benign not specified 2017-06-28 criteria provided, single submitter clinical testing
Invitae RCV000530402 SCV000636357 benign Non-ketotic hyperglycinemia 2020-12-05 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000248102 SCV000919472 benign not specified 2018-09-27 criteria provided, single submitter clinical testing Variant summary: GLDC c.1545G>A alters a non-conserved nucleotide resulting in a synonymous change. The variant allele was found at a frequency of 0.022 in 277184 control chromosomes in the gnomAD database, including 99 homozygotes. The observed variant frequency is approximately 7-fold above the estimated maximal expected allele frequency for a pathogenic variant in GLDC causing Glycine Encephalopathy (Non-Ketotic Hyperglycinemia) phenotype (0.0031), strongly suggesting that the variant is benign. c.1545G>A has been reported in the literature in an individual affected with Glycine Encephalopathy (Non-Ketotic Hyperglycinemia), though this patient had two pathogenic mutations in trans, supporting a benign impact of the variant. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and both classified the variant as benign. Based on the evidence outlined above, the variant was classified as benign.
Illumina Clinical Services Laboratory,Illumina RCV000530402 SCV001331500 likely benign Non-ketotic hyperglycinemia 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
SingHealth Duke-NUS Institute of Precision Medicine RCV000530402 SCV000853163 uncertain significance Non-ketotic hyperglycinemia 2017-06-07 no assertion criteria provided curation
Natera, Inc. RCV000530402 SCV001457130 benign Non-ketotic hyperglycinemia 2020-09-16 no assertion criteria provided clinical testing

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