ClinVar Miner

Submissions for variant NM_000170.3(GLDC):c.643A>G (p.Lys215Glu)

dbSNP: rs907616957
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001368269 SCV001564656 uncertain significance Glycine encephalopathy 2024-02-24 criteria provided, single submitter clinical testing This sequence change replaces lysine, which is basic and polar, with glutamic acid, which is acidic and polar, at codon 215 of the GLDC protein (p.Lys215Glu). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with GLDC-related conditions. ClinVar contains an entry for this variant (Variation ID: 1059059). 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 not expected to disrupt GLDC protein function with a negative predictive value of 80%. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Ambry Genetics RCV002547885 SCV003558672 uncertain significance Inborn genetic diseases 2021-03-30 criteria provided, single submitter clinical testing The c.643A>G (p.K215E) alteration is located in exon 5 (coding exon 5) of the GLDC gene. This alteration results from a A to G substitution at nucleotide position 643, causing the lysine (K) at amino acid position 215 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
GeneDx RCV004783962 SCV005396729 uncertain significance not provided 2024-05-02 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Natera, Inc. RCV001368269 SCV002075802 uncertain significance Glycine encephalopathy 2021-09-27 no assertion criteria provided clinical testing

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