ClinVar Miner

Submissions for variant NM_145262.4(GLYCTK):c.1478T>G (p.Phe493Cys)

gnomAD frequency: 0.00009  dbSNP: rs121909448
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Total submissions: 6
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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 RCV000023821 SCV000746317 likely pathogenic D-Glyceric aciduria 2018-03-05 criteria provided, single submitter clinical testing
Invitae RCV001852029 SCV002117592 uncertain significance not provided 2022-08-09 criteria provided, single submitter clinical testing This sequence change replaces phenylalanine, which is neutral and non-polar, with cysteine, which is neutral and slightly polar, at codon 493 of the GLYCTK protein (p.Phe493Cys). This variant is present in population databases (rs121909448, gnomAD 0.06%). This missense change has been observed in individual(s) with D-glyceric aciduria (PMID: 20949620). ClinVar contains an entry for this variant (Variation ID: 30836). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. Experimental studies have shown that this missense change affects GLYCTK function (PMID: 20949620). 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.
GeneDx RCV001852029 SCV002571112 likely pathogenic not provided 2023-06-26 criteria provided, single submitter clinical testing Published functional studies demonstrate F493C damages protein expression with no enzymatic activity (Sass et al., 2010); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 31589614, 20949620, 31980526, 34426522)
Revvity Omics, Revvity RCV000023821 SCV003816919 uncertain significance D-Glyceric aciduria 2021-09-08 criteria provided, single submitter clinical testing
OMIM RCV000023821 SCV000045112 pathogenic D-Glyceric aciduria 2010-12-01 no assertion criteria provided literature only
Universitäts-Kinderspital Zürich RCV000023821 SCV000109694 not provided D-Glyceric aciduria no assertion provided not provided

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