ClinVar Miner

Submissions for variant NM_000291.4(PGK1):c.278T>C (p.Val93Ala)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV002617614 SCV002955491 uncertain significance not provided 2023-04-09 criteria provided, single submitter clinical testing 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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on PGK1 protein function. ClinVar contains an entry for this variant (Variation ID: 1922599). This variant has not been reported in the literature in individuals affected with PGK1-related conditions. This variant is present in population databases (rs782807093, gnomAD 0.005%). This sequence change replaces valine, which is neutral and non-polar, with alanine, which is neutral and non-polar, at codon 93 of the PGK1 protein (p.Val93Ala).
Revvity Omics, Revvity RCV003130729 SCV003814904 uncertain significance Glycogen storage disease due to phosphoglycerate kinase 1 deficiency 2023-07-19 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV004738593 SCV005345552 uncertain significance PGK1-related disorder 2024-04-23 no assertion criteria provided clinical testing The PGK1 c.278T>C variant is predicted to result in the amino acid substitution p.Val93Ala. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0037% of alleles in individuals of European (Non-Finnish) descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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