ClinVar Miner

Submissions for variant NM_006623.4(PHGDH):c.119A>G (p.Glu40Gly)

gnomAD frequency: 0.00001  dbSNP: rs778630047
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001763487 SCV001990942 uncertain significance not provided 2020-09-03 criteria provided, single submitter clinical testing In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Has not been previously published as pathogenic or benign to our knowledge
Labcorp Genetics (formerly Invitae), Labcorp RCV002540343 SCV003473542 uncertain significance PHGDH deficiency 2022-10-04 criteria provided, single submitter clinical testing This sequence change replaces glutamic acid, which is acidic and polar, with glycine, which is neutral and non-polar, at codon 40 of the PHGDH protein (p.Glu40Gly). This variant is present in population databases (rs778630047, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with PHGDH-related conditions. ClinVar contains an entry for this variant (Variation ID: 1308575). 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 PHGDH protein function. 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.
Genome-Nilou Lab RCV003339735 SCV004049038 uncertain significance Neu-Laxova syndrome 1 2023-04-11 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV002540343 SCV004049039 uncertain significance PHGDH deficiency 2023-04-11 criteria provided, single submitter clinical testing

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