ClinVar Miner

Submissions for variant NM_006623.4(PHGDH):c.566A>C (p.Gln189Pro)

gnomAD frequency: 0.00001  dbSNP: rs750124525
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001243143 SCV001416280 uncertain significance PHGDH deficiency 2022-07-26 criteria provided, single submitter clinical testing This sequence change replaces glutamine, which is neutral and polar, with proline, which is neutral and non-polar, at codon 189 of the PHGDH protein (p.Gln189Pro). This variant is present in population databases (rs750124525, gnomAD 0.002%). 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: 968090). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). 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 RCV002462872 SCV002757634 uncertain significance not provided 2022-05-24 criteria provided, single submitter clinical testing Has not been previously published as pathogenic or benign to our knowledge; 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
Genome-Nilou Lab RCV003339560 SCV004049075 uncertain significance Neu-Laxova syndrome 1 2023-04-11 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV001243143 SCV004049076 uncertain significance PHGDH deficiency 2023-04-11 criteria provided, single submitter clinical testing
Natera, Inc. RCV001243143 SCV002094685 uncertain significance PHGDH deficiency 2020-01-17 no assertion criteria provided clinical testing

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