ClinVar Miner

Submissions for variant NM_006623.4(PHGDH):c.689G>A (p.Arg230His)

gnomAD frequency: 0.00011  dbSNP: rs777155018
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001732714 SCV001983244 uncertain significance not provided 2021-04-15 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Invitae RCV002032723 SCV002181793 uncertain significance PHGDH deficiency 2022-10-17 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 230 of the PHGDH protein (p.Arg230His). This variant is present in population databases (rs777155018, gnomAD 0.03%). 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: 1300937). 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 RCV003339725 SCV004049082 uncertain significance Neu-Laxova syndrome 1 2023-04-11 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV002032723 SCV004049083 uncertain significance PHGDH deficiency 2023-04-11 criteria provided, single submitter clinical testing

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