ClinVar Miner

Submissions for variant NM_006623.4(PHGDH):c.1534T>G (p.Ser512Ala)

gnomAD frequency: 0.00001  dbSNP: rs375098288
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001926245 SCV002204466 uncertain significance PHGDH deficiency 2022-10-24 criteria provided, single submitter clinical testing This sequence change replaces serine, which is neutral and polar, with alanine, which is neutral and non-polar, at codon 512 of the PHGDH protein (p.Ser512Ala). This variant is present in population databases (rs375098288, gnomAD 0.006%). 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: 1422796). 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.
GeneDx RCV003332362 SCV004039967 uncertain significance not provided 2023-03-30 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); 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
Genome-Nilou Lab RCV003339827 SCV004049140 uncertain significance Neu-Laxova syndrome 1 2023-04-11 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV001926245 SCV004049141 uncertain significance PHGDH deficiency 2023-04-11 criteria provided, single submitter clinical testing

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