ClinVar Miner

Submissions for variant NM_006623.4(PHGDH):c.418G>A (p.Gly140Arg)

dbSNP: rs587777770
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Department Of Translational Genomics (developmental Genetics Section), King Faisal Specialist Hospital & Research Centre RCV000171157 SCV000221353 likely pathogenic not provided criteria provided, single submitter research
Invitae RCV002514704 SCV003523348 uncertain significance PHGDH deficiency 2022-07-04 criteria provided, single submitter clinical testing This missense change has been observed in individual(s) with Neu-Laxova syndrome (PMID: 24836451, 26960553). 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 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: "Probably Damaging"; Align-GVGD: "Class C0"). ClinVar contains an entry for this variant (Variation ID: 139534). This variant is present in population databases (rs587777770, gnomAD 0.007%). This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 140 of the PHGDH protein (p.Gly140Arg).
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center RCV002514704 SCV004801211 likely pathogenic PHGDH deficiency 2024-03-14 criteria provided, single submitter research
OMIM RCV000128433 SCV000172114 pathogenic Neu-Laxova syndrome 1 2014-06-05 no assertion criteria provided literature only

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