ClinVar Miner

Submissions for variant NM_006623.4(PHGDH):c.400G>A (p.Glu134Lys)

gnomAD frequency: 0.00002  dbSNP: rs139129607
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV001099159 SCV001255589 uncertain significance PHGDH deficiency 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Invitae RCV001099159 SCV002197458 uncertain significance PHGDH deficiency 2022-08-22 criteria provided, single submitter clinical testing This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 134 of the PHGDH protein (p.Glu134Lys). This variant is present in population databases (rs139129607, gnomAD 0.02%). 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: 875371). 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: "Tolerated"; 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 RCV002464386 SCV002759160 uncertain significance not provided 2022-06-02 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously reported as pathogenic or benign to our knowledge
Genome-Nilou Lab RCV003339491 SCV004049062 uncertain significance Neu-Laxova syndrome 1 2023-04-11 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV001099159 SCV004049063 uncertain significance PHGDH deficiency 2023-04-11 criteria provided, single submitter clinical testing

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