ClinVar Miner

Submissions for variant NM_006623.4(PHGDH):c.262G>A (p.Ala88Thr)

gnomAD frequency: 0.00005  dbSNP: rs142988234
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Baylor Genetics RCV001330262 SCV001521893 uncertain significance Neu-Laxova syndrome 1 2019-10-12 criteria provided, single submitter clinical testing This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].
Invitae RCV002546378 SCV003263567 uncertain significance PHGDH deficiency 2022-07-22 criteria provided, single submitter clinical testing This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 88 of the PHGDH protein (p.Ala88Thr). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. 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: 1029061). 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"). 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 RCV001330262 SCV004049047 uncertain significance Neu-Laxova syndrome 1 2023-04-11 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV002546378 SCV004049048 uncertain significance PHGDH deficiency 2023-04-11 criteria provided, single submitter clinical testing

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