ClinVar Miner

Submissions for variant NM_058179.4(PSAT1):c.467C>T (p.Thr156Met)

gnomAD frequency: 0.00003  dbSNP: rs369944396
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001879894 SCV002140367 uncertain significance Neu-Laxova syndrome 2 2022-09-07 criteria provided, single submitter clinical testing This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 156 of the PSAT1 protein (p.Thr156Met). This variant is present in population databases (rs369944396, gnomAD 0.08%). This missense change has been observed in individual(s) with phosphoserine aminotransferase deficiency (PMID: 34089226). ClinVar contains an entry for this variant (Variation ID: 976941). 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"). Experimental studies have shown that this missense change affects PSAT1 function (PMID: 32077105). 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.
Dudley Research Group, Pacific Northwest Research Institute RCV001254449 SCV001430428 not provided not provided no assertion provided research
OMIM RCV003991539 SCV004811988 pathogenic PSAT deficiency 2024-04-08 no assertion criteria provided literature only

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