ClinVar Miner

Submissions for variant NM_058179.4(PSAT1):c.299A>C (p.Asp100Ala)

gnomAD frequency: 0.00001  dbSNP: rs118203967
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV003586121 SCV004294333 pathogenic Neu-Laxova syndrome 2 2024-12-19 criteria provided, single submitter clinical testing This sequence change replaces aspartic acid, which is acidic and polar, with alanine, which is neutral and non-polar, at codon 100 of the PSAT1 protein (p.Asp100Ala). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with phosphoserine aminotransferase deficiency (PMID: 17436247). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 1082). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is not expected to disrupt PSAT1 protein function with a negative predictive value of 80%. Experimental studies have shown that this missense change affects PSAT1 function (PMID: 17436247, 32077105). For these reasons, this variant has been classified as Pathogenic.
OMIM RCV000001137 SCV000021287 pathogenic PSAT deficiency 2007-05-01 no assertion criteria provided literature only
Dudley Research Group, Pacific Northwest Research Institute RCV001254373 SCV001430350 not provided not provided no assertion provided research
Genome Diagnostics Laboratory, University Medical Center Utrecht RCV001254373 SCV001931628 likely pathogenic not provided no assertion criteria provided clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV001254373 SCV001973837 likely pathogenic not provided no assertion criteria provided clinical testing

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