ClinVar Miner

Submissions for variant NM_058179.4(PSAT1):c.748G>A (p.Val250Ile)

gnomAD frequency: 0.00003  dbSNP: rs368071286
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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 RCV001879912 SCV002248081 uncertain significance Neu-Laxova syndrome 2 2023-11-27 criteria provided, single submitter clinical testing This sequence change replaces valine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 250 of the PSAT1 protein (p.Val250Ile). This variant is present in population databases (rs368071286, gnomAD 0.03%). This variant has not been reported in the literature in individuals affected with PSAT1-related conditions. ClinVar contains an entry for this variant (Variation ID: 977054). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae 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 does not substantially affect 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.
Breakthrough Genomics, Breakthrough Genomics RCV001254574 SCV005195445 uncertain significance not provided criteria provided, single submitter not provided
Dudley Research Group, Pacific Northwest Research Institute RCV001254574 SCV001430553 not provided not provided no assertion provided research

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