ClinVar Miner

Submissions for variant NM_000019.4(ACAT1):c.890C>A (p.Thr297Lys)

dbSNP: rs886041122
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Department of Pediatrics, Gifu University RCV000844817 SCV000966093 likely pathogenic Deficiency of acetyl-CoA acetyltransferase 2019-05-05 criteria provided, single submitter literature only
Labcorp Genetics (formerly Invitae), Labcorp RCV000844817 SCV002293953 pathogenic Deficiency of acetyl-CoA acetyltransferase 2024-02-27 criteria provided, single submitter clinical testing This sequence change replaces threonine, which is neutral and polar, with lysine, which is basic and polar, at codon 297 of the ACAT1 protein (p.Thr297Lys). This variant is present in population databases (no rsID available, gnomAD 0.007%). This missense change has been observed in individual(s) with beta-ketothiolase deficiency (PMID: 28875337). ClinVar contains an entry for this variant (Variation ID: 666510). 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 expected to disrupt ACAT1 protein function with a positive predictive value of 80%. This variant disrupts the p.Thr297 amino acid residue in ACAT1. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 7728148, 7749408). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.

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