β-Ketothiolase Deficiency via the ACAT1 Gene

β-ketothiolase deficiency is an inborn error of ketone body metabolism that usually presents as intermittent ketoacidotic episodes. Onset of the first ketoacidotic episode is usually early in life; the median age is 15 months, with a range of 3 days to 48 months. Frequency of attacks tends to decrease or cease with age, making the consequences avoidable if diagnosed early and managed properly. Affected individuals are typically asymptomatic between episodes, but the extent of the clinical features varies based on the patient and the severity of the attack. Some of the first symptoms of an episode can be vomiting, lethargy, and fever. In about half of the affected patients, a severe attack is associated with unconsciousness/coma, which can result in subsequent intellectual disability or death (Fukao et al. 2001; Nakamura et al. 2001). Following an attack, some patients have also experienced severe headaches, developmental delay, basal ganglion abnormalities, dystonia, dilated cardiomyopathy, prolonged QT interval, neutropenia and thrombocytopenia (Mitchell and Fukao et al. 2014). β-ketothiolase deficient patients are usually identified after an attack through a urinary organic acid analysis, with results showing elevated excretion of the isoleucine catabolism intermediates 2-methyl-3-hydroxybutyrate, 2-methylacetoacetate, and tiglyglycine (Catanzano et. al. 2010; Fukao et al. 2010a; Akella et. al. 2014). These patients have also been known to have elevated levels of 2-methyl-3-hydroxybutyrylcarnitine (C5OH) and tiglylcarnitine (C5:1) in blood plasma (Catanzano et. al. 2010; Akella et. al. 2014).

β-ketothiolase deficiency is inherited in an autosomal recessive manner and is caused by variations in the ACAT1 gene, which is the only gene known to be involved. Approximately 70 different pathogenic variants have been identified to date, with approximately half of those being missense variants. The remainder are a mix of nonsense variants, splice site variants, and small insertions and deletions. Only two gross deletions and one tandem duplication of multiple exons have been identified at this time (Zhang et. al. 2006; Fukao et. al. 2007; Fukao et al. 2013; Human Gene Mutation Database). Pathogenic variants in the ACAT1 gene are heterogeneous and no common pathogenic variants have yet been identified.

Normally, the mitochondrial acetoacetyl-CoA thiolase (T2) enzyme catalyzes the processing of isoleucine. Pathogenic variants in the ACAT1 gene can greatly reduce or eliminate the activity of this enzyme, causing ketoacidosis and elevated isoleucine catabolism intermediates in the urine (Fukao et al. 2010a).

Test sensitivity should be high in patients with clinical symptoms of β-ketothiolase deficiency. Fukao et al. (2001) reported 2 alleles in 100% of the 26 patients studied, and in a second study, they reported reported 2 alleles in 100% of the 10 patients studied (Fukao et al. 2010b). Sakurai et al. (2007) reported 2 alleles in 100% of the 6 patients studied.

This test provides full coverage of all coding exons of the ACAT1 gene plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define full coverage as >20X NGS reads or Sanger sequencing. PGnome panels typically provide slightly increased coverage over the PGxome equivalent. PGnome sequencing panels have the added benefit of additional analysis and reporting of deep intronic regions (where applicable).

Dependent on the sequencing backbone selected for this testing, discounted reflex testing to any other similar backbone-based test is available (i.e., PGxome panel to whole PGxome; PGnome panel to whole PGnome).