D-2-Hydroxyglutaric Aciduria Type I via the D2HGDH Gene

D-2-Hydroxlglutaric Aciduria Type I (D2HGA-I) is a rare inborn error of metabolism caused by a defect in the processing of D-2-hydroxyglutaric acid (D2HG). Affected individuals have ranged from severely affected to asymptomatic. The patients with severe D2HGA-I have presented in infancy or early childhood, usually by 6 years of age, with early infantile-onset epileptic encephalopathy with hypotonia, cerebral visual failure or delayed cerebral visual development, developmental delay, episodic vomiting, stridor, apnea and facial dysmorphism. Disturbed cerebral maturation, white abnormalities and subependymal cysts are often observed on magnetic resonance images (MRIs). Spondyloenchondrodysplasia has also been reported. Symptoms are generally slowly progressive, but non-fatal in most patients (Misra et al. 2005; Struys et al. 2005a; Haliloglu et al. 2009; Struys et al. 2016). More mildly affected patients have also been reported. These patients typically have a more variable clinical presentation which may also include macrocephaly and peripheral neuropathy. In addition, they tend to have less consistent MRI findings (Struys et al. 2005a; Haliloglu et al. 2009). Some asymptomatic individuals have been identified via family screening (Misra et al. 2005). Biochemically, all D2HGA-I patients are found to have increased levels of D2HG in body fluids (urine, plasma and cerebral spinal fluid), and decreased activity of the D-2-hydroxyglutarate dehydrogenase enzyme (Struys et al. 2005a; Kranendijk et al. 2010; Struys et al. 2016).

Pathogenic variants in other genes may also lead to increased levels of D2HG in body fluids. These genes include IDH1, IDH2, SLC25A1, and possibly ALDH5A1 and ETFA, ETFB and ETFDH (Struys et al. 2006; Struys et al. 2016). Additional metabolic investigations may be able to distinguish the various causes of elevated D2HG levels.

D2HGA-I is an autosomal recessive disorder caused by pathogenic variants in the D2HGDH gene. Over 30 pathogenic variants have been described in this gene. Approximately two-thirds of the reported variants are missense variants, though splice variants, small frameshift deletions and duplications, and multi-exonic deletions have also been reported (Human Gene Mutation Database). There is no apparent genotype-phenotype correlation, and thus far there are no commonly reported pathogenic variants (Kranendijk et al. 2010).

The D2HGDH gene encodes the D-2-hydroxyglutarate dehydrogenase enzyme, which converts the metabolite D-2-hydroxyglutaric acid to 2-ketoglutarate, an intermediate in the citric acid cycle (Struys et al. 2005b; Struys et al. 2016).

In the largest cohort published of patients with elevated D2HG levels, 24 out of 50 patients were found to be homozygous or compound heterozygous for presumed pathogenic D2HGDH sequence variants. Two of these patients were found to harbor multi-exon deletions. Therefore, 46 D2HGDH alleles detectable by sequencing were identified out of a total of 100 alleles, for a sensitivity of ~46%. Enzyme activity was only studied in 25 of these patients, and D2HGDH activity was only found to be decreased in 7 of the 25. However, all 7 of these patients were found to harbor two D2HGDH sequence variants, suggesting a clinical sensitivity closer to 100% in patients with a confirmed enzyme defect (Kranendijk et al. 2010). In another study, two unrelated patients with elevated D2HG in body fluids and a confirmed enzymatic defect were found to carry presumed pathogenic D2HGDH variants on both alleles (Struys et al. 2005b).

This test provides full coverage of all coding exons of the D2HGDH 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).

This testing also includes coverage for the intronic splice variant c.293-23A>G.

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).