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

  • Summary and Pricing
  • Clinical Features and Genetics
  • Citations
  • Methods
  • Ordering/Specimens
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Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
4772 D2HGDH$810.00 81479 Add to Order
Targeted Testing

For ordering targeted known variants, please proceed to our Targeted Variants landing page.

Turnaround Time

The great majority of tests are completed within 18 days.

Clinical Sensitivity

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).

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Deletion/Duplication Testing via aCGH

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
600 D2HGDH$690.00 81479 Add to Order
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Turnaround Time

The great majority of tests are completed within 28 days.

Clinical Sensitivity

In a study of 50 patients with elevated D2HG in body fluids, 24 of the patients were found to be homozygous or compound heterozygous for presumed pathogenic D2HGDH sequence variants. Two of these patients carried unique multi-exonic deletions (Kranendijk et al. 2010).

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Clinical Features

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).

Testing Strategy

This test involves bidirectional Sanger sequencing using genomic DNA of all coding exons of the D2HGDH gene plus ~10 bp of flanking non-coding DNA on each side. We will also sequence any single exon (Test #100) or pair of exons (Test #200) in family members of patients with known pathogenic variants or to confirm research results.

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

Indications for Test

Patients with clinical and biochemical features consistent with D2HGA-I are good candidates for this test, particularly if they have been shown to have reduced D2HGDH enzyme activity. Family members of patients who have known D2HGDH pathogenic variants are also good candidates. We will also sequence the D2HGDH gene to determine carrier status.


Official Gene Symbol OMIM ID
D2HGDH 609186
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
D-2-Alpha Hydroxyglutaric Aciduria AR 600721

Related Tests

Autism Spectrum Disorders and Intellectual Disability (ASD-ID) Comprehensive Sequencing Panel with CNV Detection
Organic Aciduria Sequencing Panel


Genetic Counselors
  • Haliloglu G. et al. 2009. Journal of Inherited Metabolic Disease. 32 Suppl 1: S21-5. PubMed ID: 19169842
  • Human Gene Mutation Database (Bio-base).
  • Kranendijk M. et al. 2010. Human Mutation. 31: 279-83. PubMed ID: 20020533
  • Misra V.K. et al. 2005. Molecular Genetics and Metabolism. 86: 200-5. PubMed ID: 16081310
  • Struys E.A. et al. 2005a. Annals of Neurology. 58: 626-30. PubMed ID: PubMed ID: 16037974
  • Struys E.A. et al. 2005b. American Journal of Human Genetics. 76: 358-60. PubMed ID: 15609246
  • Struys E.A. et al. 2006. Molecular Genetics and Metabolism. 88: 53-7. PubMed ID: 16442322
  • Struys E.A., van der Knapp M.S., Salomons G.S. 2016. 2-Hydroxyglutaric Acidurias. In: Hollak C.E.M. and Lachmann R.H., editors. Inherited Metabolic Disease in Adults: A Clinical Guide. New York: Oxford University Press, p 145-147.
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Bi-Directional Sanger Sequencing

Test Procedure

Nomenclature for sequence variants was from the Human Genome Variation Society (  As required, DNA is extracted from the patient specimen.  PCR is used to amplify the indicated exons plus additional flanking non-coding sequence.  After cleaning of the PCR products, cycle sequencing is carried out using the ABI Big Dye Terminator v.3.0 kit.  Products are resolved by electrophoresis on an ABI 3730xl capillary sequencer.  In most cases, sequencing is performed in both forward and reverse directions; in some cases, sequencing is performed twice in either the forward or reverse directions.  In nearly all cases, the full coding region of each exon as well as 10 bases of non-coding DNA flanking the exon are sequenced.

Analytical Validity

As of February 2018, we compared 26.8 Mb of Sanger DNA sequence generated at PreventionGenetics to NextGen sequence generated in other labs. We detected only 4 errors in our Sanger sequences, and these were all due to allele dropout during PCR. For Proficiency Testing, both external and internal, in the 14 years of our lab operation we have Sanger sequenced roughly 14,300 PCR amplicons. Only one error has been identified, and this was an error in analysis of sequence data.

Our Sanger sequencing is capable of detecting virtually all nucleotide substitutions within the PCR amplicons. Similarly, we detect essentially all heterozygous or homozygous deletions within the amplicons. Homozygous deletions which overlap one or more PCR primer annealing sites are detectable as PCR failure. Heterozygous deletions which overlap one or more PCR primer annealing sites are usually not detected (see Analytical Limitations). All heterozygous insertions within the amplicons up to about 100 nucleotides in length appear to be detectable. Larger heterozygous insertions may not be detected. All homozygous insertions within the amplicons up to about 300 nucleotides in length appear to be detectable. Larger homozygous insertions may masquerade as homozygous deletions (PCR failure).

Analytical Limitations

In exons where our sequencing did not reveal any variation between the two alleles, we cannot be certain that we were able to PCR amplify both of the patient’s alleles. Occasionally, a patient may carry an allele which does not amplify, due for example to a deletion or a large insertion. In these cases, the report contains no information about the second allele.

Similarly, our sequencing tests have almost no power to detect duplications, triplications, etc. of the gene sequences.

In most cases, only the indicated exons and roughly 10 bp of flanking non-coding sequence on each side are analyzed. Test reports contain little or no information about other portions of the gene, including many regulatory regions.

In nearly all cases, we are unable to determine the phase of sequence variants. In particular, when we find two likely causative mutations for recessive disorders, we cannot be certain that the mutations are on different alleles.

Our ability to detect minor sequence variants, due for example to somatic mosaicism is limited. Sequence variants that are present in less than 50% of the patient’s nucleated cells may not be detected.

Runs of mononucleotide repeats (eg (A)n or (T)n) with n >8 in the reference sequence are generally not analyzed because of strand slippage during PCR and cycle sequencing.

Unless otherwise indicated, the sequence data that we report are based on DNA isolated from a specific tissue (usually leukocytes). Test reports contain no information about gene sequences in other tissues.

Deletion/Duplication Testing via Array Comparative Genomic Hybridization

Test Procedure

Equal amounts of genomic DNA from the patient and a gender matched reference sample are amplified and labeled with Cy3 and Cy5 dyes, respectively. To prevent any sample cross contamination, a unique sample tracking control is added into each patient sample. Each labeled patient product is then purified, quantified, and combined with the same amount of reference product. The combined sample is loaded onto the designed array and hybridized for at least 22-42 hours at 65°C. Arrays are then washed and scanned immediately with 2.5 µM resolution. Only data for the gene(s) of interest for each patient are extracted and analyzed.

Analytical Validity

PreventionGenetics' high density gene-centric custom designed aCGH enables the detection of relatively small deletions and duplications within a single exon of a given gene or deletions and duplications encompassing the entire gene. PreventionGenetics has established and verified this test's accuracy and precision.

Analytical Limitations

Our dense probe coverage may allow detection of deletions/duplications down to 100 bp; however due to limitations and probe spacing this cannot be guaranteed across all exons of all genes. Therefore, some copy number changes smaller than 100-300 bp within a targeted large exon may not be detected by our array.

This array may not detect deletions and duplications present at low levels of mosaicism or those present in genes that have pseudogene copies or repeats elsewhere in the genome.

aCGH will not detect balanced translocations, inversions, or point mutations that may be responsible for the clinical phenotype.

Breakpoints, if occurring outside the targeted gene, may be hard to define.

The sensitivity of this assay may be reduced when DNA is extracted by an outside laboratory.

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Ordering Options

myPrevent - Online Ordering
  • The test can be added to your online orders in the Summary and Pricing section.
  • Once the test has been added log in to myPrevent to fill out an online requisition form.
  • A completed requisition form must accompany all specimens.
  • Billing information along with specimen and shipping instructions are within the requisition form.
  • All testing must be ordered by a qualified healthcare provider.


(Delivery accepted Monday - Saturday)

  • Collect 3 ml -5 ml (5 ml preferred) of whole blood in EDTA (purple top tube) or ACD (yellow top tube). For Test #500-DNA Banking only, collect 10 ml -20 ml of whole blood.
  • For small babies, we require a minimum of 1 ml of blood.
  • Only one blood tube is required for multiple tests.
  • Ship blood tubes at room temperature in an insulated container. Do not freeze blood.
  • During hot weather, include a frozen ice pack in the shipping container. Place a paper towel or other thin material between the ice pack and the blood tube.
  • In cold weather, include an unfrozen ice pack in the shipping container as insulation.
  • At room temperature, blood specimen is stable for up to 48 hours.
  • If refrigerated, blood specimen is stable for up to one week.
  • Label the tube with the patient name, date of birth and/or ID number.


(Delivery accepted Monday - Saturday)

  • Send in screw cap tube at least 5 µg -10 µg of purified DNA at a concentration of at least 20 µg/ml for NGS and Sanger tests and at least 5 µg of purified DNA at a concentration of at least 100 µg/ml for gene-centric aCGH, MLPA, and CMA tests, minimum 2 µg for limited specimens.
  • For requests requiring more than one test, send an additional 5 µg DNA per test ordered when possible.
  • DNA may be shipped at room temperature.
  • Label the tube with the composition of the solute, DNA concentration as well as the patient’s name, date of birth, and/or ID number.
  • We only accept genomic DNA for testing. We do NOT accept products of whole genome amplification reactions or other amplification reactions.


(Delivery preferred Monday - Thursday)

  • PreventionGenetics should be notified in advance of arrival of a cell culture.
  • Culture and send at least two T25 flasks of confluent cells.
  • Some panels may require additional flasks (dependent on size of genes, amount of Sanger sequencing required, etc.). Multiple test requests may also require additional flasks. Please contact us for details.
  • Send specimens in insulated, shatterproof container overnight.
  • Cell cultures may be shipped at room temperature or refrigerated.
  • Label the flasks with the patient name, date of birth, and/or ID number.
  • We strongly recommend maintaining a local back-up culture. We do not culture cells.
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