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L-2-Hydroxyglutaric Aciduria Type I via the L2HGDH Gene

  • Summary and Pricing
  • Clinical Features and Genetics
  • Citations
  • Methods
  • Ordering/Specimens
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TEST METHODS

Sequencing

Test Code TestIndividual Gene PriceCPT Code Copy CPT Codes
4774 L2HGDH$940.00 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

Based on a collective total of patients with elevated L2HG levels reported in several studies, the clinical sensitivity of this test is expected to range from approximately 83% to nearly 100% (Topçu et al. 2004; Vilarinho et al. 2005; Sass et al. 2008; Vilarinho et al. 2010). Several patients were reported to carry large deletions, which would not be detectable via sequencing (Steenweg et al. 2010).

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Clinical Features

L-2-Hydroxyglutaric Aciduria (L2HGA) is a rare inborn error of metabolism caused by a defect in the processing of L-2-hydroxyglutaric acid (L2HG). Affected individuals typically present before the age of 7 years with mild developmental or intellectual delays, epilepsy, and/or cerebellar ataxia (Topçu et al. 2004; Steenweg et al. 2010; Struys et al. 2016). The disease shows a slowly progressive course, with worsening cerebellar ataxia, dysarthria, mild to moderate intellectual disability, and characteristic brain abnormalities that can be differentiated from other leukodystrophies via MRI. The MRI results will typically show a pattern of signal abnormalities of the subcortical cerebral white matter, putamen, caudate nucleus, globus pallidus and dentate nucleus (Steenweg et al. 2010; Struys et al. 2016). Additional features that may be observed in these patients are seizures, variable macrocephaly, and pyramidal and extrapyramidal signs (Topçu et al. 2004). Due to the progressive nature of the disease, patients may lose skills, such as walking, over time (Steenweg et al. 2010). In addition, it has been reported that L2HGA patients have an increased tendency to develop malignant tumors of the central nervous system (Haliloglu et al. 2008; Struys et al. 2016). Biochemically, these patients are found to have elevated levels of L2HG in the urine, plasma, and cerebrospinal fluid. They may also show a decrease in N-acetylaspartate and choline and an increase in myo-inositol peaks via MR spectroscopy (Topçu et al. 2004).

Pathogenic variants in the SLC25A1 gene cause combined D-2- and L-2-hydroxyglutaric aciduria, leading to increased levels of both L2HG and D-2-hydroxyglutaric acid (D2HG) in body fluids (Struys et al. 2016). As enantiomeric separation is required to distinguish L2HG from D2HG, it is possible that initial biochemical test results may look similar for L2HGDH and SLC25A1 patients. Additional metabolic or molecular genetic investigations should be able to distinguish these disorders.

Genetics

L2HGA is an autosomal recessive disorder caused by pathogenic variants in the L2HGDH gene. Over 70 pathogenic variants have been described in this gene. Approximately half of the reported variants are missense variants and in-frame amino acid deletions. Nonsense and splice variants, small frameshift deletions, duplications and indels, and multi-exonic deletions have also been reported (Human Gene Mutation Database). There is no apparent genotype-phenotype correlation (Steenweg et al. 2010). The only two variants commonly reported in different populations are c.905C>T (p.Pro302Leu) and the frameshift variant c.530_533delinsATT (p.Pro177Hisfs*6). In addition, the variant c.241A>G (p.Lys81Glu) has been reported to be a founder mutation in the Tunisian population (Jellouli et al. 2014).

The L2HGDH gene encodes the L-2-hydroxyglutarate dehydrogenase enzyme, which converts the metabolite L-2-hydroxyglutaric acid to 2-ketoglutarate, an intermediate in the citric acid cycle (Struys et al. 2016).

Testing Strategy

This test involves bidirectional Sanger sequencing using genomic DNA of all coding exons of the L2HGDH gene plus ~20 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 test also includes coverage for the c.906+354G>A intronic variant, as well as ~20 bp of adjacent sequence.

Indications for Test

Patients with clinical and biochemical features consistent with L2HGA are good candidates for this test. Family members of patients who have known L2HGDH pathogenic variants are also good candidates. We will also sequence the L2HGDH gene to determine carrier status.

Gene

Official Gene Symbol OMIM ID
L2HGDH 609584
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Disease

Name Inheritance OMIM ID
L-2-Hydroxyglutaric Aciduria AR 236792

Related Tests

Name
Autism Spectrum Disorders and Intellectual Disability (ASD-ID) Comprehensive Panel
Hydroxyglutaric Aciduria Sequencing Panel
Organic Aciduria Sequencing Panel

CONTACTS

Genetic Counselors
Geneticist
Citations
  • Haliloglu G. et al. 2008. Neuropediatrics. 39: 119-22. PubMed ID: 18671189
  • Human Gene Mutation Database (Bio-base).
  • Jellouli N.K. et al. 2014. Journal of Human Genetics. 59: 216-22. PubMed ID: 24573090
  • Sass J.O. et al. 2008. Journal of Inherited Metabolic Disease. 31 Suppl 2: S275-9. PubMed ID: 18415700
  • Steenweg M.E. et al. 2010. Human Mutation. 31: 380-90. PubMed ID: 20052767
  • 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.
  • Topçu M. et al. 2004. Human Molecular Genetics. 13: 2803-11. PubMed ID: 15385440
  • Vilarinho L. et al. 2005. Human Mutation. 26: 395-6. PubMed ID: 16134148
  • Vilarinho L. et al. 2010. Journal of Human Genetics. 55: 55-8. PubMed ID: 19911013
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TEST METHODS

Bi-Directional Sanger Sequencing

Test Procedure

Nomenclature for sequence variants was from the Human Genome Variation Society (http://www.hgvs.org).  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 20 bases of non-coding DNA flanking the exon are sequenced.

Analytical Validity

As of March 2016, we compared 17.37 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 12 years of our lab operation we have Sanger sequenced roughly 8,800 PCR amplicons. Only one error has been identified, and this was due to sequence analysis error.

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 20 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.

Order Kits

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.
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.

SPECIMEN TYPES
WHOLE BLOOD

(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.

DNA

(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.

CELL CULTURE

(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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