Hyperammonemia Panel

Hyperammonemia is the occurrence of elevated levels of ammonia in the plasma. Normal ammonia levels are considered to be <110 μmol/L (190 μg/dL) in newborns and <80 μmol/L (140 μg/dL) in older infants and adults (Nyhan et al. 2017). Ammonia is toxic to the brain and is typically removed quickly from circulation via the urea cycle (Rabier. 2016). When this does not occur properly and ammonia levels increase substantially above these cutoffs, a number of clinical symptoms can occur. These include rapid, acute encephalopathy, decreased consciousness, psychiatric symptoms (such as personality changes, agitated and aggressive behavior, and decreased cognition), vomiting, abnormal gait and/or posturing, and seizures (LaBuzetta et al. 2010. PubMed ID: 20920686; Rabier 2016). Hyperammonemia can lead to irreversible brain damage, coma and death if not identified and treated rapidly, and is considered a medical emergency (LaBuzetta et al. 2010. PubMed ID: 20920686; Lachmann and Murphy. 2016; Ali et al. 2020. PubMed ID: 32491436).

The various conditions that cause hyperammonemia can be classified as either primary or secondary hyperammonemias. Primary hyperammonemia is due to a dysfunction of the urea cycle that leads directly to the build-up of ammonia. Classical urea cycle defects are caused by pathogenic variants in the ARG1, ASL, ASS1, CPS1, NAGS or OTC genes. These genes all encode proteins that play direct roles in the urea cycle, and are only active in the liver (Häberle. 2013. PubMed ID: 23628343).

Secondary hyperammonemias occur when the urea cycle is inhibited due to substrate deficiencies or the accumulation of metabolites that inhibit the action of one or more of the urea cycle enzymes (Häberle. 2013. PubMed ID: 23628343). In addition, as the urea cycle operates only in the liver, factors that affect liver function can also disrupt the urea cycle and lead to hyperammonemia (Häberle. 2013. PubMed ID: 23628343; Monch. 2015; Rabier. 2016). Genetic causes of secondary hyperammonemias can include the organic acidemias (primarily methylmalonic acidemia, propionic acidemia, and isovaleric acidemia), lysinuric protein intolerance, pyrroline-5-carboxylate synthetase deficiency, glutamine synthase deficiency, disorders that cause a decrease in the availability of acetyl-CoA (such as fatty acid oxidation defects), and defects in the carnitine cycle (Häberle. 2013. PubMed ID: 23628343).

Three of the genes in this panel (HCFC1, associated with methylmalonic acidemia and homocysteinemia, cblX type; OTC, associated with ornithine transcarbamylase deficiency; and TAFAZZIN, associated with Barth syndrome) are inherited in an X-linked manner. Female carriers of HCFC1 pathogenic variants are generally unaffected (Sloan et al. 2018. PubMed ID: 20301503), whereas females carriers of pathogenic OTC variants can experience serious symptoms early in life or in adulthood (Lichter-Konecki et al. 2016. PubMed ID: 24006547). Female carriers of pathogenic TAFAZZIN variants are typically unaffected, although in rare cases females with other X chromosome abnormalities (such as 45,X, structural abnormalities of the X chromosome, or skewed X-inactivation) may be symptomatic (Ferreira et al. 2020. PubMed ID: 25299040; Sabbah. 2020. PubMed ID: 33001359).   

Although it is difficult to estimate the overall prevalence of the various genetic causes of hyperammonemia, the estimated incidence of urea cycle disorders is ~1/250,000 live births in the United States, and ~1/440,000 live births internationally (Ali et al. 2020. PubMed ID: 32491436). The most common genetic cause of primary hyperammonemia in adults has been reported to be OTC deficiency in symptomatic, heterozygous female carriers (Rabier. 2016).

Additional, non-genetic causes of hyperammonemia can include transient hyperammonemia of the newborn, infection (particularly urinary tract infections caused by urease-producing bacteria), alcohol and/or drug misuse, hepatic disease, increased protein load, cancer and chemotherapy, and vascular shunts (Häberle. 2013. PubMed ID: 23628343; Monch. 2015; Rabier. 2016; Ali et al. 2020. PubMed ID: 32491436).

Molecular testing is useful to confirm a genetic cause of a hyperammonemic episode, which may then be useful for determining appropriate treatment and management measures, assessment of recurrence risks, and may allow for appropriate screening for potential future symptoms. Testing may also be useful for at-rick family members and reproductive planning.

This sequencing panel currently includes genes that have been associated with primary or secondary hyperammonemia. The majority of the disorders associated with these genes are inherited in an autosomal recessive manner. The only exceptions are GLUD1, which exhibits autosomal dominant inheritance, ALDH18A1 and CPT2, which can exhibit both autosomal dominant and recessive inheritance, and HCFC1, OTC, and TAFAZZIN, which exhibit X-linked inheritance. Pathogenic defects in the genes in this panel include missense, nonsense, splicing site variants, small deletions, small insertions/duplications, small indels, and exon-level large deletions (Human Gene Mutation Database).

The genes included in this test are associated with disorders that can be broadly classified into several categories based on the pathways within the cell that are disrupted:

Disorders of Ammonia Detoxification: ARG1, ASL, ASS1, CA5A, CPS1, NAGS, OTC, SLC25A13, SLC25A15

Disorders of Amino Acid Metabolism and/or Transport: ALDH18A1, BCKDHA, BCKDHB, DBT, DLD, GLUD1, GLUL, HMGCL, IVD, MCCC1, MCCC2, MLYCD, MMUT, OAT, PCCA, PCCB, SLC7A7 

Disorders of Carnitine Metabolism: CPT1A, CPT2, SLC22A5, SLC25A20

Disorders of Cobalamin Metabolism: ABCD4, HCFC1, LMBRD1, MMAA, MMAB, MMACHC, MMADHC, MTR, MTRR

Disorders of Fatty Acid Oxidation and Transport, and Ketone Metabolism: ACADM, ACADS, ACADVL, ACAT1, HADH, HADHA, HADHB, HMGCS2, TANGO2

Disorders of Biotin, Pantothenate, or Riboflavin Metabolism: BTD, ETFA, ETFB, ETFDH, HLCS, SLC25A42

Mitochondrial Related Disorders: FBXL4, MRPS22, SERAC1, TAFAZZIN, TMEM70, UQCRC2

Miscellaneous Disorders: CAD (pyrimidine metabolism), NBAS (associated with infantile liver failure syndrome 2), PC 

Of the genes included in this test, no large copy number variants (gross deletions or duplications/insertions) have been observed in the ABCD4, ACADS, ACADVL, CAD, CPT2, DLD, ETFB, GLUD1, GLUL, HCFC1, MCCC2,  MMAB, MMADHC, MRPS22, MTR, MTRR, NAGS, PC, SLC25A42,  or UQCRC2 genes. Large copy number variants have been reported as a relatively common cause of disease in the BCKDHA, BCKDHB, CA5A, DBT, LMBRD1, OTC, PCCA, SLC22A5, SLC25A13, SLC7A7, TANGO2, and TAFAZZIN genes. Copy number variants have been reported as a more rare cause of disease in the remaining genes on this panel. 

It should also be noted that, to our knowledge, de novo variants are not commonly reported for the majority of genes in this panel, although they have been reported in ALDH18A1, GLUD1, HCFC1, OTC and TAFAZZIN.

See individual gene summaries for more information about molecular biology of gene products and spectra of pathogenic variants.

The clinical sensitivity of this specific grouping of genes is difficult to estimate as we are unaware of any reports in the literature in which these genes have been sequenced together in a patient cohort with hyperammonemia as the primary indication for testing. The clinical sensitivity of sequencing the individual genes is high in patient groups with biochemical and/or enzymatic diagnoses of the relevant disorders; details are available on the individual gene test description pages. Analytical sensitivity is expected to be high as the majority of variants reported in these genes are detectable via direct sequencing.

Of note, Martín-Hernández et al. (2014. PubMed ID: 25433810) reported an observational study of 104 patients diagnosed with urea cycle disorders. Among their patient cohort, 67 were diagnosed with OTC deficiency, 22 with ASS1 deficiency, 10 with ASL deficiency, 2 with ARG1 deficiency, 2 with CPS1 deficiency, and 1 with NAGS deficiency. 

This test is performed using Next-Gen sequencing with additional Sanger sequencing as necessary.

This panel typically provides 99.8% coverage of all coding exons of the genes 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 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).