• Test code: 06118
  • Turnaround time:
    10–21 calendar days (14 days on average)
  • Preferred specimen:
    3mL whole blood in a purple-top EDTA tube (K2EDTA or K3EDTA)
  • Alternate specimens:
    Saliva, assisted saliva, buccal swab and gDNA
  • Sample requirements
  • Request a sample kit

Invitae Elevated Citrulline Panel

Test description

The Invitae Elevated Citrulline Panel analyzes up to 5 genes that are associated with elevated citrulline on newborn screening (NBS) or plasma amino acids. Genetic testing of these genes may confirm a diagnosis and help guide treatment and management decisions. Identification of a disease-causing variant would also guide testing and diagnosis of at-risk relatives.

Order test

Primary panel (4 genes)
Add-on Dihydrolipoamide Dehydrogenase Deficiency Gene (1 gene)

Many cases of dihydrolipoamide dehydrogenase (DLD) deficiency have been shown to present with an elevated plasma citrulline level. It has been suggested that an elevated plasma citrulline level in the absence of a urea cycle defect warrants investigation of DLD deficiency. This gene may be included at no additional charge.


Alternative tests to consider

The Invitae Urea Cycle Disorders Panel has been designed to provide a broad genetic analysis of this class of disorders. Depending on the individual’s clinical and family history, this broader panel may be appropriate. It can be ordered at no additional cost.

  • argininosuccinate lyase (ASL) deficiency
  • argininosuccinate synthase (ASS1) deficiency – also known as citrullinemia type 1 (CTLN1)
  • citrin (SLC25A13) deficiency – also known as citrullinemia type 2 (CLTN2)
  • pyruvate carboxylase (PC) deficiency

Elevated citrulline detected during newborn screening may be associated with argininosuccinate synthetase (ASS1) deficiency, argininosuccinate lyase (ASL) deficiency, and the neonatal form of citrin (SLC25A13) deficiency.

Argininosuccinate Lyase (ASL) deficiency can present either as a severe neonatal-onset form with hyperammonemia within the first few days of life, or as a late-onset form with episodic hyperammonemia or long-term complications, including liver dysfunction, neurocognitive deficits, and hypertension. These long-term complications can occur in the absence of hyperammonemic episodes. The biochemical diagnosis of ASL deficiency is typically established with elevation of plasma citrulline together with elevated argininosuccinic acid in the plasma or urine.

ASS1 deficiency causes citrullinemia type 1 (CTLN1). CTLN1 presents as a clinical spectrum with a severe neonatal form, a milder later-onset form, and some individuals who are asymptomatic. Increased intracranial pressure can occur secondarily to hyperammonemia, resulting in increased neuromuscular tone, spasticity, and ankle clonus. Initial plasma ammonia concentration may be 1000–3000 µmol/L (normal: 40–50 µmol/L). In the milder form, symptoms manifest as recurrent lethargy and somnolence, intellectual disability, and chronic or recurrent hyperammonemia. A lower plasma ammonia concentration may be seen than in the classic form (adult upper limit of normal: <35 µmol/L). A rare form of CTLN1 occurs during and after pregnancy, with affected women experiencing vomiting, lethargy, seizures, confusion, hallucinations, behavioral changes (e.g., manic episodes, psychosis), and swelling of the brain.

The SLC25A13 gene encodes the aspartate/glutamate transporter called citrin. Citrin deficiency impairs the shuttling of aspartate and glutamate across the mitochondria, causing a mild hyperammonemia and citrullinemia (also known as citrullinemia type II [CTLN2]). The clinical presentation in adults with citrin deficiency is milder than that of CTLN1, and asymptomatic or presymptomatic individuals with citrin deficiency do not always show biochemical abnormalities. For this reason, definitive diagnosis of at-risk relatives may be dependent on the molecular genetic findings of SLC25A13 in the index case.

Citrin deficiency can manifest in newborns as neonatal intrahepatic cholestasis (NICCD), in older children as failure to thrive and lipid abnormalities, and in adults as recurrent hyperammonemia with neuropsychiatric symptoms.

Pyruvate carboxylase deficiency has a broad phenotypic spectrum with a severe neonatal-onset form (Type A), infantile form (Type B) to an intermittent or benign form (Type C). Type A generally presents with lactic acidemia, severe developmental delay, failure to thrive, hypotonia and other neurologic findings such as ataxia, nystagmus and seizures. Premature death typically occurs in infancy or early childhood. Type B presents in the neonatal period with seizures, hypotonia, anorexia, abnormal movements, ocular movement abnormalities, motor delays, hypoglycemia, hyperammonemia and hypernatremia. Most affected individuals do not survive past the first few months of life. Type C is very rare and onset typically occurs within the first year of life. Symptoms typically include episodic metabolic acidosis with lactic acidemia and ketoacidosis precipitated by metabolic stress. Neurologic development can be normal or mildly affected.

Analysis of the genes on this panel will identify pathogenic variants in 90% of patients who are diagnosed with CTLN1 or CTLN2. ASL is the only gene in which pathogenic variants are known to cause argininosuccinate lyase deficiency. PC is the only gene in which pathogenic variants are known to cause pyruvate carboxylase deficiency.

All genetic causes of elevated citrulline are inherited in an autosomal recessive manner.

The prevalence of CTLN1 is 1 in 57,000 births in the US, 1 in 22,150 births in Korea, 1 in 118,543 births in Taiwan, and 1 in 77,811 births in Austria. The prevalence of CTLN2 is unknown, though most identified patients are Japanese. The prevalence of ASL deficiency is approximately 1 in 70,000 live births. In the majority of populations the incidence of PC deficiency is 1:250,000. Type A PC deficiency has an increased incidence in native North Americans of the Ojibwa, Cree and Micmac tribes of the Algonquin-speaking peoples. Type B PC deficiency has an increased incidence in Europe.

  1. De, Meirleir, L. Disorders of pyruvate metabolism. Handb Clin Neurol. 2013; 113:1667-73. PMID: 23622387
  2. Marin-Valencia, I, et al. Pyruvate carboxylase deficiency: mechanisms, mimics and anaplerosis. Mol. Genet. Metab. 2010; 101(1):9-17. PMID: 20598931
  3. Wang, D, De, Vivo, D. Pyruvate Carboxylase Deficiency. 2009 Jun 02. In: Pagon, RA, et al, editors. GeneReviews(®) (Internet). University of Washington, Seattle. PMID: 20301764
  4. Summar, M. Current strategies for the management of neonatal urea cycle disorders. J. Pediatr. 2001; 138(1 Suppl):S30-9. PMID: 11148547
  5. Batshaw, ML, et al. Alternative pathway therapy for urea cycle disorders: twenty years later. J. Pediatr. 2001; 138(1 Suppl):S46-54; discussion S54-5. PMID: 11148549
  6. Yoon, HR, et al. Tandem mass spectrometric analysis for disorders in amino, organic and fatty acid metabolism: two year experience in South Korea. Southeast Asian J. Trop. Med. Public Health. 2003; 34 Suppl 3:115-20. PMID: 15906713
  7. Marsden, D. Expanded newborn screening by tandem mass spectrometry: the Massachusetts and New England experience. Southeast Asian J. Trop. Med. Public Health. 2003; 34 Suppl 3:111-4. PMID: 15906712
  8. Kobayashi, K, et al. Citrin Deficiency. 2005 Sep 16. In: Pagon, RA, et al, editors. GeneReviews(®) (Internet). University of Washington, Seattle. PMID: 20301360
  9. Quinonez, SC, Thoene, JG. Citrullinemia Type I. 2004 Jul 07. In: Pagon, RA, et al, editors. GeneReviews(®) (Internet). University of Washington, Seattle. PMID: 20301631
  10. Niu, DM, et al. Nationwide survey of extended newborn screening by tandem mass spectrometry in Taiwan. J. Inherit. Metab. Dis. 2010; 33(Suppl 2):S295-305. PMID: 20567911
  11. Nagamani, SCS, et al. Argininosuccinate Lyase Deficiency. 2011 Feb 03. In: Pagon, RA, et al, editors. GeneReviews(®) (Internet). University of Washington, Seattle. PMID: 21290785
  12. Nagamani, SC, et al. Argininosuccinate lyase deficiency. Genet. Med. 2012; 14(5):501-7. PMID: 22241104
  13. Woo, HI, et al. Molecular genetics of citrullinemia types I and II. Clin. Chim. Acta. 2014; 431:1-8. PMID: 24508627

Assay and technical information

Invitae is a College of American Pathologists (CAP)-accredited and Clinical Laboratory Improvement Amendments (CLIA)-certified clinical diagnostic laboratory performing full-gene sequencing and deletion/duplication analysis using next-generation sequencing technology (NGS).

Our sequence analysis covers clinically important regions of each gene, including coding exons and 10 to 20 base pairs of adjacent intronic sequence on either side of the coding exons in the transcript listed below. In addition, the analysis covers the select non-coding variants specifically defined in the table below. Any variants that fall outside these regions are not analyzed. Any limitations in the analysis of these genes will be listed on the report. Contact client services with any questions.

Based on validation study results, this assay achieves >99% analytical sensitivity and specificity for single nucleotide variants, insertions and deletions <15bp in length, and exon-level deletions and duplications. Invitae's methods also detect insertions and deletions larger than 15bp but smaller than a full exon but sensitivity for these may be marginally reduced. Invitae’s deletion/duplication analysis determines copy number at a single exon resolution at virtually all targeted exons. However, in rare situations, single-exon copy number events may not be analyzed due to inherent sequence properties or isolated reduction in data quality. Certain types of variants, such as structural rearrangements (e.g. inversions, gene conversion events, translocations, etc.) or variants embedded in sequence with complex architecture (e.g. short tandem repeats or segmental duplications), may not be detected. Additionally, it may not be possible to fully resolve certain details about variants, such as mosaicism, phasing, or mapping ambiguity. Unless explicitly guaranteed, sequence changes in the promoter, non-coding exons, and other non-coding regions are not covered by this assay. Please consult the test definition on our website for details regarding regions or types of variants that are covered or excluded for this test. This report reflects the analysis of an extracted genomic DNA sample. In very rare cases, (circulating hematolymphoid neoplasm, bone marrow transplant, recent blood transfusion) the analyzed DNA may not represent the patient's constitutional genome.

Gene Transcript reference Sequencing analysis Deletion/Duplication analysis
ASL NM_000048.3
ASS1 NM_000050.4
DLD NM_000108.4
PC* NM_000920.3
SLC25A13 NM_014251.2

PC: Analysis includes the intronic variant NM_000920.3:c.1369-29A>G.