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Cystathioninuria via the CTH Gene

Summary and Pricing

Test Method

Exome Sequencing with CNV Detection
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
CTH 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
8331CTH81479 81479,81479 $990 Order Options and Pricing

Pricing Comments

Our favored testing approach is exome based NextGen sequencing with CNV analysis. This will allow cost effective reflexing to PGxome or other exome based tests. However, if full gene Sanger sequencing is desired for STAT turnaround time, insurance, or other reasons, please see link below for Test Code, pricing, and turnaround time information. If the Sanger option is selected, CNV detection may be ordered through Test #600.

An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.

Click here for costs to reflex to whole PGxome (if original test is on PGxome Sequencing platform).

Click here for costs to reflex to whole PGnome (if original test is on PGnome Sequencing platform).

The Sanger Sequencing method for this test is NY State approved.

For Sanger Sequencing click here.

Turnaround Time

3 weeks on average for standard orders or 2 weeks on average for STAT orders.

Please note: Once the testing process begins, an Estimated Report Date (ERD) range will be displayed in the portal. This is the most accurate prediction of when your report will be complete and may differ from the average TAT published on our website. About 85% of our tests will be reported within or before the ERD range. We will notify you of significant delays or holds which will impact the ERD. Learn more about turnaround times here.

Targeted Testing

For ordering sequencing of targeted known variants, go to our Targeted Variants page.


Genetic Counselors


  • McKenna Kyriss, PhD

Clinical Features and Genetics

Clinical Features

Cystathioninuria due to γ-cystathionase deficiency is an inborn error of sulfur amino acid metabolism. Deficiency of γ-cystathionase results in the accumulation of cystathionine in various tissues, as well as elevated levels of cystathionine in plasma. Key laboratory findings include high urinary excretion of cystathionine without homocystine and normal levels of plasma methionine. Although the condition is considered benign, γ-cystathionase deficiency should be differentiated from remethylation defects, as well as transient neonatal cystathioninuria due to other causes (including vitamin B6 deficiency, generalized liver disease, thyrotoxicosis, and neural tumors) (Andria et al. 2001). Treatment has been debated since the disorder is considered benign, but individuals may show improved lab chemistries with administration of daily pyridoxine.


Screening surveys of neonatal urine samples collected in Vancouver, British Columbia have estimated the prevalence of cystathioninuria to be as high as 1 per 14,000 live births (Wong et al. 1979). Cystathioninuria due to γ-cystathionase deficiency is an autosomal recessive genetic disorder associated with mutations in the CTH gene located on chromosome 1p31.1 (Lu et al. 1992). γ-Cystathionase (otherwise known as cystathionine gamma-lyase) normally converts methionine-derived cystathionine to cysteine, and the enzyme requires pyridoxal phosphate as a cofactor. Although γ-cystathionase is expressed in cultured fibroblasts, enzyme activity is too small to allow reliable measurement by enzyme assay (Fowler 1982). Therefore, genetic testing may allow diagnostic confirmation of this disorder.

γ-Cystathionase deficiency may result from nonsynonymous (i.e., missense) mutations and small deletions leading to frameshifts (Wang and Hegele 2003). There is also a common polymorphism in exon 12, defined as c.1364G>T (p.Ser403Ile), that has been found in multiple ethnic groups and may be associated with higher concentrations of plasma total homocysteine when found in the homozygous state (T/T) (Wang et al. 2004).

Clinical Sensitivity - Sequencing with CNV PGxome

The sensitivity of this test is currently unknown, as comprehensive assessments of sensitivity using direct sequencing methods have not been cited in the published literature for this rare disorder.

The sensitivity of duplication/deletion testing for this rare disorder is currently unknown. However, at least one gross deletion spanning 14.5 kb and which includes exons 2 through 5 of the CTH gene has been reported in patients with elevated levels of cystathionine in plasma and/or urine (Kraus et al. 2009).

Testing Strategy

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

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).

Indications for Test

Candidates for this test are patients with cystathioninuria. γ-Cystathionase deficiency should be differentiated from remethylation defects, as well as transient neonatal cystathioninuria due to other causes (including vitamin B6 deficiency, generalized liver disease, thyrotoxicosis, and neural tumors) (Andria et al. 2001). Although γ-cystathionase is expressed in cultured fibroblasts, enzyme activity is too small to allow reliable measurement by enzyme assay (Fowler 1982). Therefore, genetic testing may allow diagnostic confirmation of this disorder. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in CTH.


Official Gene Symbol OMIM ID
CTH 607657
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Cystathioninuria AR 219500


  • Andria G, Fowler, B, Sebastio, G. 2012. Disorders of Sulfur Amino Acid Metabolism. In: Saudubray J-M, van den Berghe G, and Walter JH, editors.  Inborn Metabolic Diseases: Diagnosis and Treatment, 5e. Berlin, Germany: Springer-Verlag, p 317-318.
  • Fowler B. 1982. Transsulphuration and methylation of homocysteine in control and mutant human fibroblasts. Biochim. Biophys. Acta 721: 201–207. PubMed ID: 7138917
  • Kraus JP, Hašek J, Kozich V, Collard R, Venezia S, Janošíková B, Wang J, Stabler SP, Allen RH, Jakobs C, Finn CT, Chien Y-H, et al. 2009. Cystathionine γ-lyase: Clinical, metabolic, genetic, and structural studies. Molecular Genetics and Metabolism 97: 250–259. PubMed ID: 19428278
  • Lu Y, O’Dowd BF, Orrego H, Israel Y. 1992. Cloning and nucleotide sequence of human liver cDNA encoding for cystathionine gamma-lyase. Biochem. Biophys. Res. Commun. 189: 749–758. PubMed ID: 1339280
  • Wang J, Hegele RA. 2003. Genomic basis of cystathioninuria (MIM 219500) revealed by multiple mutations in cystathionine gamma-lyase (CTH). Hum. Genet. 112: 404–408. PubMed ID: 12574942
  • Wang J, Huff AM, Spence JD, Hegele RA. 2004. Single nucleotide polymorphism in CTH associated with variation in plasma homocysteine concentration. Clin. Genet. 65: 483–486.
    PubMed ID: 15151507
  • Wong LT, Hardwick DF, Applegarth DA, Davidson AG. 1979. Review of Metabolic Screening Program of Children’s Hospital, Vancouver, British Columbia. 1971-1977. Clin. Biochem. 12: 167–172. PubMed ID: 519848


Ordering Options

We offer several options when ordering sequencing tests. For more information on these options, see our Ordering Instructions page. To view available options, click on the Order Options button within the test description.

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.
  • PGnome sequencing panels can be ordered via the myPrevent portal only at this time.

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.

For Requisition Forms, visit our Forms page

If ordering a Duo or Trio test, the proband and all comparator samples are required to initiate testing. If we do not receive all required samples for the test ordered within 21 days, we will convert the order to the most effective testing strategy with the samples available. Prior authorization and/or billing in place may be impacted by a change in test code.

Specimen Types

Specimen Requirements and Shipping Details

PGxome (Exome) Sequencing Panel

PGnome (Genome) Sequencing Panel

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Note: acceptable specimen types are whole blood and DNA from whole blood only.
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