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Homocystinuria via the CBS 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
9369 CBS 81406 81406,81479 $890 Order Options and Pricing
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
9369CBS81406 81406(x1), 81479(x1) $890 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 backbone).

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

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

For Sanger Sequencing click here.

Turnaround Time

18 days on average for standard orders or 13 days 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.

EMAIL CONTACTS

Genetic Counselors

Geneticist

  • McKenna Kyriss, PhD

Clinical Features and Genetics

Clinical Features

The transsulfuration pathway involves the interconversion of methionine to homocysteine, and eventually cysteine. This pathway is the main mechanism for removal of methionine (Mudd, Levy and Kraus 2014). The pyridoxine dependent cystathionine β-synthase (CBS) enzyme catalyzes the conversion of homocysteine to cystathionine (Picker and Levy 2014; Mudd, Levy and Kraus 2014). Defects in this enzyme are the most commonly observed cause of homocystinuria without associated methylmalonic aciduria (Picker and Levy 2014; Mudd, Levy and Kraus 2014). Biochemically, patients with this disorder are found to have greatly increased concentrations of plasma and urine homocysteine, total homocysteine, and marked hypermethioninemia (Picker and Levy 2014). This is in contrast to homocystinura caused by defects in the MTR and MTRR genes, which are typically associated with hypomethioninemia (Carrillo-Carrasco et al. 2013; Watkins and Rosenblatt 2014). Clinically, the most common symptoms are developmental delay or intellectual disability, ectopia lentis and/or severe myopia, skeletal abnormalities which can include thinning and lengthening of the long bones as well as osteoporosis, and vascular disease, including potentially fatal thromboembolisms (Kraus et al. 1999; Picker and Levy 2014; Mudd, Levy and Kraus 2014). Other features observed in CBS deficient patients may include psychiatric disturbances, seizures, and extrapyramidal signs (Picker and Levy 2014; Mudd, Levy and Kraus 2014). Age of onset and expressivity of clinical features displayed by patients varies widely, even within sibships, and can range from affected newborns to adults who were previously asymptomatic first presenting with a thromboembolytic event (Carrillo-Carrasco et al. 2013; Picker and Levy 2014; Mudd, Levy and Kraus 2014).

Affected individuals may be identified via newborn screening programs designed to detect hypermethioninemia. However, certain individuals with CBS deficiency may not have increased levels of methionine within the first two to three days of life when newborn screening is performed. Thus, in cases where individuals exhibit clinical symptoms suggestive of CBS deficiency yet had negative newborn screening results, testing for CBS deficiency should still be considered (Picker and Levy 2014).

Treatment includes pyridoxine therapy, to which only about half of affected patients are responsive (Kraus et al. 1999), betaine therapy, folate and vitamin B12 supplementation, and limiting dietary intake of protein and methionine (Picker and Levy 2014). Dietary control is most effective at preventing or ameliorating symptoms when introduced early in life (Mudd, Levy and Kraus 2014).

Genetics

Classic homocystinuria is inherited in an autosomal recessive manner. The CBS gene is the only gene known to be involved. To date, nearly 200 pathogenic variants have been reported in CBS (Human Gene Mutation Database; CBS Mutation Database). The vast majority of documented variants are missense, although small deletions, insertions and splice variants are also observed. Only a handful of nonsense variants have been reported in this gene to date. In addition, gross deletions have been reported, and the CBS gene is thought to be fairly susceptible to large deletions and rearrangements due to the somewhat high number of Alu repeats at this locus (Mudd, Levy and Kraus 2014). The reported pathogenic variants are found predominantly in the conserved active core of the enzyme, encoded by exons two through seven, with approximately a quarter of missense variants identified to date found in exon three. However, pathogenic variants have been reported in all coding exons of the CBS gene (Mudd, Levy and Kraus 2014; Human Gene Mutation Database).

Three pathogenic variants in the CBS gene are most commonly reported. The first is the missense variant Ile278Thr, which is considered to be a panethnic variant and is thought to account for approximately half of all homocystinuric alleles (Kraus et al. 1999; Mudd, Levy and Kraus 2014). The second is the missense change Gly307Ser, which is the most commonly reported causative variant in patients of Celtic origin and has been reported to account for greater than 70% of alleles in affected individuals of Irish descent (Kraus et al. 1999; Mudd, Levy and Kraus 2014). Lastly, more recent reports have shown that the Thr191Met missense variant makes up approximately 20 - 75% of alleles in individuals of Iberian descent (Urreizti et al. 2006; Cozar et al. 2011).

The CBS protein is part of the transsulfuration pathway in the cell, and is responsible for catalyzing the condensation of serine with homocysteine to form cystathionine, which can then be converted to cysteine. The exact manner in which CBS deficiency leads to the observed clinical symptoms is not fully understood, although a number of possibilities have been proposed (Mudd, Levy and Kraus 2014).

Clinical Sensitivity - Sequencing with CNV PGxome

Overall, the sensitivity of this test is expected to be quite high, as most patients reported to date have been found to have two CBS variants detectable via direct sequencing. The majority of studies with larger patient cohorts have reported pathogenic variant detection via direct sequencing in ~95-98% of patient alleles (Gaustadnes et al. 2002; Kruger et al. 2003; Cozar et al. 2011; Karaca et al. 2014).

Large deletions in the CBS gene have been reported, but appear to be a rare cause of disease (Human Gene Mutation Database).

Testing Strategy

This test provides full coverage of all coding exons of the CBS 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

Individuals with hypermethioninemia and hyperhomocystinuria and/or hyperhomocystinemia are good candidates for this test, as are individuals with clinical features consistent with CBS deficiency. Family members of patients known to have CBS variants are also good candidates. We will also sequence the CBS gene to determine carrier status.

Gene

Official Gene Symbol OMIM ID
CBS 613381
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Disease

Name Inheritance OMIM ID
Homocystinuria Due To Cbs Deficiency AR 236200

Related Tests

Name
Comprehensive Cardiology Panel
Homocystinuria Panel

Citations

  • Carrillo-Carrasco N, Adams D, Venditti CP. 2013. Disorders of Intracellular Cobalamin Metabolism. In: Pagon RA, Adam MP, Ardinger HH, Bird TD, Dolan CR, Fong C-T, Smith RJ, and Stephens K, editors. GeneReviews(®), Seattle (WA): University of Washington, Seattle. PubMed ID: 20301503
  • CBS Mutation Database.
  • Cozar M. et al. 2011. Human Mutation. 32: 835-42.  PubMed ID: 21520339
  • Gaustadnes M. et al. 2002. Human Mutation. 20: 117-26.  PubMed ID: 12124992
  • Human Gene Mutation Database (Bio-base).
  • Karaca M. et al. 2014. Gene. 534: 197-203.  PubMed ID: 24211323
  • Kraus JP. et al. 1999. Human Mutation. 13: 362-75.  PubMed ID: 10338090
  • Kruger W.D. et al. 2003. Human Mutation. 22: 434-41.  PubMed ID: 14635102
  • Mudd HS, Levy HL, Kraus JP. 2014. Disorders of Transsulfuration. In: Valle D, Beaudet AL, Vogelstein B, et al., editors.New York, NY: McGraw-Hill. OMMBID. 
  • Picker JD and Levy HL. 2014. Homocystinuria Caused by Cystathionine Beta-Synthase Deficiency. In: Pagon RA, Adam MP, Ardinger HH, Bird TD, Dolan CR, Fong C-T, Smith RJ, and Stephens K, editors. GeneReviews(®), Seattle (WA): University of Washington, Seattle. PubMed ID: 20301697
  • Urreizti R. et al. 2006. Journal of Human Genetics. 51: 305-13.  PubMed ID: 16479318
  • Watkins and Rosenblatt. 2014. Inherited Disorders of Folate and Cobalamin Transport and Metabolism. In: Valle D, Beaudet A.L., Vogelstein B, et al., editors. New York, NY: McGraw-Hill. OMMBID.

Ordering/Specimens

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


Specimen Types

Specimen Requirements and Shipping Details

PGxome (Exome) Sequencing Panel

PGnome (Genome) Sequencing Panel

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ORDER OPTIONS

View Ordering Instructions

1) Select Test Method (Backbone)


1) Select Test Type


2) Select Additional Test Options

STAT and Prenatal Test Options are not available with Patient Plus.

No Additional Test Options are available for this test.

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