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Alagille Syndrome Panel

Summary and Pricing

Test Method

Exome Sequencing with CNV Detection
Test Code Test Copy Genes Gene CPT Codes Copy CPT Codes
JAG1 81407,81406
NOTCH2 81479,81479
Test Code Test Copy Genes Panel CPT Code Gene CPT Codes Copy CPT Code Base Price
10071Genes x (2)81479 81406(x1), 81407(x1), 81479(x2) $990 Order Options and Pricing

Pricing Comments

We are happy to accommodate requests for testing single genes in this panel or a subset of these genes. The price will remain the list price. If desired, free reflex testing to remaining genes on panel is available. Alternatively, a single gene or subset of genes can also be ordered via our Custom Panel tool.

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).

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


  • Ben Dorshorst, PhD

Clinical Features and Genetics

Clinical Features

Alagille syndrome is characterized by cholestasis (caused by abnormalities in the bile ducts), congenital heart defects (featured by pulmonic stenosis), ophthalmic findings (featured by posterior embryotoxon), vertebral defects (featured by butterfly vertebrae), and characteristic facies (including deep-set eyes with moderate hypertelorism, a broad forehead, a prominent pointed chin, and a long straight nose with a bulbous tip) (Emerick et al. 1999). Symptoms can start in infancy or early childhood. Phenotypes vary greatly among affected individuals, even within the same family.


Alagille syndrome is an autosomal dominant disorder caused by defects in JAG1 or NOTCH2. The JAG1 gene (26 coding exons) encodes the ligand for the receptor Notch 1 in the Notch signaling pathway. Alagille syndrome is most often caused by dominant JAG1 pathogenic variants (Oda et al. 1997; Warthen et al. 2006). Pathogenic defects in JAG1 include missense, nonsense, splicing site variants, small indels and large deletions/duplications (Human Gene Mutation Database).

The NOTCH2 gene (34 coding exons) encodes the receptor Notch 2 in the Notch signaling pathway. Dominant NOTCH2 pathogenic variants can cause both Alagille syndrome (McDaniell et al. 2006) and the skeletal disorder Hajdu-Cheney syndrome (Simpson et al. 2011). NOTCH2 defects are a minor cause for Alagille syndrome, accounting for less than 6% of all cases (McDaniell et al. 2006). Genetic defects of NOTCH2 found to date include missense, nonsense, splicing variants and small deletion/insertions (Human Gene Mutation Database). Exon-level large deletions/duplication involving NOTCH2 have not been reported.

Clinical Sensitivity - Sequencing with CNV PGxome

JAG1 pathogenic variants were found in 232 out of 247 (94%) patients with clinically well-defined Alagille syndrome overall (Warthen et al. 2006). Given that large deletions and duplications affecting JAG1 were found to be about 5% (Warthen et al. 2006; Li et al. 2015), the mutation detection rate of JAG1 via sequencing is expected to be approximately 90%. NOTCH2 defects are a minor cause for Alagille syndrome, accounting for less than 6% of all cases (McDaniell et al. 2006).

The prevalence of large deletions and duplications affecting the JAG1 gene was found to be about 5% in Alagille syndrome (Warthen et al. 2006; Li et al. 2015). Large deletions encompassing the entire JAG1 gene are the major type of copy number change affecting this gene (Warthen et al. 2006; Li et al. 2015; Kamath et al. 2009). Large deletions/duplication involving NOTCH2 have not been reported.

Testing Strategy

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

This panel typically provides 93.3% 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).

This test does not include coverage for exons 1 to 4 of the NOTCH2 gene because of high sequence similarity to one or more additional chromosomal regions. So far, no pathogenic variants have been reported in these exons.

Indications for Test

Candidates for this test are patients with Alagille syndrome.


Official Gene Symbol OMIM ID
JAG1 601920
NOTCH2 600275
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Alagille Syndrome 1 AD 118450
Alagille Syndrome 2 AD 610205

Related Test



  • Emerick K.M. et al. 1999. Hepatology. 29: 822-9. PubMed ID: 10051485
  • Human Gene Mutation Database (Bio-base).
  • Kamath B.M. et al. 2009. Human Mutation. 30: 371-8. PubMed ID: 19058200
  • Li L. et al. 2015. Plos One. 10: e0130355. PubMed ID: 26076142
  • McDaniell R. et al. 2006. American Journal of Human Genetics. 79: 169-73. PubMed ID: 16773578
  • Oda T. et al. 1997. Nature Genetics. 16: 235-42. PubMed ID: 9207787
  • Simpson M.A. et al. 2011. Nature Genetics. 43: 303-5. PubMed ID: 21378985
  • Warthen D.M. et al. 2006. Human Mutation. 27: 436-43. PubMed ID: 16575836


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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View Ordering Instructions

1) Select Test Method (Platform)

1) Select Test Type

2) Select Additional Test Options

No Additional Test Options are available for this test.

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