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HelpTest ID: ALAGP Alagille Syndrome Gene Panel, Varies
Ordering Guidance
Targeted testing for familial variants (also called site-specific or known mutations/variants testing) is available for the genes on this panel. See FMTT / Familial Variant, Targeted Testing, Varies. To obtain more information about this testing option, call 800-533-1710.
Customization of this panel and single gene analysis for any gene present on this panel are available. For more information, see CGPH / Custom Gene Panel, Hereditary, Next-Generation Sequencing, Varies.
Shipping Instructions
Specimen preferred to arrive within 96 hours of collection.
Specimen Required
Patient Preparation: A previous bone marrow transplant from an allogenic donor will interfere with testing. Call 800-533-1710 for instructions for testing patients who have received a bone marrow transplant.
Container/Tube:
Preferred: Lavender top (EDTA) or yellow top (ACD)
Acceptable: Any anticoagulant
Specimen Volume: 3 mL
Collection Instructions:
1. Invert several times to mix blood.
2. Send whole blood specimen in original tube. Do not aliquot.
Specimen Stability Information: Ambient (preferred)/Refrigerated
Forms
1. New York Clients-Informed consent is required. Document on the request form or electronic order that a copy is on file. The following documents are available:
-Informed Consent for Genetic Testing (T576)
-Informed Consent for Genetic Testing-Spanish (T826)
2. Hereditary Renal Genetic Testing Patient Information (T918)
3. If not ordering electronically, complete, print, and send a Renal Diagnostics Test Request (T830) with the specimen.
Useful For
Providing a genetic evaluation for patients with a personal or family history suggestive of Alagille syndrome
Establishing a diagnosis of Alagille syndrome
Genetics Test Information
This test utilizes next-generation sequencing to detect single nucleotide, small deletion-insertion, and copy number variants in two genes (JAG1, NOTCH2) associated with Alagille syndrome. See Targeted Genes and Methodology Details for Alagille Syndrome Gene Panel and Method Description for additional details.
Identification of a disease-causing variant may assist with diagnosis, prognosis, clinical management, familial screening, and genetic counseling for Alagille syndrome.
Method Name
Sequence Capture and Next Generation Sequencing (NGS)
Reporting Name
Alagille Syndrome Gene PanelSpecimen Type
VariesSpecimen Minimum Volume
1 mL
Specimen Stability Information
| Specimen Type | Temperature | Time | Special Container |
|---|---|---|---|
| Varies | Varies | ||
Clinical Information
Alagille syndrome (ALGS) is a multisystemic genetic condition with a wide spectrum of clinical variability. Characteristic features of ALGS include bile duct paucity, cholestasis, congenital heart defects, butterfly vertebrae, eye findings, and facial features including a broad forehead, deeply set eyes, and a small, pointed chin.(1) Approximately 40% of individuals also have kidney disease. The kidney features may include structural abnormalities (eg, small hyperechoic kidney, kidney cysts, or ureteropelvic obstruction) as well as kidney dysfunction, such as renal tubular acidosis.
Disease-causing variants in the JAG1 gene account for approximately 94% to 97% of ALGS, while disease-causing NOTCH2 gene variants account for approximately 1% to 3% of cases.(1,2) A small percentage of individuals with a clinical diagnosis of ALGS do not have an identified disease-causing variant in either JAG1 or NOTCH2.
The severity of ALGS is highly variable among individuals, ranging from mild and subclinical, to severe heart or liver disease requiring transplantation. ALGS is inherited in an autosomal dominant manner. Approximately 30% to 50% of individuals inherit ALGS from an affected parent, while about 50% to 70% of cases are de novo. Parental somatic mosaicism and germline mosaicism have been reported.
Reference Values
An interpretive report will be provided.
Interpretation
All detected variants are evaluated according to American College of Medical Genetics and Genomics recommendations.(3) Variants are classified based on known, predicted, or possible pathogenicity and reported with interpretive comments detailing their potential or known significance.
Clinical Reference
1. Spinner NB, Gilbert MA, Loomes KM, Krantz ID: Alagille syndrome. In: Adam MP, Ardinger HH, Pagon RA, et al, eds. GeneReviews [Internet]. University of Washington, Seattle; 2000. Updated December 12, 2019. Accessed June 7, 2022. Available at www.ncbi.nlm.nih.gov/books/NBK1273/
2. Turnpenny P, Ellard S: Alagille syndrome: pathogenesis, diagnosis and management. Eur J Hum Genet. 2012 Mar;20(3):251-257
3. Richards S, Aziz N, Bale S, et al: Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015 May;17(5):405-424
Day(s) Performed
Varies
Report Available
28 to 42 daysTest Classification
This test was developed and its performance characteristics determined by Mayo Clinic in a manner consistent with CLIA requirements. It has not been cleared or approved by the US Food and Drug Administration.CPT Code Information
81407
81479
81479 (if appropriate for government payers)
LOINC Code Information
| Test ID | Test Order Name | Order LOINC Value |
|---|---|---|
| ALAGP | Alagille Syndrome Gene Panel | 51966-0 |
| Result ID | Test Result Name | Result LOINC Value |
|---|---|---|
| 618031 | Test Description | 62364-5 |
| 618032 | Specimen | 31208-2 |
| 618033 | Source | 31208-2 |
| 618034 | Result Summary | 50397-9 |
| 618035 | Result | 82939-0 |
| 618036 | Interpretation | 69047-9 |
| 618037 | Additional Results | 82939-0 |
| 618038 | Resources | 99622-3 |
| 618039 | Additional Information | 48767-8 |
| 618040 | Method | 85069-3 |
| 618041 | Genes Analyzed | 48018-6 |
| 618042 | Disclaimer | 62364-5 |
| 618043 | Released By | 18771-6 |
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