ALPS Gene Panel
GTR Test Accession: Help GTR000607884.2
INHERITED DISEASEIMMUNOLOGYSYNDROMIC DISEASE ... View more
Last updated in GTR: 2024-05-15
Last annual review date for the lab: 2024-05-28 LinkOut
At a Glance
Diagnosis
Sneddon syndrome; Activated PI3K-delta syndrome; Agammaglobulinemia 7, autosomal recessive; ...
ADA2 (22q11.1), CARD11 (7p22.2), CASP10 (2q33.1), CASP8 (2q33.1), CTLA4 (2q33.2), ...
Molecular Genetics - Deletion/duplication analysis: Next-Generation (NGS)/Massively parallel sequencing (MPS); ...
Providing a comprehensive genetic evaluation for patients with a personal …
Not provided
Establish or confirm diagnosis
Ordering Information
Offered by: Help
Test short name: Help
ALPSG
Specimen Source: Help
Who can order: Help
  • Genetic Counselor
  • Health Care Provider
  • Licensed Dentist
  • Licensed Physician
  • Nurse Practitioner
  • Physician Assistant
  • Public Health Mandate
  • Registered Nurse
Lab contact: Help
Elyse Love, MS, CGC, Certified Genetic counselor, CGC, Genetic Counselor
gcmolgen@mayo.edu
1-800-533-1710
Contact Policy: Help
Laboratory can only accept contact from health care providers. Patients/families are encouraged to discuss genetic testing options with their health care provider.
How to Order: Help
https://www.mayocliniclabs.com/test-catalog/overview/619746#Specimen
Order URL
Test development: Help
Manufactured (research use only; not FDA-reviewed)
Informed consent required: Help
Based on applicable state law
Pre-test genetic counseling required: Help
Decline to answer
Post-test genetic counseling required: Help
Decline to answer
Recommended fields not provided:
Conditions Help
Total conditions: 34
Condition/Phenotype Identifier
Test Targets
Genes Help
Total genes: 26
Gene Associated Condition Germline or Somatic Allele (Lab-provided) Variant in NCBI
Methodology
Total methods: 2
Method Category Help
Test method Help
Instrument
Deletion/duplication analysis
Next-Generation (NGS)/Massively parallel sequencing (MPS)
Other
Sequence analysis of the entire coding region
Next-Generation (NGS)/Massively parallel sequencing (MPS)
Vasculitis, autoinflammation, immunodeficiency, and hematologic defects syndrome
Clinical Information
Test purpose: Help
Diagnosis
Clinical utility: Help
Establish or confirm diagnosis
View citations (3)
  • Oliveira JB, Bleesing JJ, Dianzani U, Fleisher TA, Jaffe ES, Lenardo MJ, Rieux-Laucat F, Siegel RM, Su HC, Teachey DT, Rao VK. Revised diagnostic criteria and classification for the autoimmune lymphoproliferative syndrome (ALPS): report from the 2009 NIH International Workshop. Blood. 2010;116(14):e35-40. doi:10.1182/blood-2010-04-280347. Epub 2010 Jun 10. PMID: 20538792.
  • Key diagnostic markers for autoimmune lymphoproliferative syndrome with molecular genetic diagnosis. Molnár E, et al. Blood. 2020;136(17):1933-1945. doi:10.1182/blood.2020005486. PMID: 32599613.
  • Consonni F, Gambineri E, Favre C. ALPS, FAS, and beyond: from inborn errors of immunity to acquired immunodeficiencies. Ann Hematol. 2022;101(3):469-484. doi:10.1007/s00277-022-04761-7. Epub 2022 Jan 20. PMID: 35059842.

Target population: Help
Providing a comprehensive genetic evaluation for patients with a personal or family history suggestive of autoimmune lymphoproliferative syndrome (ALPS) or related disorders Establishing a diagnosis of ALPS or a related disorder, allowing for appropriate management and surveillance for disease features based on the gene or variant involved Identifying variants within … View more
View citations (6)
  • Oliveira JB, Bleesing JJ, Dianzani U, Fleisher TA, Jaffe ES, Lenardo MJ, Rieux-Laucat F, Siegel RM, Su HC, Teachey DT, Rao VK. Revised diagnostic criteria and classification for the autoimmune lymphoproliferative syndrome (ALPS): report from the 2009 NIH International Workshop. Blood. 2010;116(14):e35-40. doi:10.1182/blood-2010-04-280347. Epub 2010 Jun 10. PMID: 20538792.
  • Price S, Shaw PA, Seitz A, Joshi G, Davis J, Niemela JE, Perkins K, Hornung RL, Folio L, Rosenberg PS, Puck JM, Hsu AP, Lo B, Pittaluga S, Jaffe ES, Fleisher TA, Rao VK, Lenardo MJ. Natural history of autoimmune lymphoproliferative syndrome associated with FAS gene mutations. Blood. 2014;123(13):1989-99. doi:10.1182/blood-2013-10-535393. Epub 2014 Jan 07. PMID: 24398331.
  • Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL, . 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;17(5):405-24. doi:10.1038/gim.2015.30. Epub 2015 Mar 05. PMID: 25741868.
  • Key diagnostic markers for autoimmune lymphoproliferative syndrome with molecular genetic diagnosis. Molnár E, et al. Blood. 2020;136(17):1933-1945. doi:10.1182/blood.2020005486. PMID: 32599613.
  • López-Nevado M, González-Granado LI, Ruiz-García R, Pleguezuelo D, Cabrera-Marante O, Salmón N, Blanco-Lobo P, Domínguez-Pinilla N, Rodríguez-Pena R, Sebastián E, Cruz-Rojo J, Olbrich P, Ruiz-Contreras J, Paz-Artal E, Neth O, Allende LM. Primary Immune Regulatory Disorders With an Autoimmune Lymphoproliferative Syndrome-Like Phenotype: Immunologic Evaluation, Early Diagnosis and Management. Front Immunol. 2021;12:671755. doi:10.3389/fimmu.2021.671755. Epub 2021 Aug 10. PMID: 34447369.
  • Consonni F, Gambineri E, Favre C. ALPS, FAS, and beyond: from inborn errors of immunity to acquired immunodeficiencies. Ann Hematol. 2022;101(3):469-484. doi:10.1007/s00277-022-04761-7. Epub 2022 Jan 20. PMID: 35059842.
Variant Interpretation:
What is the protocol for interpreting a variation as a VUS? Help
All detected variants are evaluated according to the most recent American College of Medical Genetics and Genomics (ACMG) and Association for Molecular Pathology (AMP) recommendations. Variants are classified based on known, predicted, or possible pathogenicity and reported with interpretive comments detailing their potential or known significance.

Will the lab re-contact the ordering physician if variant interpretation changes? Help
Not provided. The laboratory encourages health care providers to contact the laboratory at any time to learn how the status of a particular variant may have changed over time.
Research:
Is research allowed on the sample after clinical testing is complete? Help
Research testing is only performed under IRB approved protocol with an opt-out policy in place.
Recommended fields not provided:
Technical Information
Test Procedure: Help
Next-generation sequencing (NGS) and/or Sanger sequencing are performed to test for the presence of variants in coding regions and intron/exon boundaries of the genes analyzed, as well as some other regions that have known disease-causing variants. The human genome reference GRCh37/hg19 build was used for sequence read alignment. At least … View more
Availability: Help
Tests performed
Entire test performed in-house
Analytical Validity: Help
At least 99% of the bases are covered at a read depth >30X. Sensitivity is estimated at >99% for single nucleotide variants, >94% for indels up to 39 base pairs, >95% for deletions up to 75 base pairs and insertions up to 47 base pairs.
Assay limitations: Help
Clinical Correlations: Test results should be interpreted in the context of clinical findings, family history, and other laboratory data. Misinterpretation of results may occur if the information provided is inaccurate or incomplete. If testing was performed because of a clinically significant family history, it is often useful to first test … View more
Proficiency testing (PT):
Is proficiency testing performed for this test? Help
Yes

Method used for proficiency testing: Help
Platform PT performed

Description of internal test validation method: Help
This test was laboratory developed, and its performance characteristics determined by Mayo Clinic in a manner consistent with CLIA requirements
VUS:
Software used to interpret novel variations Help
Variants may be analyzed using any combination of the following: Alamut, REVEL, Polyphen-2, SIFT, AGVGD, MutationTaster, SpliceSiteFinder-like, MaxEntScan, NNSPLICE, GeneSplicer, SpliceAI, gene-specific online databases, ISCA, UCSC Genome Browser

Laboratory's policy on reporting novel variations Help
All novel alterations and copy number variants are evaluated for potential pathogenicity and included in the written report, accordingly.
Recommended fields not provided:
Regulatory Approval
FDA Review: Help
Category: FDA exercises enforcement discretion
Additional Information

IMPORTANT NOTE: NIH does not independently verify information submitted to GTR; it relies on submitters to provide information that is accurate and not misleading. NIH makes no endorsements of tests or laboratories listed in GTR. GTR is not a substitute for medical advice. Patients and consumers with specific questions about a genetic test should contact a health care provider or a genetics professional.