TEST CATALOG ORDERING & RESULTS SPECIMEN HANDLING CUSTOMER SERVICE EDUCATION & INSIGHTS
Test Catalog

Test ID: GATA2    
GATA-Binding Protein 2 (GATA2), Full Gene, Next-Generation Sequencing, Varies

Useful For Suggests clinical disorders or settings where the test may be helpful

A comprehensive evaluation of the GATA2 gene in patients with clinical or immunological symptoms suggestive of GATA-binding protein 2 (GATA2) deficiency

 

Screening family members of patients with confirmed GATA2 deficiency

Genetics Test Information Provides information that may help with selection of the correct genetic test or proper submission of the test request

This test includes next-generation sequencing and supplemental Sanger sequencing.

 

Identification of a pathogenic variant may assist with prognosis, clinical management, familial screening, and genetic counseling.

Testing Algorithm Delineates situations when tests are added to the initial order. This includes reflex and additional tests.

For skin biopsy or cultured fibroblast specimens, fibroblast culture and cryopreservation testing will be performed at an additional charge. If viable cells are not obtained, the client will be notified.

Clinical Information Discusses physiology, pathophysiology, and general clinical aspects, as they relate to a laboratory test

GATA-binding protein 2 (GATA2) deficiency is emerging as the second most common primary immunodeficiency disorder (PIDD) or inborn error of immunity in adults, after common variable immunodeficiency (CVID). There is a spectrum of clinical presentations associated with GATA2 deficiency, including severe viral infections (eg, human papillomavirus [HPV]), warts, fungal infections, bacterial infections (eg, atypical mycobacterial infections such as nontuberculous mycobacterial infections [NTM] or mycobacterium avium complex [MAC]), myelodysplastic syndrome (MDS), acute myeloid leukemia (AML), and Emberger syndrome (primary lymphedema with MDS). Other clinical phenotypes of GATA2 deficiency may include aplastic anemia, pulmonary alveolar proteinosis (PAP), sensorineural hearing loss, neutropenia, and congenital lymphedema without MDS at diagnosis. Immunological phenotypes include dendritic cell, monocyte, CD4+ T cell, B and natural killer (NK) cell deficiencies. Also, the loss of a specific NK-cell subset, CD56 bright NK cells, has been reported in these patients. GATA2 deficiency was first described in 2011 as being associated with either MonoMAC (monocytopenia and mycobacterial infection) syndrome or DCML deficiency (dendritic cell, monocyte, B and NK cell lymphocyte deficiency).

 

GATA2 is a zinc finger transcription factor, involved in the generation and function of hematopoietic stem cell progenitors and, therefore, affects several of the subsequent cell lineages.

 

GATA2 deficiency is a disease of haploinsufficiency, and most germline variants appear to arise de novo (spontaneously) but are then transmitted in an autosomal dominant manner. Standard genotype-phenotype correlations are difficult to make, as there is considerable clinical heterogeneity and the age of presentation varies from early childhood to late in adult life. Additionally, there may be a role for environmental factors triggering certain infectious manifestations. There has been incomplete penetrance (not every individual with a variant has a clinical phenotype) observed with GATA2 deficiency as well as variable expressivity (different clinical presentations for the same genetic variant).The genetic alterations observed in GATA2 are heterogeneous, and include missense variants, nonsense variants, and variants in the regulatory region of intron 5, in-frame deletions involving the C-terminal zinc finger domain, frameshift variants, and large deletions. The latter are associated with null alleles, while regulatory variants have been observed in the enhancer region of intron 5.

 

Somatic variants in ASXL1 have been reported in GATA2 deficiency patients and have been postulated to be associated with transformation to myeloid leukemia. The definitive treatment for GATA2 deficiency is hematopoietic cell transplantation (HCT). Additionally, systemic use of interferon-alpha may be helpful in patients with NK cell deficiency who have recurrent or severe HPV or herpes virus infections. Also, prophylactic antibiotics may be needed or mandated in the nontransplanted patient. The pulmonary alveolar proteinosis observed in GATA2 deficiency is in the context of negative results for anti-GM-CSF autoantibodies has been shown to improve after HCT and suggests correction of alveolar macrophage function.

 

Early genetic diagnosis of GATA2 deficiency is critical in determining strategies for managing the disease considering the broad clinical spectrum. Genetic diagnosis by confirmation of a pathogenic GATA2 variant may also aid in family counseling and screening.

Reference Values Describes reference intervals and additional information for interpretation of test results. May include intervals based on age and sex when appropriate. Intervals are Mayo-derived, unless otherwise designated. If an interpretive report is provided, the reference value field will state this.

An interpretive report will be provided.

Interpretation Provides information to assist in interpretation of the test results

Evaluation and categorization of variants is performed using the most recent published American College of Medical Genetics and Genomics (ACMG) recommendations. Variants are classified based on known, predicted, or possible pathogenicity and reported with interpretive comments detailing their potential or known significance.

 

Unless reported or predicted to cause disease, alterations found deep in the intron or alterations that do not result in an amino acid substitution are not reported.

Cautions Discusses conditions that may cause diagnostic confusion, including improper specimen collection and handling, inappropriate test selection, and interfering substances

The nomenclature of variants identified in the GATA2 gene may vary depending on the reference transcript used. When comparing the result to published literature this fact should be kept in mind.

 

CLINICAL CORRELATIONS:

Some individuals who have involvement of one or more of the genes on the panel may have a variant that is not identified by the methods performed (eg, promoter variants, deep intronic variants). The absence of a variant, therefore, does not eliminate the possibility of disease. Test results should be interpreted in context of clinical findings, family history, and other laboratory data. Misinterpretation of results may occur if the information provided is inaccurate or incomplete.

 

For predictive testing of asymptomatic individuals, it is often useful to first test an affected family member. Identification of a pathogenic variant in an affected individual allows for more informative testing of at-risk individuals.

 

TECHNICAL LIMITATIONS:

Next-generation sequencing may not detect all types of genetic variants. Additionally, rare variants may be present that could lead to false-negative or false-positive results. If results do not match clinical findings, consider alternative methods for analyzing these genes, such as Sanger sequencing or large deletion/duplication analysis.

 

If the patient has had an allogeneic blood or bone marrow transplant or a recent (ie, <6 weeks from time of sample collection) heterologous blood transfusion, results may be inaccurate due to the presence of donor DNA.

 

EVALUATION TOOLS:

Multiple in silico evaluation tools may be used to assist in the interpretation of these results. The accuracy of predictions made by in silico evaluation tools is highly dependent upon the data available for a given gene, and predictions made by these tools may change over time. Results from in silico evaluation tools should be interpreted with caution and professional clinical judgment.

 

Reclassification of Variants-Policy:

At this time, it is not standard practice for the laboratory to systematically review likely pathogenic variants or variants of uncertain significance that are detected and reported. 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. Consultation with a healthcare provider, or team of healthcare providers, with expertise in genetics and primary immunodeficiencies, is recommended for interpretation of this result.

 

A list of benign and likely benign variants detected is available from the lab upon request.

 

Contact the laboratory if additional information is required regarding the transcript or human genome assembly used for the analysis of results.

Clinical Reference Recommendations for in-depth reading of a clinical nature

1. Spinner MA, Sanchez LA, Hsu AP, et al: GATA2 deficiency: a protean disorder of hematopoiesis, lymphatics and immunity. Blood 2014;123:809-821

2. Dickinson RE, Griffin H, Bigley V, et al: Exome sequencing identifies GATA-2 mutation as the cause of dendritic cells, monocyte, B and NK lymphoid deficiency. Blood 2011;118:2656-2658

3. Hsu AP, Sampaio EP, Khan J, et al: Mutations in GATA2 are associated with the autosomal dominant and sporadic monocytopenia and mycobacterial infection (MonoMAC) syndrome. Blood 2011;118:2653-2655

4. Mace EM, Hsu AP, Monaco-Shawver L, et al: Mutations in GATA2 cause human NK cell deficiency with specific loss of the CD56bright subset. Blood 2013;121:2669-2677

5. Ostergaard P, Simpson MA, Connell FC, et al: Mutations in GATA2 cause primary lymphedema associated with a predisposition to acute myeloid leukemia (Emberger syndrome). Nature Genetics 2011;43:929-931

6. West RR, Hsu AP, Holland SM, et al: Acquired ASXL1 mutations are common in patients with inherited GATA2 mutations and correlate with myeloid transformation. Haematologica 2014;99:276-281

7. Cuellar-Rodriguez J, Gea-Banacloche J, Freeman AF, et al: Successful allogeneic hematopoietic stem cell transplantation for GATA2 deficiency. Blood 2011;118:3715-3720

8. Hsu AP, McReynolds LJ, Holland SM: GATA2 deficiency. Curr Opin Allergy Clin Immunol 2015;15:104-109

Special Instructions Library of PDFs including pertinent information and forms related to the test