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Evolving spectrum of adenosine deaminase (ADA) deficiency: Assessing genotype pathogenicity according to expressed
Ines Santisteban1, Francisco X Arredondo-Vega1, Pawan Bali1
1Department of Medicine, Division of Rheumatology and Immunology, Duke University School of Medicine, Durham, NC.
Insights
Adenosine deaminase (ADA) deficiency pathogenicity varies. Red blood cell deoxyadenosine nucleotide (dAXP) levels correlate with clinical severity and may offer better prognosis than genotype categories in screened infants.
Area of Science:
- Biochemistry
- Genetics
- Immunology
Background:
- Adenosine deaminase (ADA) deficiency presents with significant clinical and genetic variability.
- Newborn screening identifies infants with indeterminate phenotypes and unknown ADA variants.
- Understanding ADA variant pathogenicity is crucial for accurate diagnosis and prognosis.
Purpose of the Study:
- To systematically evaluate the pathogenic potential of rare ADA missense variants.
- To define the genotype-phenotype relationship concerning red blood cell (RBC) deoxyadenosine nucleotide (dAXP) content.
- To improve the prediction of ADA variant pathogenicity.
Main Methods:
- Expressed 46 ADA missense variants in E. coli to determine activity levels.
- Categorized variants (GCs I-IV) based on expressed ADA activity.
- Correlated genotype categories, RBC dAXP levels, and clinical phenotypes in 58 patients.
Main Results:
- Expressed ADA activity ranged from <0.05% to 70% of wild-type.
- RBC dAXP levels strongly correlated with clinical phenotype and inversely with total ADA activity.
- The developed GC scoring system outperformed AlphaMissense in pathogenicity assessment.
Conclusions:
- ADA deficiency pathogenicity is a continuum influenced by the combined activity of inherited variants.
- RBC dAXP levels may provide superior prognostic value over GC rank in screened infants with indeterminate phenotypes.
- Accurate assessment of ADA variants is essential for managing ADA deficiency.
Background:
Deficiency of adenosine deaminase (ADA or ADA1) has broad clinical and genetic heterogeneity. Screening techniques can identify asymptomatic infants whose phenotype and prognosis are indeterminate, and who may carry ADA variants of unknown significance.
Objective:
We systematically assessed the pathogenic potential of rare ADA missense variants to better define the relationship of genotype to red blood cell (RBC) total deoxyadenosine nucleotide (dAXP) content and to phenotype.
Methods:
We expressed 46 ADA missense variants in the ADA-deficient SØ3834 strain of Escherichia coli and defined genotype categories (GCs) ranked I to IV by increasing expressed ADA activity. We assessed relationships among GC rank, RBC dAXP, and phenotype in 58 reference patients with 50 different genotypes. We used our GC ranking system to benchmark AlphaMissense for predicting variant pathogenicity, and we used a minigene assay to identify exonic splicing variants in ADA exon 9.
Results:
The 46 missense variants expressed ∼0.001% to ∼70% of wild-type ADA activity (40% had <0.05% of wild-type ADA activity and 50% expressed >1%). RBC dAXP ranged from undetectable to >75% of total adenine nucleotides and correlated well with phenotype. Both RBC dAXP and clinical severity were inversely related to total ADA activity expressed by both inherited variants. Our GC scoring system performed better than AlphaMissense in assessing variant pathogenicity, particularly for less deleterious variants.
Conclusion:
For ADA deficiency, pathogenicity is a continuum and conditional, depending on the total ADA activity contributed by both inherited variants as indicated by GC rank. However, in patients with indeterminate phenotype identified by screening, RBC dAXP measured at diagnosis may have greater prognostic value than GC rank.
