Comprehensive analysis of ADA2 genetic variants and estimation of carrier frequency driven by a function-based approach.

Abstract

BACKGROUND\nDeficiency of adenosine deaminase 2 (DADA2) is an autoinflammatory disease caused by deleterious ADA2 variants. The frequency of these variants in the general population, and hence the expected disease prevalence, remain unknown.\n\n\nOBJECTIVE\nWe aim to characterize the functional impact and carrier frequency of ADA2 variants.\n\n\nMETHODS\nWe performed functional studies and in silico analysis on 163 ADA2 variants, including DADA2-associated variants and population variants identified in the Genome Aggregation Database (gnomAD). We estimated the carrier rate using the aggregate frequency of deleterious variants.\n\n\nRESULTS\nFunctional studies of ADA2 variants revealed that 77/85 (91%) of DADA2-associated variants reduced ADA2 enzymatic function by > 75%. Analysis of 100 ADA2 variants in gnomAD showed a full spectrum of impact on ADA2 function, rather than a dichotomy of benign versus deleterious variants. We found several in silico algorithms that effectively predicted the impact of ADA2 variants with high sensitivity and specificity, and confirmed a correlation between the residual function of ADA2 variants in vitro and the plasma ADA2 activity of individuals carrying these variants (n = 45; r = 0.649; p < 0.0001). Using < 25% residual enzymatic activity as the cut-off to define potential pathogenicity, integration of our results with gnomAD population data revealed an estimated carrier frequency of at least 1 in 236 individuals, corresponding to an expected DADA2 disease prevalence of ∼1 in 222,000 individuals.\n\n\nCONCLUSION\nFunctional annotation guides the interpretation of ADA2 variants to create a framework that enables estimation of DADA2 carrier frequency and disease prevalence.