Comprehensive functional characterization of complement factor I rare variant genotypes identified in the SCOPE geographic atrophy cohort

Abstract

Rare variants (RVs) in the gene encoding the regulatory enzyme complement factor I (CFI; FI) that reduce protein function or levels increase age-related macular degeneration (AMD) risk. A total of 3357 subjects underwent screening in the SCOPE natural history study for Geographic Atrophy (GA) secondary to AMD, including CFI sequencing followed by serum FI measurement.Eleven CFI RV genotypes that were challenging to categorise as Type I (low serum level) or Type II (normal serum level but reduced enzymatic function) were characterized in the context of pure FI protein in C3b and C4b fluid phase cleavage assays and a novel bead-based functional assay (BBFA) of surface-bound C3b cleavage. A further 4 variants predicted or previously characterized as benign, were analysed using the BBFA to add confidence to their classification.In all, 3 variants [W51S, C67R, I370T] resulted in low expression. A further 4 variants [P64L, R339Q, G527V and P528T] were identified as being highly deleterious with IC50s for C3b breakdown >1 log increased vs the WT protein, while 2 variants [K476E and R474Q] were ∼1 log reduced in function. Meanwhile, 6 variants [P50A, T203I, K441R, E548Q, P553S, S570T] had IC50s similar to wild-type (WT). Odds ratios (ORs) and BBFA IC50s were positively correlated (r=0.76, P<0.01), whilst ORs vs combined annotation dependent depletion (CADD) scores were not (r=0.43, P=0.16).Overall, 15 CFI RVs were functionally characterized which may aid future patient stratification approaches for complement-targeted therapies. Pure protein in vitro analysis remains the gold standard for determining the functional consequence of CFI RVs.