Inborn errors of immunity are a heterogeneous group of genetic disorders where patients can present with varied immune dysfunction and recurrent infections. Among these are common variable immunodeficiency (CVID) which is typically more severe in disease presentation, and specific antibody deficiency (SAD) where individuals respond poorly to polysaccharide antigens. Despite significant efforts, only 15–30% of individuals with CVID receive a genetic diagnosis, and surprisingly there have been no major studies into the genetic variation that may underlie SAD. To address this gap, we performed whole-genome short-read sequencing on a cohort of SAD (n=10) and CVID (n=10) individuals to identify novel candidate pathogenic variants. We identified previously described variants in TTC7A (K606R, S672P) and TRNT1 (S418fs) for two individuals with CVID, and an unexpected pathogenic variant in the cystic fibrosis gene CFTR (G85E) in one individual with SAD. We also report novel coding variants in known immune regulatory genes such as CLCN7, TAP1, and TAP2 with predicted deleterious function in the SAD cohort. Unexpectedly, we identified many coding variants with predicted loss-of-function in genes involved in the complement signalling pathway in both CVID and SAD, such as complement 4 (C4). Copy number variation at the C4 locus has been shown to be highly variable within the general population, therefore we quantified C4 copy number in our cohort. We observed a copy number loss at surprisingly high frequency (9/20) in CVID and SAD individuals. Copy number loss at C4 has previously been associated with systemic lupus erythematosus. This loss of heterozygosity at the C4 locus, and the identified loss-of-function variants in the complement genes suggest that dysregulation of this pathway may be implicated in CVID and SAD. Our study has provided novel insights of the genetics underlying SAD and provided further insight to the genetic factors contributing to CVID.