Thus, 10.1% of our original SLE patients (SLE1, n = 7 of 69) (Fig. 2a) and 10.9% of our replication cohort (SLE2, n = 7 of 64) had a rare or novel missense SNV in BLK. Rare or novel missense SNVs in BLK were found at significantly lower frequencies in a common variable immunodeficiency/complex immunodeficiency (CVID/CID) cohort (n = 3 of 107, 2.8%, p ⩽ 0.02) but at comparable frequency in healthy controls (n = 7 of 97, 7.2%, p = 0.5). Here, BLK is linked to common variable immunodeficiency.