Comparisons of the HLA risk allele frequencies between the PR3-cANCA positive subgroup (88% of cases) and the ANCA-negative subgroup showed that the associations with HLA–DPB1 (rs9277554, P = 4.7 × 10−57) and HLA–DPA1 (rs9277341, P = 2.30 × 10−42) were caused by the PR3-cANCA positive group, a finding, which confirms previous data suggesting genetic differences between ANCA-positive and ANCA-negative GPA. Here, PRTN3 is linked to granulomatosis with polyangiitis.