For ACPA-positive RA patients, the model reached an AUC of 0.9913 (95% CI = 0.9653–1) (Figure 6B), and the top 15 best-performing proteins were leucine-rich alpha-2-glycoprotein, SAA2, CRP, complement component C9, fibrinogen alpha chain, annexin A1, C4a anaphylatoxin, arfaptin-1, testicular tissue protein Li 70, SAA1, ITIH4 protein, ficolin-3, carbonic anhydrase, hemoglobin subunit alpha, and complement C4-A (Figure 6B). This evidence concerns the gene PRTN3 and rheumatoid arthritis.