The model including AFP (p = 0.0001, β = 0.00069 ± 0.00016, OR = 0.985 [0.973–0.997])), AFP-L3 (p = 0.0031, β = 0.005 ± 0.0016, OR = 1.084 [1.008–1.166]), GPC3 (p = 0.0013, β = 0.000066 ± 0.000020, OR = 0.924 [0.913–0.961]), CK-19 (p = 0.038, β = 0.01 ± 0.005, OR = 0.942 [0.924–0.976]), and serum albumin levels (p < 0.0001, β = 0.235 ± 0.041) was the best model for predicting the presence of HCC (p < 0.001). The gene discussed is GPC3; the disease is hepatocellular carcinoma.