The results revealed that LAT2/SPRY2 (odds ratio [OR]: 0.4974, 95% confidence interval [CI]: 0.2506–0.9871; p = 0.045), FAP/THBS4 (OR: 0.6537, 95% CI: 0.4919–0.8687), ICA1/IRAK1 (OR: 1.3014, 95% CI: 1.0345–1.637; p = 0.024), ERBIN/LAT2 (OR: 1.9763, 95% CI: 1.3009–3.0026; p < 0.005), and ITGB1BP2/LAT2 (OR: 1.5055, 95% CI: 1.0418–2.1755; p = 0.029), a total of 93 protein pairs, were associated with increased risk of HCC. This evidence concerns the gene FAP and hepatocellular carcinoma.