In summary, the present study identified N-glycosylated PHKB (Asn-935, H5N2F0S0; Asn-935, H4N4F0S0; Asn-935, H5N4F0S0), CEACAM5 (Asn-197, H5N4F0S0) and ATP6V0A4 (Asn-367, H6N4F0S0) as promising cyst fluid biomarkers that exhibited high accuracy and outperformed traditional protein biomarkers in distinguishing malignant PCNs. The gene discussed is ATP6V0A4; the disease is cyst.