Although TP53 mutations or SVs were not observed in the malignant cases with KIT Δ557–558 except in one case, the p53 inactivation signature was significantly higher (P = 0.019), along with the CIN signature (P = 0.030) and the hypoxia signature (P = 0.00096; Supplementary Data S4). Here, KIT is linked to cervical squamous intraepithelial neoplasia.