Figure 4C shows the locations of the CNV alterations of these genes on chromosomes. Gene mutations were found in 47 (9.29%) of the 506 samples. Indeed, we found that PLOD2 was the most frequently mutated gene in patients with HNSCC, followed by ASNS, CCT6A, P4HA1, STIP1, HSPA5, MTHFD2, and STC1; the other 17 genes showed no mutations or mutations in less than 1% of samples. The missense mutation ranked as the top variant classification, and C > T was the most common single-nucleotide variant (SNV) class (Figure 4D). Here, MTHFD2 is linked to head and neck squamous cell carcinoma.