In the current study, through the low-frequency variants association studies by SKAT method, we identified several genes significantly associated with isolated unilateral microtia, including MUC4, MUC6, COL4A4, MYO7A, AKAP12, COL11A1, DSPP, ESPN, GPR98, PCDH15, BSN, CACNA1D, TPRN, and USH1C. Of these genes, two were related to the pathways we identified using KEGG pathway enrichment analysis. Here, COL4A4 is linked to microtia.