Parry–Romberg syndrome is a rare craniofacial disorder which is characterized by progressive facial atrophy. The etiology and pathogenesis of the disease are not known. Herein, we report the genetic variants in patient with this disease. A 25-year-old woman was diagnosed with Parry–Romberg syndrome according to her clinical manifestation, which presented with typical progressive unilateral facial soft tissue atrophy. Using peripheral blood samples, Whole exome sequencing (WES) was conducted on this patient and her parents. Variant loci of the genes were validated by Sanger sequencing in her twin sister who had no Parry–Romberg syndrome. Subsequently, we searched the GeneCards®: the Human Gene Database for variant genes, annotated them and analyzed their functions. The results of WES showed that 2 genes (MTOR, DHX37) were mutated, and the variant loci were MTOR: NM_004958.4: exon31: c.4487A>T: p.Q1496L and DHX37: NM_032656.4: exon17: c.2180C>T: p.T727M, respectively. However, the variant loci were also detected in her twin sister by Sanger sequencing. The Human Gene Database for variant genes shows that the two genes may be associated with craniomaxillofacial developmental abnormalities. Although MTOR and DHX37 genes were tested and found to have mutations in patient with Parry–Romberg syndrome, these variants may not directly determine the clinical phenotype. When studying clinical etiology, other factors, such as the environment, should also be taken into account.