Introduction: Gorlin syndrome (GS) or basal cell nevus syndrome type 1 (BCNS1) is a rare genetic disease belonging to the spectrum of genodermatoses. Here, we present a case with BCNS1 that was caused by haploinsufficiency of PTCH1 gene, which is associated with BCNS1. Methods: A diagnosis for BCNS1 was clinically set for a 15-year-old female patient who presented with four nevoid skin lesions, four radiolucent osteolytic lesions of the jaws, macrocephaly, unilateral congenital cataracts, strabismus, hypertelorism, and calcification of the falx cerebri. The patient’s parents bore no clinical findings indicative of the syndrome. Results: Whole exome sequencing and array comparative genomic hybridization revealed a heterozygous 2.5 million base pair deletion in the long arm of chromosome 9 (9q22.32q22.33), which encompasses PTCH1 gene among others. Conclusion: The suggested clinical diagnosis for Gorlin syndrome type 1 was confirmed by genetic analysis. Loss-of-function mutations in PTCH1 gene, including large deletions, are known to promote the formation of neoplasms and craniomaxillofacial phenotype observed in BCNS1 by relieving the inhibition of the sonic hedgehog pathway, which is implicated in cell proliferation.