We identified a three-generation Gorlin Syndrome (GS) family and collected six pairs of skin samples from the three patients (II-2, II-4, II-6) to detect mutational genes. We found the germline mutation c.1341_1342dupA (p.L448Tfs*49) in PTCH1. Moreover, additional driver mutations in ERBB2 and PPP6C were found in two of the six BCCs. Loss of heterozygosity of PPP6C and PTCH1 were observed in two and three of the six BCCs, respectively. Transcriptional analysis by RNA-seq showed up-regulation of the Hh pathway genes in BCCs. We quantified the expression of PTCH1 and its target GLI1 genes in six pairwise samples to confirm the results obtained by RNA-seq, and found that the relatively higher transcript levels of PTCH1 and GLI1 were observed in BCCs compared with ANCT.