Objective To construct and analyze the mutant genetic profile of hereditary gingival fibromatosis (HGF) and to predict specific mutations and genes relevant to pathogenesis. Methods Samples from a family with obvious maternal inheritance were collected and whole exome sequencing was performed by Agilent SureSelect exome capture and Illumina Solxa sequencing platform. Single nucleotide polymorphisms (SNP) and genes relevant to the onset of HGF were screened by bioinformatic methods and experimental verification and verified against normal people. Results A total of 17 SNPs relevant to the onset of HGF were screened. Verification against about 200 normal people only found a small number of same mutations. Five novel mutations were screened from 5 maternal imprint genes by analyzing the results of expression profile chip. Conclusion The mutation profile of exome of HGF was successfully constructed. Some SNPs were found in normal people with low frequency. Novel mutations were found in 5 maternal imprint genes. Pioneering study has been conducted by introducing the whole exome sequencing technique and can provide reference for the further study.