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Background  Primary hepatic mucoepidermoid carcinoma (HMEC) is extremely rare and the molecular etiology is still unknown. The  CRTC1-MAML2  fusion gene was previously detected in a primary HMEC, which is often associated with MEC of salivary gland in the literature.    Methods  A 64-year-old male was diagnosed with HMEC based on malignant squamous cells and mucus-secreting cells in immunohistochemical examination. Fluorescence in situ hybridization (FISH) was used to detect the  CRTC1-MAML2  fusion gene in HMEC. Whole-exome sequencing and Sanger sequencing were used to reveal the molecular characteristics of HMEC and analysis was performed with public data. Pedigree investigation was performed to identify susceptibility genes.    Results  Hematoxylin–eosin staining and immunohistochemistry revealed that the tumor cells were composed of malignant epidermoid malignant cells and mucous cells, indicating a diagnosis of HMEC. The  CRTC1-MAML2  fusion gene was not detected in the primary HMEC, and somatic mutations in  GNAS ,  KMT2C  and  ELF3  genes were identified by sequencing. Analyses of public data revealed somatic  GNAS  alterations in 2.1% hepatobiliary tumors and relation with parasite infection. Heterozygous germline mutations of  FANCA ,  FANCI ,  FANCJ/BRIP1  and  FAN1  genes were also identified. Pedigree investigation verified that mutation of Fanconi’s anemia susceptibility genes were present in the pedigree.    Conclusions  Here we provide the first evidence of the molecular etiology of a rare HMEC associated with germline Fanconi’s anemia gene mutations and somatic GNAS R201H mutation.    Supplementary Information  The online version contains supplementary material available at 10.1186/s13000-021-01086-3.

Whole-exome sequencing reveals the etiology of the rare primary hepatic mucoepidermoid carcinoma