Abstract Objective Muscle segment homeobox gene 1 ( MSX1 ) is widely expressed in craniofacial development and tooth formation. The aim of this study was to report a novel MSX1 mutation in a Chinese family with selective tooth agenesis and abnormal median maxillary labial frenum (MMLF). Materials and Methods Mutation analysis was carried out by whole exome sequencing. The pMD18‐T vector was used to verify the mutations. PubMed and Human Gene Mutation Database were searched to analyze the relationship between the mutations in MSX1 and related phenotypes. Results A novel heterozygous mutation (c.75delG) in MSX1 was detected in the proband and her mother. They presented as oligodontia and lower attached hypertrophy median maxillary labial frenum. 60 MSX1 mutations from 39 reports did not declare malformed MMLF except our cases. Meanwhile, we found that the types and sites of MSX1 mutations may affect the selectivity of tooth agenesis and orofacial cleft. Conclusion This study suggests malformed MMLF as a new phenotype of MSX1 mutation and a specific relationship between MSX1 genotype and phenotype.