IntroductionA previous study suggested that loss of CFAP47 function is involved in multiple morphological abnormalities of the sperm flagella (MMAF) in humans and mice. However, the comprehensive role ofCFAP47in spermatogenesis is largely unknown.MethodsWhole-exome sequencing (WES) was conducted to identify pathogenic variant in two patients with MMAF. The functional effect of the identified mutations was investigated by immunofluorescence staining and western blotting. Intracytoplasmic sperm injection (ICSI) was used to assist fertilization for the patient with MMAF.ResultsIn this study, we identified a novel missense mutation (c.1414G>A; p.V472M) inCFAP47 in two unrelated patients with oligoasthenoteratozoospermia. Intriguingly, in addition to the MMAF phenotype very analogous to the previous report, the two patients notably presented abnormal morphology of sperm heads, the sperm mitochondrial sheath was obviously disorganized, and the sperm annulus were almost defective. Further functional experiments confirmed that the expression of CFAP47 was markedly reduced in the spermatozoa of the patients. Mechanism analysis suggested that CFAP47 might regulate the expression of CFAP65, CFAP69 and SEPTIN4 through their physical interactions and thus modulating sperm morphogenesis.Conclusionwe revealed a novel mutation inCFAP47and further expanded the phenotype and mutation spectrum ofCFAP47, as well as the potential mechanism ofCFAP47manipulating spermatogenesis, finally providing important guidance for genetic counseling and targeted treatment forCFAP47mutation-related male infertility.