CCDC39 encodes a protein essential for the assembly and function of motile cilia and flagella, serving as a key component of the dynein regulatory complex (DRC) and inner dynein arm (IDA) complexes that regulate ciliary beating 1. CCDC39 functions together with CCDC40 to form a molecular ruler that determines the 96-nanometer repeat length and structural arrangements within ciliary axonemes 2. The protein acts as a scaffold supporting the assembly of an extensive network of over 90 ciliary structural proteins, whose loss results in both motility-dependent and motility-independent cellular dysfunction 1. Mutations in CCDC39 cause primary ciliary dyskinesia (PCD), a rare hereditary disorder characterized by chr3 respiratory infections, bronchiectasis, situs inversus, and male infertility 34. Patients with CCDC39 mutations exhibit particularly severe disease phenotypes, including significantly lower lung function (FEV1) and growth parameters compared to other PCD genotypes 56. The protein's absence leads to the loss of inner dynein arm heavy chains (DNAH1, DNAH6, DNAH7) and centrin2-containing IDAs, resulting in defective ciliary ultrastructure and impaired motility 2. CCDC39 variants are among the most common causes of PCD globally, with distinct founder mutations showing regional clustering patterns 6.