Molecular analysis revealed homozygous variants in RAG1:NM_000448.3:c.554delG;p.(Lys186Serfs*15) and TXNDC15:NM_024715.4:c.703 C > T;p.(Arg235Trp) fully explaining the individual’s immunodeficiency and ciliopathy phenotypes, respectively. Here, RAG1 is linked to ciliopathy.