AbstractBackgroundX‐linked hyper‐IgM (X‐HIGM), which results from mutations in the CD40LG gene located on chromosome Xq26.3, is the most common form of HIGM. To date, more than 130 variants of the CD40L gene have been reported. We described a patient with novel de novo nuclear mitochondrial DNA sequences (NUMTs) in the CD40LG gene that have resulted in X‐HIGM.MethodsWhole‐exome sequencing (WES) analysis was used to screen for causal variants in the genome, and the candidate breakpoint was confirmed by Sanger sequencing.ResultsA new mutation of CD40LG, which deletes A at position 17 followed by a 147‐nucleotide from mitochondrial DNA copies insertion in exon 1, was detected in a 20‐month‐old boy harbouring an X‐HIGM combined with immunodeficiency syndrome.ConclusionThis is one of the few cases of a human genetic disease caused by nuclear mitochondrial DNA sequences (NUMTs). The presented data serve to demonstrate that de novo NUMT transfer of nucleic acid is a novel mechanism of X‐HIGM.