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Background: Immunoglobulin A (IgA) nephropathy is a disorder of the immune system affecting kidney function, and genome‐wide association studies (GWAS) have defined numerous loci with associated variation, all implicating components of innate or adaptive immunity. Among these, single nucleotide polymorphisms (SNPs) in a region including the multiallelic copy number variation (CNV) of DEFA1A3 are associated with IgA nephropathy in both European and Asian populations. At present, the precise factors underlying the observed associations at DEFA1A3 have not been defined, although the key alleles differ between Asian and European populations, and multiple independent factors may be involved even within a single population. Methods: In this study, we measured DEFA1A3 copy number in UK family trios with an offspring affected by IgA nephropathy, used the population distributions of joint SNP–CNV haplotypes to infer the likely segregation in trios, and applied transmission disequilibrium tests (TDT) to examine joint SNP–CNV haplotypes for over‐ or undertransmission into affected offspring from heterozygous parents. Results and Conclusions: We observed overtransmission of 3‐copy class 2 haplotypes (raw p = 0.029) and some evidence for under‐transmission of 3‐copy class 1 haplotypes (raw p = 0.051), although these apparent effects were not statistically significant after correction for testing of multiple haplotypes. [ABSTRACT FROM AUTHOR]