Causative variants in the TRAPPC11 gene are associated with muscular dystrophy and a broad spectrum of other clinical features. We present clinical and molecular genetic findings in three patients who are compound heterozygotes for a missense variant and a multiexon deletion in the TRAPPC11 gene. These are the first structural variants identified in this gene in association with a disease. We analysed the breakpoint junctions and estimated that nonhomologous end joining is a possible mechanism of deletion origin in two patients and nonallelic homologous recombination in one patient. We also report on the mitochondrial function in the skeletal muscles of these patients. (https://jmg.bmj.com/content/early/2024/07/01/jmg-2024-110016 )