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. (By MSc Johana Kopčilová, https://jmg.bmj.com/content/early/2024/07/01/jmg-2024-110016 )