Mutations in the SPATA5-gene are associated with the Epilepsy, Hearing Loss and Mental Retardation Syndrome (EHLMRS). While SPATA5 is ubiquitously expressed and is attributed a role in mitochondrial morphogenesis during spermatogenesis, there is only limited knowledge on the associated muscular and molecular pathology. We report on a case of EHLMRS in an 8-year-old girl with typical clinical presentation, where exome analysis revealed two clinically relevant, compound-heterozygous variants in SPATA5 and a comprehensive workup of muscular pathology was performed including proteomic profiling and microscopic studies. Proteomic profiling of a quadriceps biopsy showed the dysregulation of 82 proteins, out of whom 15 are localized in the mitochondrion, while 19 are associated to diseases presenting with phenotypical overlap to EHLMRS. Histological and immunofluorescence staining of our patient’s muscle biopsy confirmed mitochondrial pathology, while the examination of dysregulated proteins assessed vulnerability of the cell beyond the mitochondria. Through our study we provide insights into the molecular etiology of EHLMRS and provide further evidence for a muscle pathology associated with SPATA5-deficiency, including a pathological histochemical pattern accompanied by dysregulated protein expression.