The type VI variant of Ehlers-Danlos syndrome (EDS) is a heritable connective tissue disorder caused by a deficiency in the activity of lysyl hydroxylase, an enzyme required for the post-translational processing of collagens. We have characterized a novel type of mutation in a young female patient with type VI EDS, in which cells possess only 12% of the lysyl hydroxylase activity that is detected in unaffected cells. The syndrome was found to be caused by a homozygous insertion of two thymidines at the 5' splice site consensus sequence of intron 9 in the lysyl hydroxylase gene. The insertion interfered with normal splicing of the primary RNA transcript and resulted in an inframe deletion of the 132 nucleotides coded by exon 9 from the lysyl hydroxylase mRNA. In addition, the mutation caused a marked reduction in the steady-state level of the truncated mRNA, which was less than 15% of the level found in unaffected cells. The mutation also reduced the amount of the enzyme protein produced, which was estimated to be about 20% of that in control cells. However, the mutation did not affect the stability of the abnormally spliced mRNA nor the normal localization of the enzyme protein in the endoplasmic reticulum. According to our results, the reduction in enzymatic activity observed in this patient is caused by low levels of both lysyl hydroxylase mRNA and enzyme protein. The primary cellular defect associated with this mutation, therefore, appears to be at the level of nuclear mRNA metabolism even though the mutation did not create a premature translation termination codon.