A new dominant mutation in the COL2A1 gene was found in a 38-week-old fetus with hypochondrogenesis. Denaturing gradient gel electrophoresis was used to analyze all 44 exons coding for the triple-helical domain of COL2A1 gene and the corresponding exon-intron boundaries. The technique detected a new sequence variation in exon 35. Sequencing of exon 35 demonstrated a single base mutation that converted the codon for glycine at position 604 to a codon for alanine. Electrophoresis of pepsin-digested collagen extracted from the diseased cartilage showed a doublet band of the alpha 1(II) chain of type II collagen and the presence of alpha 1(I) and alpha 2(I) chains of type I collagen. Two-dimensional analysis of cyanogen bromide peptides from the type II collagen revealed post-translational overmodification of peptides CB12, CB11, CB8, and CB10.5, whereas peptide CB9.7 migrated normally. Microscopic examination of cartilage showed that the mutation altered the organization of the growth plate. Also, articular chondrocytes contained large cisternae of rough endoplasmic reticulum. The density of the extracellular matrix was reduced, and the intensity of the staining with an antibody to type II collagen was diminished. In contrast, a significant staining with an antibody to type I collagen was observed. In situ hybridization with cRNA probes revealed a significant level of alpha 1(I) mRNA in the cytoplasm of the patient's chondrocytes. The signal for alpha 1(II) mRNA was about the same in control samples. The results indicated, therefore, that the genes for both type I and type II procollagens were simultaneously expressed in chondrocytes from the patient.