A child with spondyloepiphyseal dysplasia congenita was shown to be heterozygous for a mutation of the COL2A1 gene that encodes the alpha 1 (II) chain of type II collagen. The alpha 1 (II) chains extracted from cartilage contained disulfide-bonded dimeric and trimeric alpha 1 (II) chains. Carboxymethylation confirmed that some of the type II collagen chains contained cysteine residues that are not normally present in alpha 1 (II) chains. Cyanogen bromide peptide mapping showed that the abnormal cysteine residue was located in the alpha 1 (II) CB10.5 peptide. Amplification products of the corresponding region of alpha 1 (II) cDNA prepared from cultured dermal fibroblasts were shown by chemical cleavage and single strand conformation polymorphism analyses to contain a sequence anomaly. DNA sequencing showed a transition of C2913T in exon 41 of one allele of the COL2A1 gene resulting in the substitution of arginine 789 by cysteine in the alpha 1 (II) chain. The mutation resulted in the loss of a MaeII cleavage site that was used to confirm that the proband was heterozygous for the mutation and that neither parent showed evidence of the mutation. The type II collagen extracted from cartilage and from chondrocytes cultured in alginate beads showed similar characteristics. Approximately a third of the type II collagen chains were mutant, and the secretion of molecules containing mutant chains was impaired. The thermal stability of the collagen extracted from cartilage was normal. This study confirmed the importance of dominant negative mutations of the COL2A1 gene in producing the spondyloepiphyseal dysplasia congenita phenotype.