Complete sequence of the 23-kilobase human COL9A3 gene - Detection of GLY-X-Y triplet deletions that represent neutral variants

We report the complete sequence of the human COL9A3 gene that encodes the a lpha 3 chain of heterotrimeric type IX collagen, a member of the fibril-ass ociated collagens with interrupted triple helices family of collagenous pro teins. Nucleotide sequencing defined over 23,000 base pairs (bp) of the gen e and about 3000 bp of the 5'-flanking sequences. The gene contains 32 exon s, The domain and exon organization of the gene is almost identical to a re lated gene, the human COL9A2 gene. However, exon 2 of the COL9A3 gene codes for one -Gly-X-Y- triplet less than exon 2 of the COL9A2 gene. The differe nce is compensated by an insertion of 9 bp coding for an additional triplet in exon 4 of the COL9A3 gene. As a result, the number of -Gly-X-Y- repeats in the third collagenous domain remains the same in both genes and ensures the formation of an in-register triple helix. In the course of screening t his gene for mutations, heterozygosity for separate 9-bp deletions within t he COL1 domain were identified in two kindreds, In both instances, the dele tions did not co-segregate with any disease phenotype, suggesting that they were neutral variants, In contrast, similar deletions in triple helical do main of type I collagen are lethal, To study whether alpha 3(IX) chains wit h the deletion will participate in the formation of correctly folded hetero trimeric type IX collagen, we expressed mutant alpha 3 chains together with normal alpha 1 and alpha 2 chains in insect cells, We show here that despi te the deletion, mutant alpha 3 chains were secreted as heterotrimeric, tri ple helical molecules consisting of three alpha chains in a 1:1:1 ratio. Th e results suggest that the next noncollagenous domain (NC2) is capable of c orrecting the alignment of the alpha chains, and this ensures the formation of an in-register triple helix.