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The gene encoding adrenal steroid 21-hydroxylase, CYP21, is located in the MHC class III region. Most cases of congenital adrenal hyperplasia (CAH) are caused by mutations in this gene, and most mutations appear to arise from gene conversion-like events involving the transfer of deleterious sequences from the pseudogene, CYP21P, which is located within 30 kb of CYP21. Approximately 20-30% of mutations are caused by deletions of CYP21. The second intron of CYP21 is polymorphic, and several base substitutions that include nt395, nt453, and nt601 have been reported; however, the frequencies of these polymorphisms are unknown. Using a combination of cleavase fragment length polymorphism analysis and direct sequencing, we examined the sequence of intron 2 in seven wild-type CYP21 genes and determined the frequency of polymorphisms at nt395, nt453, and nt601 in 48 chromosomes from the parental generation of Centre d'Etude du Polymorphisme Humain families. The observed frequencies of bases at these positions were as follows: 395C, 0.17; 395T, 0.83; 453C, 0.71; 453T, 0.29; 601A, 0.1; and 601C, 0.9. Using a PCR/restriction digestion approach to examine these intragenic markers, we could follow the segregation of alleles in informative families with 21-hydroxylase deficiency and identify deletions of CYP21. We emphasize that this method should be used in conjunction with other molecular genetic techniques for diagnosis of CAH. In addition to their potential use in families with CAH, these markers may be of use in genetic studies of the MHC in humans.

Characterization of frequent polymorphisms in intron 2 of CYP21: application to analysis of segregation of CYP21 alleles