The primary etiologic factor is genetic. CAH is an autosomal recessive disorder and the gene encoding 21-hydroxylase enzyme, CYP21A2, is mapped to the short arm of chromosome 6 (6p21.3). To date, more than 100 mutations have been described, including point mutations, small deletions, small insertions, and complex rearrangements of the gene.  Approximately 95% to 98% of the mutations causing 21-hydroxylase deficiency have been identified through molecular genetic studies of gene rearrangement and point mutations arrays.  Hormonally and clinically defined forms of 21-hydroxylase-deficient CAH are associated with distinct genotypes. Image 2
The classical phenotype is predicted when a patient carries 2 severe mutations. The nonclassical phenotype is caused by a mild/mild or severe/mild genotype, as is expected in an autosomal recessive disorder. It is not always possible, however, to accurately predict the phenotype on the basis of the genotype. Such predictions have been shown to be approximately 50% concordant.  A study demonstrated that the genotype-phenotype concordance is 90.5% for salt-wasting CAH, 85.1% for simple-virilizing CAH, and 97.8% for non-classical CAH. 
The production of cortisol occurs in the zona fasciculata of the adrenal cortex through 5 enzymatic steps.
Scheme of adrenal corticosteroid synthesis
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The internal female reproductive tract remains normal, as the ovaries do not produce anti-Mullerian hormone. Postnatal virilization includes rapid growth, premature development of pubic hair, and advanced epiphyseal maturation leading to secondary precocious puberty, early epiphysis fusion, and short final adult height. Short stature may be the combined result of elevated adrenal androgens causing advanced epiphyseal maturation and premature epiphyseal fusion. Glucocorticoid over treatment leads to growth suppression and short stature.  Gonadal dysfunction usually occurs as the excess adrenal androgens suppress pituitary gonadotropins and thus impair gonadal growth and function.
When the loss of 21-hydroxylase function is severe, adrenal aldosterone secretion is insufficient to stimulate sodium reabsorption by the distal renal tubules, resulting in salt-wasting as well as cortisol deficiency, in addition to androgen excess.