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The traditional morphologic classification of holoprosencephaly into alobar, semilobar, and lobar forms is grades of severity, and each occurs in all of the genetic mutations known. Of the four defective genes identified as primary in human holoprosencephaly, three exhibit a ventrodorsal gradient of expression (SHH, SIX3, and TGIF) and one a dorsoventral gradient (ZIC2). But, in addition to the vertical axis, genes expressed in the neural tube also may have rostrocaudal and mediolateral gradients in the other axes. These other gradients may be equally as important as the vertical. If the rostrocaudal gradient extends as far as the mesencephalic neuromere, it may interfere with the formation, migration, or apoptosis of the mesencephalic neural crest, which forms membranous bones of the face, orbits, nose, and parts of the eyes, and may explain the midfacial hypoplasia seen in many, but not all, children with holoprosencephaly. This rostrocaudal gradient also causes noncleavage of the caudate nucleus, thalamus, and hypothalamus and contributes to the formation of the dorsal cyst of holoprosencephaly, which is probably derived from an expanded suprapineal recess of the 3rd ventricle with secondary dilation of the telencephalic monoventricle and at times may produce a unique transfontanellar encephalocele. The extent of the mediolateral gradient may explain the severe disorganization of cerebral cortical architecture in medial parts of the forebrain and normal cortex in lateral parts, including the radial glial fibers. This preserved lateral cortex may explain why some children with holoprosencephaly have better intellectual function than expected and may also be important in the pathogenesis of epilepsy, by contrast with malformations such as lissencephaly, in which the entire cerebral cortex is involved. Epilepsy in some, but not all, cases also may be related to the sequential maturation of axonal terminals in relation to the neurons they innervate. Diabetes insipidus is a complication in a majority of patients; other neuroendocrinopathies occur less frequently. Secondary down-regulation of the OTP gene or of downstream genes such as BRN2 or SIM1 may result in failure of terminal differentiation of magnocellular neurons of the supraoptic and paraventricular hypothalamic nuclei. Disoriented radial glial fibers or abnormal ependyma may allow aberrant migration of neuroepithelial cells into the ventricle. A new classification of holoprosencephaly is needed to integrate morphologic and genetic criteria. 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