We report 22 patients with normal neuropsychological development and a holoprosencephaly-like (HPE-like) phenotype screened for SHH, SIX3, TGIF, and GLI2. These patients were divided into two groups: (1) 6 patients with SHH and GLI2 mutations and (2) 16 patients with no detectable mutations. We discuss the phenotypic manifestations, evolution of the phenotype, and neuroimaging in the two groups. Conclusions about the HPE-like phenotype include (1) initial appearance as an unusually wide, and very severe unilateral cleft lip-palate in some cases; (2) variability with the expression of minor anomalies in some cases, such as single maxillary central incisor; (3) identifiable mutations in some cases and absence of mutations in others; (4) essentially normal MRI in the most cases (pituitary tumor in two cases and choroid fissure cyst in one case in Group 1; empty sella turcica in one case in Group 2); (5) intelligence within the normal range; and (6) familial aggregation in some instances. Implications include (1) thorough examination of family members for minor anomalies; (2) MRI and developmental assessment for the proband; and (3) molecular analysis.