We present an autosomal-recessive frontonasal dysplasia (FND) characterized by 
bilateral extreme microphthalmia, bilateral oblique facial cleft, complete cleft 
palate, hypertelorism, wide nasal bridge with hypoplasia of the ala nasi, and 
low-set, posteriorly rotated ears in two distinct families. Using Affymetrix 
250K SNP array genotyping and homozygosity mapping, we mapped this clinical 
entity to chromosome 12q21. In one of the families, three siblings were 
affected, and CNV analysis of the critical region showed a homozygous 3.7 Mb 
deletion containing the ALX1 (CART1) gene, which encodes the aristaless-like 
homeobox 1 transcription factor. In the second family we identified a homozygous 
donor-splice-site mutation (c.531+1G > A) in the ALX1 gene, providing evidence 
that complete loss of function of ALX1 protein causes severe disruption of early 
craniofacial development. Unlike loss of its murine ortholog, loss of human ALX1 
does not result in neural-tube defects; however, it does severely affect the 
orchestrated fusion between frontonasal, nasomedial, nasolateral, and maxillary 
processes during early-stage embryogenesis. This study further expands the 
spectrum of the recently recognized autosomal-recessive ALX-related FND 
phenotype in humans.