The splotch (Sp) mouse mutant displays defects in neural crest cell migration and neural tube closure and serves as a model for the study of spina bifida, exencephaly, and Waardenburg syndrome type I in humans. Recently, we have described alterations in the Pax-3 gene for the radiation-induced Spr and Sp2H alleles and for the original, spontaneously arising Sp allele. Another allele that arose spontaneously at the Sp locus, termed splotch-delayed (Spd), shows a less severe phenotype than the other Sp alleles, including the delayed death of homozygous embryos. To determine the molecular basis underlying this unique phenotype, we have analyzed the integrity of the Pax-3 gene in Spd mutant embryos. Nucleotide sequence analysis of cDNA and genomic clones revealed a G to C transversion at nucleotide 421 of the Pax-3 mRNA transcript, which results in a Gly to Arg substitution at position 42 of the Pax-3 protein (position 9 of the paired domain). The location of the mutated residue, its conservation in all other paired domain-containing proteins described to date, and the nonconservative nature of the substitution suggest that this mutation is responsible for the phenotype observed in the Spd mouse mutant.