Isolated sucrase deficiency has been demonstrated in a line of house musk shrew, Suncus murinus (laboratory name: suncus). This animal belongs to the order Insectivore and is phylogenetically different from ordinarily used laboratory animals. They are believed to have evolved with mainly animal food without sucrose. To study the molecular basis of the sucrase deficiency in suncus, we cloned 6. 0-kilobase (kb) sucrase-isomaltase (SI, EC 3.2.1.48-10) cDNA from suncus intestinal cDNA library. The cDNA clone contained a 5442-base pair (bp)-long open reading frame preceded by an in frame termination codon. The deduced 1813-amino acid sequence showed 68.6, 71.2, and 74.7% similarity with those of rat, rabbit, and human, respectively. A cleavage site between isomaltase and sucrase as well as the region surrounding the catalytic sites for sucrase and isomaltase were conserved among the species. Out of 18 potential N-linked glycosylation sites, 5 were common among all 4 species. In the connecting segment which was enriched with O-linked glycosylation sites in the other species, only two sites were present in suncus. Northern blot analysis revealed that the 6.0-kb SI mRNA was expressed in the KAT line with intact sucrase-isomaltase activity. In contrast, 3.0-kb SI mRNA was expressed in suncus of the MI line with isolated sucrase deficiency. The 3.0-kb mRNA cosegregated with sucrase deficiency phenotype as an autosomal recessive trait. Sequence analysis revealed a 2-nucleotide deletion at position 2767-2768, which results in a frameshift and an immature termination codon. The cDNA of the MI line diverged from that of the KAT line at position 2865, having an 18-bp unique sequence followed by a poly(A) tail. The mutant cDNA encodes 922 amino acid residues which preserves the region for isomaltase but lacks that for whole sucrase. While the cells transfected with the plasmids expressing SI in the KAT line showed both sucrase and isomaltase activity, the plasmids expressing MI line cDNA showed only isomaltase activity. Thus it was concluded that the mutation in the SI gene was responsible for isolated sucrase deficiency in the MI line.