We report two sisters born to consanguineous parents with an identical syndrome consisting of severe mental retardation and epilepsy, hypoplastic terminal phalanges, and anteriorly displaced anus. Further metabolic and genetic testing failed to detect the etiology. A whole genome linkage scan showed homozygosity for a 28-Mb region on chromosome 1p, and a 65-Mb region spanning most of chromosome 14. These results are consistent with an autosomal recessive condition that is similar to, but likely distinct from, Coffin-Siris syndrome.