We demonstrate that a mutation in the homeobox gene, MSX1, causes a co
mmon developmental anomaly, familial tooth agenesis. Genetic linkage a
nalyses in a family with autosomal dominant agenesis of second premola
rs and third molars identified a locus on chromosome 4p, where the MSX
1 gene resides. Sequence analyses demonstrated an Arg31Pro missense mu
tation in the homeodomain of MSX1 in all affected family members. Arg
31 is a highly conserved homeodomain residue that interacts with the r
ibose phosphate backbone of target DNA. We propose that the Arg31 Pro
mutation compromises MSX1 interactions, and suggest that MSX1 function
s are critical for normal development of specific human teeth.