Most mutations in Crouzon, Pfeiffer, and Apert syndromes are in the 
extracellular, third immunoglobulin-like domain and adjacent linker regions 
(exons IIIa and IIIc) of the fibroblast growth factor receptor 2 (FGFR2) gene. 
Using the published primers for PCR, a patient with Crouzon syndrome was found 
to be homozygous for a mutation that results in a Q289P amino acid substitution 
in FGFR2. Two additional patients; one with Apert syndrome and P253R mutation, 
the other with Pfeiffer syndrome and S267P mutation, also appeared to be 
homozygous. Using a new primer located 146 bp 5' of exon IIIa for PCR followed 
by sequencing revealed an A to G polymorphism at -62 [corrected] position of 
exon IIIa. All three patients were heterozygous for both the mutation and the 
polymorphism. These results indicate that the polymorphism and the mutation are 
not on the same chromosome. The single nucleotide polymorphism is located at the 
second to the last base of the 3' end of the published primer. This primer 
mismatch caused the failure of amplification of the normal chromosome and thus, 
the apparent homozygosity. The frequency of this novel polymorphism was 
determined to be 0.03 by studying 326 chromosomes from the general population. 
We propose that a new primer should be used for mutational analysis of exon IIIa 
of FGFR2 to avoid misdiagnosis caused by primer mismatch.