In this study, we have identified a novel mechanism of mutation involving translocation between the HPRT1 loci and other loci on the X chromosome. In HRT-25's cDNA obtained from a patient with Lesch-Nyhan syndrome, the upstream region of exon 3 was amplified, but the full-length region was not amplified. The use of 3' rapid amplification of cDNA ends polymerase chain reaction (3'RACE-PCR) for HRT-25 revealed part of intron 3 and an unknown sequence which have not identified the HPRT1 gene starting at the 3' end of exon 3. We analyzed HPRT1 genomic DNA in order to confirm the mutation with the unknown sequence in the genomic DNA. Unknown sequence compared through BLAST analysis of human genome (NCBI; http://www.ncbi.nlm.nih.gov/BLAST/) showed that at least 0.5 to 0.6-Mb telomeric to HPRT1 on chromosome Xq where located near LOC340581. This study provides the molecular basis for the involvement of genomic instability in germ cells.