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Homozygote DNA but Heterozygote RNA? - (Mar/21/2013 )

I have a problem that I am not able to solve. I have sequenced the DNA of a patient and found an homozygote mutation at the end of exon 6 (PCR was done several times and with more than a pair of primers). As this mutation is responsible for an aberrant splicing (loosing the exon 6) we have looked in the RNA (obtained from the patient lymphocytes) and we have found two amplifications, one without the exon (smaller) and the other including the exon (larger).
The sequence of the larger RT-PCR product (includes the exon) revealed the normal base and not the mutation.
In summary, in the patient DNA we found homozygote mutation but in the RNA we found only the normal base.
There is not any amplification of the RNA without retrotranscriptase.

Thank you in advance for any idea !!




My first thought was the pseudogene but PCR amplification of patient DNA with primers for RT-PCR (binding in exons 5 and 8) did not reveal any band.