Lowering of IQ can be found in babies born to women with thyroid problems that have not been treated with proper thyroid medications. If your wife's thyroid has been properly maintained with medication and her levels are closely monitored during pregnancy and kept in check, there is no reason to think that the child should suffer any ill effects. Only if her TSH, T4 and T3 levels become quite abnormal and stay in that state for a considerably long time without being corrected would you find the possibility of problems of that nature.
I have had problems with my thyroid for years and I am 7 months pregnant. As stated, there is a possibility of problems only if it is untreated and if it is more than a slight problem. My thyroid gland was almost completely killed by radiation so I am almost solely dependant on synthryoid. My doctor encouraged me that my pregnancy would be normal and he has keep a very close eye on my levels. It is important to test often and test not just the tsh but t4. I am shocked that your wife's doctor would say something like that. Having a low thyroid function i s not that rare for women so think of how many women have the problem and don't even know it. I would consider a new doctor and if it would ease your mind, maybe even a specialist.
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