2005 which includes:
A woman is five months pregnant and physicians have unanimously agreed that the fetus is deformed; this is the third time for her to go through the same experience. Is it permissible for her to abort this deformed fetus?
 

If the case is as mentioned in the question and the embryo has been ensouled, then it is a complete human and it is not permissible to encroach upon its life even if it is deformed provided that continuing the pregnancy will not result in harm to the mother. If medical specialists determine that the pregnancy does pose risks to the mother, then – in this case – there is no harm in terminating the pregnancy after consulting a Muslim physician.
Allah Almighty knows best.
The above answers the question.