At the end of the day you have to live with your own choices and convictions, I did read somewhere that if the life of the mother is in danger or she has many other children and cannot provide for another or it would take a great toll on her health that it is permissible. I am sure it has to be very early in the pregnancy although I can't remember the exact weeks specified. I will try to find this information again and add a comment or link to this answer. I am nearly certain it is also permissible in the case of rape.
It would certainly be a hard life for a mother and child, even the whole family to deal with a child with special needs, but we never know on the other hand what gifts these children could bring to the world or to our own lives. Look at Steven Hawkings for example and what gifts and genius he has brought to the scientific community.
It's truly a very hard place to be in to make this kind of decision regardless of religion. Allah does not make mistakes but humans... we do.
This link does include fetal deformity and it must be done within the first 4 months of pregnancy. It is mentioned that while it is allowed in some circumstance, most muslims consider abortion to be haram, forbidden.
****://en.wikipedia.org/wiki/Islam_and_abortion