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Thank you for asking on Just Answer about this problem you had with one of your puppies. I have seen this before in m,any other animals, and almost answered it when you posted a few weeks ago, but dogs are not my specialty and I wanted to leave it for someone that it was. Since no one if that field answered it, I am going to this time for you and hope this provides the information you need.
My specialty is reptiles, and I have seen this probably a dozen times in them. I was also raised on a teaching farm that taught vet students, zoo keepers and care staff from Ringling Circus the care of many species of animals and worked with many mammals at that time and have seen it in those animals at least a dozen times also. What you are describing is not seen that often in the animal world but does occur and it is not known to be genetic or to reoccur in the same pairing. It is unique to that one offspring, and not in the line.
It is a congenital defect that occurs early in the development and is a form of Hydrocephalus, it happens when there is a build-up of cerebrospinal fluid inside the skull of the developing animal, the fluids can not drain properly. This causes pressure on the brain resulting in swelling and displacement, this often affects the eyes too. Other common birth defects that are seen are failure of the tissue of the spine and/or around the umbilicus to close properly, bulging that can be anywhere from slight to the fontanelle to the head expanding.grossly. seizures, ataxia and internal organ defects. If he had lived, you would have seen more symptoms over the next few days including problems keeping food down and if he survived that time even more problems occur later. You did the right thing putting him down, not having him go through more and chances are also that he was blind with detached retinas or a minimum had serious vision problems.
I am sorry you had to deal with this, it is heartbreaking to ever have to put down a newborn of any species, but it was for the best and is not a result of any genetic problem with the parents. Please let me know if you need any further information on this condition or you have other questions. Again I am sorry in not answering this before but I thought a canine specialist would answer it, but then many would never have seen this. It is more common in the short nose/heads for some reason, and even then often not visual at birth and disgnosed later when neurological symptims occur or if they have visual problems they often do not even survive being born so it is not something they would see that often. I would say with what you were able to see on this puppy, that he had an advance case of it and would not have survived long or had any quality of life