There are a number of reasons why this could happen both genetic and environmental like cob-web said.
Genetically things are a bit more complicated than just dominant and recessive, u have co-dominant, epistatic, mosaics, modifiers, incomplete penetrance, masking genes, chromosomal breaks and transposition....bla bla bla.
It is very rarely you will have a disease or a trait that affected by 'only gene' or which follows Mendel's inheritance i.e dominant/recessive.
With something such as an over shot jaw it is more like to be a fault in the genes which control general development i.e turn on the genes for growth via transcription factors, than one or several genes which 'cause' it, if that makes sense? If I had to take an educated guess I would say the IGF1, SMAD3 pathway, COL13A1, DKK1, PRG1, ADAMTS14, EGR2, SIRT1 or PLEKHK1 genes are likely to be involved.
I think that it is good that ur are not planning on breeding from him......not that there is something wrong with him!!! its just that if there is something wrong with the way his genes are controlled that could manifest its self more severely in his puppies.
Also it could not be anything wrong with his DNA
sequence , which is the only part which is inherited. But DNA is more complex than a row of A, C, T and G's. It has to be tightly packed by proteins in able to fit inside the cell (ur DNA stretched out would reach to the moon and back!) but it can only be read when the proteins release it, so they do so a little bit at a time. However the way the proteins work can affect how u are made and they can also be affected by environmental factors (this is epigenetics). So his sequence might be ok but his histones (the proteins) might not be.
So to answer ur question.......eh without doing a genome scan on him it might be impossible to say for sure.......
