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Cleft lip and palate is due to tissues of the face not properly joining together during development. They are a type of birth defect. The cause in most cases is unknown. Risk factors include smoking during pregnancy, diabetes, an older mother, obesity, and certain medications such as some used to treat seizures.
If a syndrome is involved, the chances of passing on a cleft is all down to the heritability of the syndrome, which in some cases can be as high as 50%. An isolated cleft palate (where the lip is not affected) is believed to have a different cause to cleft lip and palate. So a family affected by cleft palate (but not cleft lip) may only be likely to pass on cleft palate.