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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.
What this means is that now the appearance of a feature like a cleft chin is dependent on two genes, the modifier gene and the cleft gene itself. If both copies of the modifier gene lead to no cleft chin, then the cleft chin gene won't matter -- it will be silenced.