David is afraid for Sophie.  He knows if anyone discovers her that she and her family are in danger.

Sophie is a young girl he befriended who has to stay in hiding because she has six toes.  In David’s society, anyone who is not perfect is considered an abomination, and people are sent away for trivial reasons such as having an arm that someone considers short.  Something obvious, like an extra toe, would cause someone to be expelled for sure.

When David accidentally says he wishes he had a third hand, his father goes ballistic.  He gets angry because according to him David is asking to be a Mutant.

What is a Mutant?'

'"A thing accursed in the sight of God and man",' I mumbled.

'And that is what you wished to be! What have you to say?' (ch 3)

His father does not know about Sophie, but after what David says about wanting a third hand his father beats him severely and tells him to pray.  That night, David has a dream that his father kills Sophie.

My father held Sophie with one arm just as he had held the struggling calf. He raised his other hand high, and as he swept it down the knife flashed in the light of the rising sun throat... (ch 3)

This dream is actually foreshadowing.  Later, someone sees David with Sophie and since they have never seen the child before they assume she is a Mutant.  David returns home and an inspector is talking to his father.  He asks who the girl was, and David does not tell.  However, David’s father beats him until he does tell.  Sophie’s family has to flee.

Of course, David has other fears.  He is generally afraid of his father, and he is also afraid that someone will discover that he, too, is a mutant because he is a telepath.