I assumed he was an uncle and father. It's clear the protagonist never knew her father. Yet, the mother (who was also mentally ill) felt the need to keep her brother close.
My take is that while Judas was full-blown homicidal, the mother was simply "not right in the head." But, while she did harm her daughters, they were dragged to the closet in an attempt to keep them alive. The mother would locked the girls in the closet with their hair tied to pipes so they couldn't wander the house and accidentally get killed.
As far as the girls parentage, we aren't introduced to any other significant older male character in the movie. There isn't even mention of the mother caring for any other man. And, at her funeral, hardly anyone showed. So, I'm inclined to believe this mentally ill woman only had contact with the brother she obsessed over.
And as further evidence that the uncle is also the brother, both girls seem to have mental illness, which is likely hereditary. One sister self-medicated while the other was wayward with her mannerism's having her accused of being "off." I'd wager the girls got this not just from their mother but their father too.
Finally, the holes in the walls. Why would the uncle even need to see in the house? He knows to exit at night, while the girls are tied up....unless her also cared for them too. He wanted to see them grow up as well. And while his illness would be a threat to them, the walls kept him from interacting with the girl. We see him crying on the bed because he's ashamed of what he does. He WANTS to be well. But, he's not. So, he sadly watched his daughters/nieces and sister/lover from afar, only to exit when they are out of sight.
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