New rule: Only clear your firearm when your hand is firmly on the grip, finger off the trigger, and you can make eye contact with your firearm, and it is in safe direction.
We must always be mindful of gun safety. A lot of us start taking it for granted when we become very familiar with them, but it is a discipline we still have to be mindful.
If you are proper with your gun safety, then a loaded gun doesn't make you feel uncomfortable, because you are already handling it in a safe manner.
This experience of your nephew also teaches us something important: Pick a holster, and pick a wise one.
So my pseudo nephew, his dad and I were best friends growing up had an AD and shot himself. I’ve only been to the range with him one time and I never really got to teach him right. He’s very lucky to be alive and he knows it. The story I got from him is he was clearing his gun while it was in his pocket (still can’t wrap my head around that rationale) and the gun discharged. Went through his hip and missed everything important. His wife is going to beat him when he heals up and I may help.
He said it was a burning hot feeling all over his right butt/hip. Like your nephew, it went though flesh but didn't sever anything important. He swapped places with his wife, who was just sitting down in the car when it fired, for the ride to the hospital. 
