wow...looks like someone got chomped on. Fish can be durable and resilient little guys. I had a feeder gold fish that had one of it's gill covers removed by a crayfish. Ended up living for 10+ years like that, with partially exposed gills and all.
For awhile I had assumed that it took some damage along the way, but after having seen pictures of other "notched" fish, and having firsthand knowledge of what that area of the fish looks like, i'm about 98% sure it's a genetic defect.