Arduino Fried? Power is being delivered to Arduino but COM not found
If you were powering from 12V and shorted the 5V to GND then yes, it is all dead. The regulator will have stopped regulating. 12V will have then been sent to every component on the board. The USB chip, the main MCU, the 5V regulator - all will be toast.  

You could repair it by replacing almost every component on the board, but when they're so cheap, why would you bother?