OK, it’s a little bit slanted toward the computer nerd, but many things apply to general geekage.
Your nerd might come off as not liking people. Small talk. Those first awkward five minutes when two people are forced to interact. Small talk is the bane of the nerd’s existence because small talk is a combination of aspects of the world that your nerd hates. When your nerd is staring at a stranger, all he’s thinking is, “I have no system for understanding this messy person in front of me”. This is where the shy comes from. This is why nerds hate presenting to crowds.
The skills to interact with other people are there. They just lack a well-defined system.