A protein is, at its heart, a chain of amino acids. These can be numbered from 1 to however many amino acids are there. In this case, the mutation name means that amino acid 2019 is usually a glycine (G), but has been mutated to a serine (S). Each amino acid has a one-letter abbreviation which can be found by Googling. The mutation can also be written as a DNA change: A6209G means that the adenine (A) which is usually at nucleotide #6209 has been changed to a guanine (G).
The only way to tell for sure if they're talking about amino acids or nucleotides is to look at the letters. It it's DNA, you'll only see A, C, G, and T. Any other letter means you're dealing with amino acids.
As for projects, well:
"write a program that compares the DNA sequence between a normal sequence and those afflicted with Parkinson's?"
That's already been done. That's how they know that that mutation is important.
"Should I write a program to find the 3d structure of LRRK2?"
If you can do that, you'll not only win the science fair, but also a Nobel Prize. People have been working on that problem for decades without much progress.