In real life, the San Andreas Fault is a large continental fault from San Francisco to Bombay Beach, California, and it marks the boundary between two tectonic plates.
The San Andreas Fault Line can be seen in GTA San Andreas. It is an underwater ridge, located in the San Fierro Bay. The crack starts just north of Jizzy's Pleasure Domes in San Fierro, and it runs along the seabed and comes to an end at a wall of sandstone that goes back up towards the land. The crack is based on the real-life San Andreas Fault in California (where the game takes place) which is also presumably what GTA San Andreas is named after. This is probably why the Fault Line is in the game. It most likely contributed to the San Andreas Earthquake.