SCA1 affects 1 to 2 per 100,000 people worldwide.

Mutations in the ATXN1 gene cause SCA1. The ATXN1 gene provides instructions for making a protein called ataxin-1. This protein is found throughout the body, but its function is unknown. Within cells, ataxin-1 is located in the nucleus. Researchers believe that ataxin-1 may be involved in regulating various aspects of producing proteins, including the first stage of protein production (transcription) and processing RNA, a chemical cousin of DNA.

The ATXN1 gene mutations that cause SCA1 involve a DNA segment known as a CAG trinucleotide repeat. This segment is made up of a series of three DNA building blocks (cytosine, adenine, and guanine) that appear multiple times in a row. Normally, the CAG segment is repeated 4 to 39 times within the gene. In people with SCA1, the CAG segment is repeated 40 to more than 80 times. People with 40 to 50 repeats tend to first experience signs and symptoms of SCA1 in mid-adulthood, while people with more than 70 repeats usually have signs and symptoms by their teens.

An increase in the length of the CAG segment leads to the production of an abnormally long version of the ataxin-1 protein that folds into the wrong 3-dimensional shape. This abnormal protein clusters with other proteins to form clumps (aggregates) within the nucleus of the cells. These aggregates prevent the ataxin-1 protein from functioning normally, which damages cells and leads to cell death. For reasons that are unclear, aggregates of ataxin-1 are found only in the brain and spinal cord (central nervous system). Cells within the cerebellum, which is the part of the brain that coordinates movement, are particularly sensitive to changes in ataxin-1 shape and function. Over time, the loss of the cells of the cerebellum causes the movement problems characteristic of SCA1.