These haplotypes influence <i>C9orf72</i> expression levels in motor neurons and stratify C9-ALS patients into four subgroups; using clinical disease duration data and longitudinal ALSFRS-R scores, we show that these subgroups exhibit different survival trajectories, indicating that wild-type <i>C9orf72</i> expression acts as a genetic modifier of disease duration. Here, C9 is linked to amyotrophic lateral sclerosis.