In MS participants only, PVRL2 and IRX1 had clearer associations with 30-year EDSS [PVRL2: + 2.60, bootstrapped 95% CI: (1.30, 3.87), P = 2.02 × 10−3; IRX1: −2.12, bootstrapped 95% CI: (−0.87, −3.44), P = 5.02 × 10−3] and both influenced risk of SPMS [PVRL2: OR 15.16, bootstrapped 95% CI: (1.16, 26.67), P = 0.031; IRX1: OR 0.19, 95% CI: (0.04, 0.92), P = 0.042). Here, IRX1 is linked to secondary progressive multiple sclerosis.