Case-case subphenotype analysis available on a subset of 1,751 SLE case subjects demonstrated that rs140490 was associated with increased risk of lupus nephritis (p = 0.0036, OR 1.27, 95% CI: 1.08–1.49), suggesting that UBE2L3 is associated with increased disease severity. Here, UBE2L3 is linked to systemic lupus erythematosus.