Background: Systemic lupus erythematosus is a condition characterized by the immune system destroying multiple organs in the body.
Aim: To assess and characterize C1q rs 631090 polymorphism in a group of Egyptian children with juvenile systemic lupus erythematosus (jSLE) and to investigate the relationship between this polymorphism, phenotypes, presenting manifestations, activity, and damage indices. This mutation was previously studied in adult systemic lupus erythematosus (SLE) patients in Egypt but not in pediatrics, also C1q deficiency was the diagnosis of one of our SLE patients who presented with severe skin manifestations and recurrent infections.  
Patients and Methods: 114 children were recruited in this study, 67 Egyptian juvenile SLE patients and 47 healthy age matched children as control group. Whole blood (EDTA) samples were collected from studied population then DNA was genotyped for rs631090(c.187+267T>C).
Results: Out of our study population, 24 patients (35.8%) had gene mutation either homozygous or heterozygous (C/C and C/T); homozygous mutation C/C in (13.4%), which was significantly greater than the control group. Lupus nephritis incidence significantly varied among patients with homozygous and heterozygous mutations, with the homozygous group showing lower incidence (p value 0.002). Vasculitis was highest in homozygous C/C in (33.3%) compared to (11.6%) in non-mutant group T/T and none (0%) of the heterozygous group C/T.
Conclusion: Our study suggests that a homozygous mutation in the gene C1q rs631090 may be a beneficial prognostic factor for juvenile SLE patients with milder disease complications.