rs2300747 — CD58

Intronic variant in CD58 (LFA-3) that modulates T-cell costimulation and Treg function; the protective G allele raises CD58 expression and reduces multiple sclerosis risk

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CD58 — The T-Cell Costimulatory Gatekeeper in Multiple Sclerosis

CD58, also known as LFA-3 (Lymphocyte Function-Associated Antigen 3)11 LFA-3 (Lymphocyte Function-Associated Antigen 3)
LFA-3 is a cell-surface glycoprotein expressed on antigen-presenting cells, endothelium, and non-immune cells, plays a pivotal role in the immune synapse. By binding CD2 on T cells22 CD2 on T cells
The CD2–CD58 interaction is one of the earliest and strongest adhesion contacts formed between a T cell and an antigen-presenting cell, it stabilises the interaction between T cells and antigen-presenting cells, transmits costimulatory signals, and — critically for multiple sclerosis — promotes the expansion and function of regulatory T cells. The rs2300747 variant sits within the first intron of the CD58 gene, not in coding sequence, yet it is the single most associated marker across the CD58 locus for MS risk.

The Mechanism

The rs2300747(G) allele is associated with higher CD58 mRNA in a dose-dependent fashion, measurable both in lymphoblastic cell lines (P = 1.1 × 10⁻¹⁰) and in peripheral blood mononuclear cells from MS patients (P = 0.0037). The variant is in high linkage disequilibrium with rs12044852 (r² = 0.929)33 high linkage disequilibrium with rs12044852 (r² = 0.929)
r² measures how tightly two variants travel together; values above 0.8 mean they are almost always inherited as a unit, suggesting the functional effect is shared across this intronic haplotype block.

The raised LFA-3 levels driven by the protective G allele amplify CD2 signalling in CD4+CD25high regulatory T cells44 CD2 signalling in CD4+CD25high regulatory T cells
Regulatory T cells (Tregs) suppress self-reactive immune responses; their deficiency is a central feature of MS. CD2 engagement upregulates FoxP355 FoxP3
FoxP3 is the master transcription factor that programs Treg identity and function, the master transcription factor of Treg identity. MS patients have defective Treg function; elevated CD58 expression partially rescues this defect. Supporting this model, CD58 mRNA levels on circulating mononuclear cells vary with clinical disease status, with expression changes correlating with immune regulatory activity.

Adding biological complexity, the first intron of CD58 also encodes hsa-miR-548ac66 the first intron of CD58 also encodes hsa-miR-548ac
A microRNA is a short non-coding RNA that fine-tunes gene expression by degrading or silencing target mRNAs. The risk allele inversely affects CD58 mRNA and miR-548ac levels from the same primary transcript — as CD58 mRNA falls, miR-548ac rises. Hecker et al. propose that the risk allele alters Drosha (the microRNA-processing enzyme) cleavage activity, partially uncoupling the two RNA products during co-transcriptional processing. The elevated miR-548ac in risk carriers may further suppress immune regulatory targets, compounding the CD58 deficit.

This pathway was the biological rationale behind testing alefacept (Amevive)77 alefacept (Amevive)
Alefacept is a recombinant LFA-3/IgG1 fusion protein that blocks the CD2–LFA-3 interaction; it was approved for psoriasis and explored in autoimmune settings — a recombinant LFA-3/IgG1 fusion protein — in autoimmune diseases. Alefacept selectively depletes memory-effector T cells through CD2 ligation, illustrating the therapeutic relevance of this pathway.

The Evidence

The original PNAS study by De Jager et al. 200988 De Jager et al. 2009
931 MS cases and 2,431 controls; the CD58 association was identified in a genome-wide scan and functionally validated in lymphoblastic cell lines and patient blood samples established rs2300747 as the peak MS association signal in the CD58 locus (P = 1.1 × 10⁻⁶, OR 0.82, 95% CI 0.75–0.89). The protective G allele effect was dose-dependent: carriers of two G alleles showed the greatest CD58 mRNA induction.

A meta-analysis by Liu et al. 201699 meta-analysis by Liu et al. 2016
16 independent case-control studies from 12 publications; allelic OR 0.86, 95% CI 0.78–0.94, P < 0.01 confirmed the G allele is consistently protective across allelic, heterozygous, and dominant genetic models. An independent replication across three cohorts (total n = 3,981)1010 replication across three cohorts (total n = 3,981)
P = 4 × 10⁻⁹, meeting genome-wide significance threshold confirmed CD58 as a genome-wide significant MS locus. The landmark Sawcer et al. 2011 Nature GWAS1111 Sawcer et al. 2011 Nature GWAS
9,772 cases of European descent collected by 23 research groups across 15 countries further cemented CD58 among the 52 confirmed MS susceptibility loci, all enriched for T-cell pathway genes.

Population genetics add an interesting layer: the protective G allele is relatively rare in Europeans (~13%) but common in East Asians (~62%), mirroring the considerably lower MS prevalence in East Asian populations. This parallels the HLA-DRB1*15:01 story, where high-frequency risk alleles in Europeans partly explain the European-predominant MS burden.

Practical Actions

For individuals carrying the AA genotype (no G alleles), the practical implications centre on MS awareness, early detection, and preserving Treg function through vitamin D optimisation. There is no supplement that directly compensates for reduced CD58 expression, but vitamin D robustly upregulates FoxP3 and Treg function through parallel mechanisms, and vitamin D deficiency is an established environmental risk modifier for MS.

For AG carriers, the picture is similar but the absolute risk increase is modest — the OR per copy of the A allele is ~1.2, meaning background MS risk is elevated rather than dramatically elevated.

Interactions

The CD58 pathway converges with other confirmed MS susceptibility genes. rs3135388 (HLA-DRB1 tagging variant) and rs6897932 (IL7R) both influence T-cell priming and survival in the same adaptive immune cascade. HLA-DRB1*15:01 shapes the antigen-presentation context in which CD2–CD58 costimulation occurs; IL7R regulates T-cell homeostasis and Treg maintenance. Individuals carrying high-risk alleles at multiple loci in this T-cell activation pathway would be expected to have substantially higher MS susceptibility than any single variant predicts alone, though formal interaction statistics across these three loci in a single cohort are not yet available in the literature.

Genotype Interpretations

What each possible genotype means for this variant.

GG Full CD58 Protection Beneficial

Two protective G alleles associated with highest CD58 expression and most effective regulatory T cell function

You carry two copies of the protective G allele at rs2300747, the genotype associated with the highest CD58 mRNA levels and the most robust CD2-mediated stimulation of FoxP3-positive regulatory T cells. This genotype is found in approximately 2% of Europeans but is common in East Asian populations (~38% GG). Evidence consistently shows the G allele is the most protective configuration at this locus for MS susceptibility. The GG genotype is used as the reference category against which the risk of AA and AG are measured.

AG One Protective Allele Intermediate

One protective G allele provides intermediate CD58 expression and partial Treg support

The AG genotype represents a mixed haplotype state: one CD58 allele produces higher mRNA (the G haplotype) and one produces lower mRNA with elevated miR-548ac (the A haplotype). The net CD58 expression is intermediate. In dose-response analyses of the original De Jager et al. cohort, AG carriers showed intermediate CD58 mRNA in both lymphoblastic cell lines and patient blood samples, consistent with an additive allelic dosage effect. The partial Treg rescue conferred by the G allele is reflected in the heterozygous OR of 0.85 in the 2016 meta-analysis.

AA Reduced CD58 Expression High Risk

Two copies of the risk allele associated with lower CD58 levels and reduced regulatory T cell function

The AA genotype at rs2300747 is associated with the lowest CD58 mRNA levels measurable in both lymphoblastic cell lines and peripheral blood mononuclear cells from MS subjects. Because rs2300747 is a haplotype tag for a broader intronic regulatory region (r² = 0.929 with rs12044852), the AA haplotype also drives higher expression of the intronic microRNA hsa-miR-548ac, which further suppresses downstream immune-regulatory targets. The net result is a CD58/Treg axis operating at reduced efficiency. MS is a complex disease requiring multiple genetic and environmental hits — most AA individuals never develop MS — but this genotype contributes meaningfully to susceptibility, particularly in populations of European descent where it is highly prevalent and where MS incidence is elevated.

Vitamin D is the best-studied environmental modifier: deficiency synergises with genetic MS risk factors including CD58, while sufficiency independently supports FoxP3 expression and Treg function through the vitamin D receptor signalling axis.