rs6910071 — TSBP1

TSBP1 rs6910071 — The MHC Sentinel for Rheumatoid Arthritis Risk

The rs6910071 variant sits within an intron of TSBP1 (testis-expressed basic protein 1, formerly C6orf10), a gene embedded in the major histocompatibility complex (MHC) on chromosome 6p21. The MHC is the most densely associated genetic region for rheumatoid arthritis (RA), driven principally by HLA-DRB1 alleles encoding a five-amino-acid sequence called the shared epitope¹¹ shared epitope
A conserved sequence in the third hypervariable region of the HLA-DRβ chain (positions 70–74) that shapes the peptide-binding groove and is the dominant genetic risk factor for seropositive RA. Because rs6910071 sits in strong linkage disequilibrium with HLA-DRB1*04 shared-epitope haplotypes, it functions as a reliable GWAS tag for this high-risk haplotype block — catching much of the MHC-mediated RA susceptibility in a single testable SNP.

The Mechanism

TSBP1 itself is broadly expressed at low levels throughout adult tissues, with highest expression in the testis and modest expression in immune-relevant tissues including blood and lymph nodes. The gene activates protein kinase A (PKA) signaling and interacts with at least 14 genes implicated in autoimmune pathways. However, the primary clinical signal at rs6910071 is almost certainly indirect: the G allele tags a chromosomal haplotype block that includes HLA-DRB1*04:01 and related shared-epitope alleles, which together shape antigen presentation by class II MHC molecules to CD4+ T cells.

Shared-epitope HLA-DRB1 alleles promote autoimmunity through two mechanisms. First, they preferentially present citrullinated peptides — peptides carrying arginine residues enzymatically converted by PAD enzymes — leading to the anti-citrullinated protein antibodies (ACPA/anti-CCP) that are the serological hallmark of seropositive RA. Five amino-acid positions within HLA-DRB1, HLA-B, and HLA-DPB1 explain most of the MHC-wide RA association²² Five amino-acid positions within HLA-DRB1, HLA-B, and HLA-DPB1 explain most of the MHC-wide RA association
Fine-mapping study by Raychaudhuri et al. 2012 using imputed HLA alleles across 5,539 RA cases and 20,169 controls. Second, epigenetic dysregulation in the region may amplify risk: whole-blood bisulfite sequencing in RA patients identified differential hypomethylation at C6ORF10 CpG sites³³ differential hypomethylation at C6ORF10 CpG sites
Pearson correlation between C6ORF10 methylation and anti-CCP/RF levels was significantly negative, p<0.05, and the degree of hypomethylation correlated with serological risk markers anti-CCP and rheumatoid factor.

The Evidence

rs6910071 has been independently replicated in multiple large datasets. The most rigorous demonstration comes from a phenome-wide association study (PheWAS) across 29,349 Europeans in two biorepositories (MyCode/Geisinger and BioVU/Vanderbilt), which identified rs6910071 as the top replicating signal for rheumatoid arthritis and inflammatory polyarthropathies (pMETAL = 2.58 × 10⁻⁹⁴⁴ pMETAL = 2.58 × 10⁻⁹
60 cases/2,964 controls in MyCode; 81 cases/2,818 controls in BioVU). A separate genomic phenotype study identified the same variant as a novel locus for polymyalgia rheumatica⁵⁵ polymyalgia rheumatica
OR = 1.5, 95% CI 1.3–1.6, P = 1.3 × 10⁻¹⁰ in 413 PMR cases vs. 5,782 controls, a closely related inflammatory condition also strongly associated with HLA-DRB1*04.

A network analysis of 116 pleiotropic RA-associated genes identified C6orf10 as a hub gene⁶⁶ identified C6orf10 as a hub gene
Shared across nine autoimmune diseases including RA, psoriasis, SLE, multiple sclerosis, Graves' disease, and type 1 diabetes, consistent with the broader role of the HLA region in determining autoimmune susceptibility across organ systems. The G allele is notably more common in Europeans (~20%) than in African (~6%) or East Asian (~8%) populations, mirroring the higher prevalence of seropositive RA in northern European populations.

Practical Actions

Carriers of the G allele — particularly GG homozygotes — carry a meaningfully elevated prior probability of developing seropositive RA. The most evidence-based response to this genetic signal is early serological surveillance. ACPA (anti-CCP) and rheumatoid factor (RF) testing can identify preclinical seropositive RA years before joint damage begins; positive serology in the context of a high-risk genetic profile warrants rheumatology referral even before arthritis is clinically apparent.

Smoking is the primary modifiable environmental amplifier of shared-epitope RA risk: citrullination of lung proteins by cigarette smoke creates the neoantigens that, in shared-epitope carriers, trigger ACPA production. GG carriers who smoke face a combined gene-environment risk substantially larger than either factor alone.

Interactions

rs6910071 does not act in isolation. The strongest compound risk in RA comes from combining MHC-region HLA-DRB1 risk alleles (tagged by rs6910071) with non-HLA variants including PTPN22 R620W ([rs2476601 | The strongest non-HLA RA risk allele, increasing T-cell activation threshold]) and smoking exposure. When rs6910071-G is combined with rs2476601-A (PTPN22 R620W), the combined risk for seropositive RA exceeds either allele alone — a well-documented epistatic interaction where both T-cell and antigen-presentation pathways are simultaneously dysregulated.