CXCR6
Chr 3C-X-C motif chemokine receptor 6
Also known as: BONZO, CD186, CDw186, STRL33, TYMSTR
The protein is a G protein-coupled receptor that serves as the exclusive receptor for chemokine CXCL16 and regulates T lymphocyte migration to peripheral tissues including liver, spleen, intestine, lungs, and skin. Mutations cause autosomal recessive combined immunodeficiency characterized by recurrent infections and impaired T cell responses. The gene primarily affects the immune system through disruption of T lymphocyte trafficking and positioning in lymphoid and non-lymphoid tissues.
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Highly tolerant — LoF variants common in population
Mild missense constraint
This gene has evidence for multiple mechanisms of pathogenicity (dominant-negative and gain-of-function). Both the Badonyi & Marsh prediction and the broader genomic evidence point to dominant-negative as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.
Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.
Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.
ClinVar Variant Classifications
47 submitted variants in ClinVar
Classification Summary
Curated Variants Distribution
Classified variants from ClinVar · 5 ACMG categories
| Classification | LoF | Missense + Inframe | Non-coding | Synonymous | Total |
|---|---|---|---|---|---|
Pathogenic | 0 | 0 | 7 | 0 | 7 |
Likely Pathogenic | 0 | 0 | 1 | 0 | 1 |
VUS | 0 | 28 | 3 | 0 | 31 |
Likely Benign | 0 | 1 | 1 | 2 | 4 |
Benign | 0 | 0 | 0 | 1 | 1 |
| Total | 0 | 29 | 12 | 3 | 44 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
CXCR6 · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
3D Protein StructureAlphaFold
External Resources
Links to major genomics databases and tools
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
No active trials found for this gene.
Search ClinicalTrials.gov →External Resources
Links to major genomics databases and tools