CXCR5

Chr 11

C-X-C motif chemokine receptor 5

Also known as: BLR1, CD185, MDR15

NCBI Gene: 643 ENSG00000160683 UniProt: P32302

This gene encodes a multi-pass membrane protein that belongs to the CXC chemokine receptor family. It is expressed in mature B-cells and Burkitt's lymphoma. This cytokine receptor binds to B-lymphocyte chemoattractant (BLC), and is involved in B-cell migration into B-cell follicles of spleen and Peyer patches. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Aug 2011]

GeneReviews Research

GeneReviews ResearchGenerating clinical summary…

Clinical highlights

Interpreting a novel variant

This gene is strongly intolerant of loss-of-function variation in the population, so LoF variants warrant close attention. No curated mechanism annotation is available — see the mechanism card for the computational prediction and its caveats.Based on population constraint only.

Active trials

278

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.55

LOEUF

Multiple*

Mechanism· predicted

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GeneReview available — CXCR5

Authoritative clinical overview · Recommended first read

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Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Moderate LoF intolerance

LoF Constraint?

0.55LOEUF

pLI 0.729

Z-score 2.41

OE 0.12 (0.04–0.55)

Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?

2.15Z-score

OE missense 0.61 (0.54–0.70)

149 obs / 243.1 exp

Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios?

LoF OE?0.12 (0.04–0.55)

0≤0.351.4

Missense OE?0.61 (0.54–0.70)

0≤0.61.4

Synonymous OE?0.94

0≤1.21.6

LoF obs/exp: 1 / 8.6Missense obs/exp: 149 / 243.1Syn Z: 0.46

Background carrier burden — how many people carry a rare variant somewhere in CXCR5?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 160

345 rare PASS variants

Rare truncating (LoF)

1 in 13,000

25 rare PASS variants

Rare synonymous (reference)

1 in 150

234 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for CXCR5. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 180	1 in 14,000
South Asian	~43k	1 in 150	1 in 2,400
Remaining (unassigned)	~30k	1 in 130	≈ 1 in 28,000
European (Finnish)	~27k	1 in 340	≈ 1 in 24,000
Admixed American	~22k	1 in 140	≈ 1 in 22,000
African / African American	~21k	1 in 130	≈ 1 in 21,000
East Asian	~20k	1 in 290	≈ 1 in 20,000
Ashkenazi Jewish	~13k	1 in 690	≈ 1 in 13,000
Middle Eastern	~2,884	1 in 130	≈ 1 in 2,600

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): All 2 coding exons well covered in gnomAD exomes and genomes.? see exons ↓