CXCL9

Chr 4

C-X-C motif chemokine ligand 9

Also known as: CMK, Humig, MIG, SCYB9, crg-10

NCBI Gene: 4283 ENSG00000138755 UniProt: Q07325 OMIM: 601704

The encoded protein is a chemokine that functions as a chemoattractant for activated T cells and binds to the CXCR3 receptor, playing a role in immune and inflammatory responses. Mutations in this gene are associated with neurological disorders, though this gene shows low constraint to loss-of-function variation (pLI = 0.003, LOEUF = 1.69). A GeneReviews entry is available for detailed clinical information about associated conditions and inheritance patterns.

GeneReviews OMIM ResearchSummary from RefSeq, UniProt

This antimicrobial gene is part of a chemokine superfamily that encodes secreted proteins involved in immunoregulatory and inflammatory processes. The protein encoded is thought to be involved in T cell trafficking. The encoded protein binds to C-X-C motif chemokine 3 and is a chemoattractant for lymphocytes but not for neutrophils. [provided by RefSeq, Aug 2020]

GeneReviews OMIM ResearchGenerating clinical summary…

Active trials

865

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

—

LOEUF

Mechanism· predicted

📖

GeneReview available — CXCL9

Authoritative clinical overview · Recommended first read

Open GeneReview ↗

Some data sources returned errors (1)

gnomad: Error: gnomAD API error: 400

Population Genetics & Constraint

gnomAD

Constraint data not available from gnomAD.

Background carrier burden — how many people carry a rare variant somewhere in CXCL9?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 700

139 rare PASS variants

Rare truncating (LoF)

1 in 2,400

40 rare PASS variants

Rare synonymous (reference)

1 in 1,700

48 rare PASS variants

Rare missense and truncating variants are carried at similar rates in CXCL9; this gene does not show strong loss-of-function constraint by this measure. 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 1,000	1 in 2,200
South Asian	~43k	1 in 180	1 in 2,800
Remaining (unassigned)	~30k	1 in 370	1 in 2,500
European (Finnish)	~27k	1 in 1,300	≈ 1 in 26,000
Admixed American	~22k	1 in 390	1 in 1,200
African / African American	~21k	1 in 320	1 in 800
East Asian	~20k	1 in 420	1 in 2,300
Ashkenazi Jewish	~13k	1 in 2,600	none seen
Middle Eastern	~2,884	1 in 580	none seen

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): 2 of 4 coding exons well covered in gnomAD exomes; exons 1, 4 marginal. Genomes: all 4.? see exons ↓