CXCL9

Chr 4

C-X-C motif chemokine ligand 9

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

NCBI Gene: 4283ENSG00000138755UniProt: Q07325

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]

GeneReviewsResearchGenerating clinical summary…
DNmechanismLOEUF 1.69
Clinical Summary— CXCL9
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
19 VUS of 24 total submissions
💊
Clinical Trials
9 active or recruiting trials — potential therapeutic options may be available
Explore recent and relevant literature in Research Assistant →
📖
GeneReview available — CXCL9
Authoritative clinical overview · Recommended first read
Open GeneReview ↗
Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?
1.69LOEUF
pLI 0.003
Z-score 0.40
OE 0.81 (0.39–1.69)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?
-0.03Z-score
OE missense 1.01 (0.83–1.24)
66 obs / 65.3 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios?
LoF OE?0.81 (0.39–1.69)
0≤0.351.4
Missense OE?1.01 (0.83–1.24)
0≤0.61.4
Synonymous OE?1.20
0≤1.21.6
LoF obs/exp: 4 / 5.0Missense obs/exp: 66 / 65.3Syn Z: -0.72

This gene — mechanism propensity

DN
0.77top 25%
GOF
0.3094th %ile
LOF
0.2873th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

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

24 submitted variants in ClinVar

ClinVar

Classification Summary

VUS19
Likely Benign1
Benign1
19
VUS
1
Likely Benign
1
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
0
0
0
Likely Pathogenic
0
0
0
0
0
VUS
0
19
0
0
19
Likely Benign
0
1
0
0
1
Benign
0
0
0
1
1
Total0200121

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

24 pathogenic / likely-pathogenic (of 32) ClinVar copy-number / structural variants overlap CXCL9 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →

Protein Context — Lollipop Plot

CXCL9 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov
COVID-19Influenza

Clinical Study on the Immune Response Characteristics of Novel Coronavirus and Influenza Virus Infection

RECRUITING
NCT06667063Zhongnan HospitalStarted 2024-09-19
Nasal swab/Nasopharyngeal swab/Blood sample collectionNasal swab/Nasopharyngeal swab/Blood drawNasal swab/Nasopharyngeal swab/Blood draw
Glioma

The Role of B7-H4 in Tumor Vaccine

RECRUITING
NCT06156150Huashan HospitalStarted 2023-11-26
tumor vaccine
Haemophagocytic Lymphohistiocytosis

Ruxolitinib as First Line Treatment in Primary Haemophagocytic Lymphohistiocytosis (R-HLH)

RECRUITING
NCT05762640Phase PHASE2Assistance Publique - Hôpitaux de ParisStarted 2024-11-10
Ruxolitinib
Cutaneous Squamous Cell Carcinoma (CSCC)

Next-gen Flow Cytometry to Find Immune Profiles, Treatment Response, and Toxicity Markers in Skin Cancer Patients Treated With Cemiplimab.

RECRUITING
NCT07064330Instituto de Investigación Biomédica de SalamancaStarted 2025-07-17
Cemiplimab
Central Centrifugal Cicatricial AlopeciaFrontal Fibrosing Alopecia

Deucravacitinib in the Treatment of Cicatricial Alopecias

RECRUITING
NCT07508488Phase PHASE2Icahn School of Medicine at Mount SinaiStarted 2026-05-28
Deucravacitinib
Rejection; Transplant, Liver

Transcriptomics as an Aid in the Histological Diagnosis of Acute Rejection After Liver Transplantation

RECRUITING
NCT06734013Phase NAIRCCS Azienda Ospedaliero-Universitaria di BolognaStarted 2024-10-17
Molecular diagnostic
Kidney TransplantRejection

Detection of Circulating Kidney DNA in Kidney Transplant Patients Facing an Episode of Graft Rejection

RECRUITING
NCT06351488Assistance Publique - Hôpitaux de ParisStarted 2024-08-21
MetforminAging

Pilot Study on Evaluating the Geroprotective Effect of Metformin

RECRUITING
NCT06459310Phase PHASE2Xuanwu Hospital, BeijingStarted 2024-06-30
Metformin Hydrochloride tabletPlacebo
Breast NeoplasmTriple Negative Breast Cancer (TNBC)HRD

PHOENIX DDR/Anti-PD-L1 Trial: A Pre-surgical Window of Opportunity and Post-surgical Adjuvant Biomarker Study of DNA Damage Response Inhibition With or Without Anti-PD-L1 Immunotherapy in Patients With Neoadjuvant Treatment Resistant Residual Triple Negative Breast Cancer

RECRUITING
NCT03740893Phase PHASE2Institute of Cancer Research, United KingdomStarted 2019-10-15
AZD6738OlaparibDurvalumab

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients