CXCL9

C-X-C motif chemokine ligand 9, the group of Chemokine ligands

Basic information

Region (hg38): 4:76001275-76007509

Previous symbols: [ "CMK", "MIG" ]

Links

ENSG00000138755 ∙ NCBI:4283 ∙ OMIM:601704 ∙ HGNC:7098 ∙ Uniprot:Q07325 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CXCL9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CXCL9 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			10	1		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	1	1

Variants in CXCL9

This is a list of pathogenic ClinVar variants found in the CXCL9 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
4-76003601-T-C			Benign (Jun 05, 2018)
4-76003623-C-T		not specified	Uncertain significance (Nov 26, 2024)
4-76003635-C-T		not specified	Uncertain significance (Dec 11, 2023)
4-76003665-T-G		not specified	Uncertain significance (Dec 13, 2023)
4-76003686-T-G		not specified	Uncertain significance (Jun 23, 2023)
4-76004849-G-A		not specified	Uncertain significance (May 17, 2023)
4-76004876-C-G		not specified	Uncertain significance (Jun 16, 2023)
4-76006164-C-T		not specified	Uncertain significance (Aug 02, 2022)
4-76006185-A-C		not specified	Uncertain significance (Dec 05, 2022)
4-76006205-G-A		not specified	Uncertain significance (Aug 20, 2024)
4-76006220-G-C			Likely benign (Mar 29, 2018)
4-76006236-T-C		not specified	Uncertain significance (Feb 13, 2024)
4-76006265-A-G		not specified	Uncertain significance (Feb 28, 2023)
4-76007418-C-T		not specified	Uncertain significance (Jan 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CXCL9	protein_coding	protein_coding	ENST00000264888	4	6214

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00293	0.599	118368	0	3	118371	0.0000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0329	66	65.3	1.01	0.00000340	810
Missense in Polyphen		13	17.121	0.75931		216
Synonymous	-0.721	26	21.7	1.20	0.00000101	232
Loss of Function	0.401	4	4.96	0.806	2.09e-7	60

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000125	0.000106
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000188	0.0000182
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cytokine that affects the growth, movement, or activation state of cells that participate in immune and inflammatory response. Chemotactic for activated T-cells. Binds to CXCR3.
• Pathway: Chemokine signaling pathway - Homo sapiens (human);Toll-like receptor signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);Regulation of toll-like receptor signaling pathway;Allograft Rejection;Chemokine signaling pathway;Type II interferon signaling (IFNG);Toll-like Receptor Signaling Pathway;Signaling by GPCR;Signal Transduction;Chemokine receptors bind chemokines;Peptide ligand-binding receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;G alpha (i) signalling events;GPCR downstream signalling;IL23-mediated signaling events;CXCR3-mediated signaling events (Consensus)

Recessive Scores

• pRec: 0.355

Intolerance Scores

• loftool: 0.745
• rvis_EVS: 0.26
• rvis_percentile_EVS: 69.83

Haploinsufficiency Scores

• pHI: 0.0642
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Low	Low
Primary Immunodeficiency	Medium	Low	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Cxcl9
• Phenotype: immune system phenotype; hematopoietic system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: chemotaxis;defense response;inflammatory response;immune response;cellular defense response;signal transduction;G protein-coupled receptor signaling pathway;adenylate cyclase-activating G protein-coupled receptor signaling pathway;cell-cell signaling;regulation of signaling receptor activity;neutrophil chemotaxis;leukocyte chemotaxis;regulation of cell population proliferation;positive regulation of cAMP-mediated signaling;positive regulation of myoblast differentiation;positive regulation of release of sequestered calcium ion into cytosol;defense response to virus;antimicrobial humoral immune response mediated by antimicrobial peptide;chemokine-mediated signaling pathway;cellular response to lipopolysaccharide;positive regulation of myoblast fusion
• Cellular component: extracellular region;extracellular space;external side of plasma membrane
• Molecular function: cytokine activity;protein binding;chemokine activity;CXCR3 chemokine receptor binding