CXCL11

C-X-C motif chemokine ligand 11, the group of Chemokine ligands

Basic information

Region (hg38): 4:76033681-76041415

Previous symbols: [ "SCYB9B", "SCYB11" ]

Links

ENSG00000169248 ∙ NCBI:6373 ∙ OMIM:604852 ∙ HGNC:10638 ∙ Uniprot:O14625 ∙ 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 CXCL11 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CXCL11 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						0
missense			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	0

Variants in CXCL11

This is a list of pathogenic ClinVar variants found in the CXCL11 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-76034815-T-G		not specified	Uncertain significance (Mar 06, 2023)
4-76035066-T-A		not specified	Uncertain significance (Sep 27, 2022)
4-76035074-T-G		not specified	Uncertain significance (Mar 22, 2023)
4-76035118-T-C		not specified	Uncertain significance (Aug 08, 2023)
4-76035929-T-G		not specified	Uncertain significance (Dec 19, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CXCL11	protein_coding	protein_coding	ENST00000306621	4	7734

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.314	0.622	125733	0	5	125738	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.320	45	51.5	0.875	0.00000250	620
Missense in Polyphen		11	12.693	0.8666		162
Synonymous	-0.0981	16	15.5	1.03	7.27e-7	169
Loss of Function	1.43	1	4.13	0.242	1.72e-7	58

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000872	0.0000872
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000880	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.0000330	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Chemotactic for interleukin-activated T-cells but not unstimulated T-cells, neutrophils or monocytes. Induces calcium release in activated T-cells. Binds to CXCR3. May play an important role in CNS diseases which involve T-cell recruitment. May play a role in skin immune responses.
• 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;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;CXCR3-mediated signaling events (Consensus)

Recessive Scores

• pRec: 0.238

Intolerance Scores

• loftool: 0.599
• rvis_EVS: 0.28
• rvis_percentile_EVS: 70.87

Haploinsufficiency Scores

• pHI: 0.426
• hipred: N
• hipred_score: 0.146
• ghis: 0.395

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	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Cxcl11

Gene ontology

• Biological process: chemotaxis;inflammatory response;immune 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;T cell chemotaxis;neutrophil chemotaxis;leukocyte chemotaxis;regulation of cell population proliferation;positive regulation of cAMP-mediated signaling;positive regulation of release of sequestered calcium ion into cytosol;antimicrobial humoral immune response mediated by antimicrobial peptide;chemokine-mediated signaling pathway;cellular response to lipopolysaccharide
• Cellular component: extracellular region;extracellular space;cell
• Molecular function: protein binding;chemokine activity;heparin binding;CXCR3 chemokine receptor binding