XCL2

gene
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Also known as SCM-1b

Summary

XCL2 (X-C motif chemokine ligand 2, HGNC:10646) is a protein-coding gene on chromosome 1q24.2, encoding Cytokine SCM-1 beta (Q9UBD3). Chemotactic activity for lymphocytes but not for monocytes or neutrophils.

Predicted to enable CCR chemokine receptor binding activity and chemokine activity. Predicted to be involved in several processes, including antimicrobial humoral immune response mediated by antimicrobial peptide; cell chemotaxis; and chemokine-mediated signaling pathway. Predicted to be located in extracellular region. Predicted to be active in extracellular space.

Source: NCBI Gene 6846 — RefSeq curated summary.

At a glance

  • GWAS associations: 4
  • Clinical variants (ClinVar): 21 total
  • MANE Select transcript: NM_003175

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:10646
Approved symbolXCL2
NameX-C motif chemokine ligand 2
Location1q24.2
Locus typegene with protein product
StatusApproved
AliasesSCM-1b
Ensembl geneENSG00000143185
Ensembl biotypeprotein_coding
OMIM604828
Entrez6846

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000367819

RefSeq mRNA: 1 — MANE Select: NM_003175 NM_003175

CCDS: CCDS1273

Canonical transcript exons

ENST00000367819 — 3 exons

ExonStartEnd
ENSE00001445685168540768168541120
ENSE00001445686168543904168543997
ENSE00002347798168541993168542107

Expression profiles

Bgee: expression breadth ubiquitous, 119 present calls, max score 91.02.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 1.2395 / max 146.6482, expressed in 124 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
158221.2395124

Top tissues by expression

148 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
granulocyteCL:000009491.02gold quality
spleenUBERON:000210680.83gold quality
bloodUBERON:000017878.06gold quality
vastus lateralisUBERON:000137975.92gold quality
lymph nodeUBERON:000002975.38gold quality
thymusUBERON:000237075.04gold quality
quadriceps femorisUBERON:000137771.94gold quality
bone marrowUBERON:000237171.85gold quality
cerebellar vermisUBERON:000472071.14gold quality
duodenumUBERON:000211471.05gold quality
vermiform appendixUBERON:000115470.91gold quality
colonic epitheliumUBERON:000039768.83gold quality
placentaUBERON:000198767.77gold quality
right lobe of liverUBERON:000111467.26gold quality
smooth muscle tissueUBERON:000113566.05gold quality
gall bladderUBERON:000211064.98gold quality
mucosa of transverse colonUBERON:000499164.92gold quality
liverUBERON:000210764.68gold quality
right uterine tubeUBERON:000130264.03gold quality
rectumUBERON:000105263.70gold quality
bone marrow cellCL:000209262.73silver quality
upper lobe of left lungUBERON:000895262.55gold quality
lungUBERON:000204861.70gold quality
endometriumUBERON:000129561.25gold quality
fallopian tubeUBERON:000388961.23gold quality
small intestine Peyer’s patchUBERON:000345461.22gold quality
small intestineUBERON:000210860.44gold quality
olfactory segment of nasal mucosaUBERON:000538659.91gold quality
tracheaUBERON:000312659.07gold quality
dorsal plus ventral thalamusUBERON:000189759.03gold quality

Single-cell (SCXA)

Detected in 24 experiment(s), a significant marker in 23.

ExperimentMarker?Max mean expression
E-HCAD-36yes4998.77
E-MTAB-6701yes4607.50
E-HCAD-24yes3313.67
E-MTAB-8142yes2735.83
E-MTAB-10042yes2310.92
E-CURD-79yes976.86
E-CURD-84yes802.81
E-HCAD-32yes794.77
E-GEOD-70580yes645.83
E-HCAD-1yes110.56
E-HCAD-4yes109.31
E-CURD-122yes62.49
E-MTAB-10287yes34.65
E-MTAB-9467yes29.43
E-MTAB-6678yes27.78

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): ESR1

miRNA regulators (miRDB)

44 targeting XCL2, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-5692A100.0074.406850
HSA-MIR-548N99.9871.944170
HSA-MIR-477599.9875.006394
HSA-MIR-590-3P99.9674.346478
HSA-MIR-548AB99.9571.313488
HSA-MIR-55999.9572.283609
HSA-MIR-6772-5P99.9467.01577
HSA-MIR-548A-5P99.9471.273482
HSA-MIR-548AD-5P99.9471.233502
HSA-MIR-548AE-5P99.9471.233502
HSA-MIR-548AK99.9471.243488
HSA-MIR-548AM-5P99.9471.243488
HSA-MIR-548AP-5P99.9471.143489
HSA-MIR-548AQ-5P99.9471.343426
HSA-MIR-548AR-5P99.9471.283515
HSA-MIR-548AS-5P99.9471.223482
HSA-MIR-548AU-5P99.9471.243488
HSA-MIR-548AY-5P99.9471.233502
HSA-MIR-548B-5P99.9471.233502
HSA-MIR-548BB-5P99.9471.273509
HSA-MIR-548C-5P99.9471.243488
HSA-MIR-548D-5P99.9471.233502
HSA-MIR-548H-5P99.9471.243488
HSA-MIR-548I99.9471.253481
HSA-MIR-548J-5P99.9471.143489
HSA-MIR-548O-5P99.9471.243488
HSA-MIR-548W99.9471.243488
HSA-MIR-548Y99.9471.283514
HSA-MIR-3617-5P99.7569.411968
HSA-MIR-64199.7569.351975

Literature-anchored findings (GeneRIF, showing 9)

  • The G carrier of the -2510A/G promoter polymorphism was found to be associated with primary knee knee osteoarthritis among Koreans. (PMID:17763208)
  • Wag31 was found to specifically stimulate XCL2 expression in macrophages (PMID:18618175)
  • S1P induced the macrophage-recruiting factor CCL2 expression in NB cells via S1P2, providing new insights into the complicated functions of S1P2 in cancer. (PMID:25092091)
  • identified 13 ADCC-activated genes. Six gene expression assays including 8 of the 13 genes (CCL3, CCL4/CCL4L1/CCL4L2, CD160, IFNG, NR4A3 and XCL1/XCL2) were analyzed in 127 kidney biopsies (PMID:25449536)
  • analysis of XCL1 and XCL2, members of the C-chemokine subfamily, in the immune system (PMID:25497737)
  • XCL2 and CX3CL1 expression in lung cancers and adjacent non-cancerous tissues was detected by quantitative PCR and ELISA. The expression of XCL2 and CX3CL1 increases with increasing degree of malignancy, indicating that both chemokines might be important targets in gene therapy for lung cancer. (PMID:27156946)
  • Upregulated X-C motif chemokine ligand 2 (XCL2) is associated with poor prognosis and increased immune infiltration in clear cell renal cell carcinoma. (PMID:36503163)
  • The effect of ITLN1, XCL2 and DOT1L variants on knee osteoarthritis risk in the Han population. (PMID:36773049)
  • Comprehensive analysis reveals XCL2 as a cancer prognosis and immune infiltration-related biomarker. (PMID:37905956)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriocxcl32b.1ENSDARG00000071499
mus_musculusXcl1ENSMUSG00000026573
rattus_norvegicusXcl1ENSRNOG00000002964

Paralogs (26): CX3CL1 (ENSG00000006210), CCL26 (ENSG00000006606), CCL22 (ENSG00000102962), CCL17 (ENSG00000102970), CCL24 (ENSG00000106178), CCL7 (ENSG00000108688), CCL2 (ENSG00000108691), CCL8 (ENSG00000108700), CCL1 (ENSG00000108702), CCL20 (ENSG00000115009), CCL25 (ENSG00000131142), CCL21 (ENSG00000137077), XCL1 (ENSG00000143184), CCL11 (ENSG00000172156), CCL19 (ENSG00000172724), CCL13 (ENSG00000181374), CCL5 (ENSG00000271503), CCL23 (ENSG00000274736), CCL16 (ENSG00000275152), CCL4 (ENSG00000275302), CCL18 (ENSG00000275385), CCL15 (ENSG00000275718), CCL4L2 (ENSG00000276070), CCL3L3 (ENSG00000276085), CCL14 (ENSG00000276409), CCL3 (ENSG00000277632)

Protein

Protein identifiers

Cytokine SCM-1 betaQ9UBD3 (reviewed: Q9UBD3)

Alternative names: C motif chemokine 2, XC chemokine ligand 2

All UniProt accessions (1): Q9UBD3

UniProt curated annotations — full annotation on UniProt →

Function. Chemotactic activity for lymphocytes but not for monocytes or neutrophils.

Subcellular location. Secreted.

Similarity. Belongs to the intercrine gamma family.

RefSeq proteins (1): NP_003166* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001811Chemokine_IL8-like_domDomain
IPR008105Chemokine_XCL1/XCL2Family
IPR036048Interleukin_8-like_sfHomologous_superfamily
IPR039809Chemokine_b/g/dFamily

Pfam: PF00048

UniProt features (6 total): sequence variant 2, signal peptide 1, chain 1, region of interest 1, disulfide bond 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9UBD3-F181.470.50

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Disulfide bonds (1): 32–69

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

IDPathway
R-HSA-380108Chemokine receptors bind chemokines
R-HSA-416476G alpha (q) signalling events

MSigDB gene sets: 98 (showing top): BROWNE_HCMV_INFECTION_30MIN_DN, GOBP_ANTIMICROBIAL_HUMORAL_RESPONSE, GOBP_CIRCULATORY_SYSTEM_PROCESS, GOBP_CELL_CHEMOTAXIS, GOBP_INFLAMMATORY_RESPONSE, GOBP_RESPONSE_TO_PEPTIDE, AP4_Q6, CAGCTG_AP4_Q5, GOBP_TAXIS, REACTOME_PEPTIDE_LIGAND_BINDING_RECEPTORS, GOBP_DEFENSE_RESPONSE_TO_OTHER_ORGANISM, AML_Q6, GNF2_IL2RB, GOBP_HUMORAL_IMMUNE_RESPONSE, GOMF_CHEMOKINE_ACTIVITY

GO Biological Process (9): inflammatory response (GO:0006954), signal transduction (GO:0007165), blood circulation (GO:0008015), positive regulation of cell migration (GO:0030335), cell chemotaxis (GO:0060326), antimicrobial humoral immune response mediated by antimicrobial peptide (GO:0061844), chemokine-mediated signaling pathway (GO:0070098), chemotaxis (GO:0006935), immune response (GO:0006955)

GO Molecular Function (4): chemokine activity (GO:0008009), CCR chemokine receptor binding (GO:0048020), cytokine activity (GO:0005125), protein binding (GO:0005515)

GO Cellular Component (2): extracellular region (GO:0005576), obsolete extracellular space (GO:0005615)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
Peptide ligand-binding receptors1
GPCR downstream signalling1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cell migration2
chemokine receptor binding2
defense response1
cell communication1
cellular process1
signaling1
regulation of cellular process1
cellular response to stimulus1
circulatory system process1
regulation of cell migration1
positive regulation of cell motility1
chemotaxis1
cellular response to chemical stimulus1
antimicrobial humoral response1
G protein-coupled receptor signaling pathway1
cytokine-mediated signaling pathway1
cellular response to chemokine1
response to chemical1
taxis1
immune system process1
response to stimulus1
cytokine activity1
cell chemotaxis1
receptor ligand activity1
binding1
cellular anatomical structure1

Protein interactions and networks

STRING

1094 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
XCL2XCR1P46094997
XCL2CCL3P10147751
XCL2CCR7P32248594
XCL2CCL19Q99731591
XCL2CCL21O00585582
XCL2CD8AP01732574
XCL2CCR5P51681566
XCL2CCL25O15444563
XCL2CCR2P41597552
XCL2CD160O95971507
XCL2CXCR3P49682480
XCL2CXCL10P02778469
XCL2CCL4P13236468
XCL2CXCL8P10145467
XCL2PROK2Q9HC23456

IntAct

26 interactions, top by confidence:

ABTypeScore
XCL2KRTAP10-9psi-mi:“MI:0915”(physical association)0.560
XCL2NOTCH2NLApsi-mi:“MI:0915”(physical association)0.560
XCL2CCL5psi-mi:“MI:0407”(direct interaction)0.560
XCL2CXCL12psi-mi:“MI:0407”(direct interaction)0.560
CCL5XCL2psi-mi:“MI:0407”(direct interaction)0.560
CXCL12XCL2psi-mi:“MI:0407”(direct interaction)0.560
KRTAP1-3XCL2psi-mi:“MI:0915”(physical association)0.560
CCL7XCL2psi-mi:“MI:0407”(direct interaction)0.440
CCL8XCL2psi-mi:“MI:0407”(direct interaction)0.440
CCL20XCL2psi-mi:“MI:0407”(direct interaction)0.440
CCL21XCL2psi-mi:“MI:0407”(direct interaction)0.440
CCL26XCL2psi-mi:“MI:0407”(direct interaction)0.440
CCL28XCL2psi-mi:“MI:0407”(direct interaction)0.440
CXCL2XCL2psi-mi:“MI:0407”(direct interaction)0.440
CXCL3XCL2psi-mi:“MI:0407”(direct interaction)0.440
PF4XCL2psi-mi:“MI:0407”(direct interaction)0.440
PF4V1XCL2psi-mi:“MI:0407”(direct interaction)0.440
CXCL5XCL2psi-mi:“MI:0407”(direct interaction)0.440
CXCL17XCL2psi-mi:“MI:0407”(direct interaction)0.440
XCL2KRTAP1-3psi-mi:“MI:0915”(physical association)0.000

BioGRID (18): KRTAP10-9 (Two-hybrid), NOTCH2NL (Two-hybrid), KRTAP1-3 (Two-hybrid), XCL2 (Reconstituted Complex), XCL2 (Reconstituted Complex), XCL2 (Reconstituted Complex), XCL2 (Reconstituted Complex), XCL2 (Reconstituted Complex), XCL2 (Reconstituted Complex), XCL2 (Reconstituted Complex), XCL2 (Reconstituted Complex), XCL2 (Reconstituted Complex), XCL2 (Reconstituted Complex), XCL2 (Reconstituted Complex), XCL2 (Reconstituted Complex)

ESM2 similar proteins: A0A0R4INB9, A9QWP9, B0R191, K7XWG4, O00175, O35903, O43927, O55038, O62812, O70460, P02775, P02778, P10146, P10720, P17515, P18340, P22362, P26894, P27784, P28292, P41324, P43030, P47992, P47993, P48298, P48973, P49113, P50228, P51672, P79255, P84444, P86792, P86793, P97545, P97885, Q07325, Q08782, Q2KIQ8, Q5KSV9, Q62401

Diamond homologs: K7XWG4, P16619, P42831, P47992, P47993, P49873, P51671, P51672, P52203, P80075, P80343, P82943, P97545, Q03366, Q09141, Q62401, Q68AY9, Q68Y88, Q8MIT7, Q99616, Q9JKC0, Q9QXY8, Q9TTQ4, Q9TTS6, Q9UBD3, F5HET8, O00626, O15467, O55145, O70460, O88430, O89093, O97919, P10147, P10148, P10855, P13236, P13500, P13501, P14097

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 17 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Chemokine receptors bind chemokines10133.7×2e-19
Class A/1 (Rhodopsin-like receptors)631.8×1e-07
Peptide ligand-binding receptors631.8×1e-07
GPCR ligand binding627.5×2e-07
G alpha (i) signalling events925.1×1e-10
Signaling by GPCR617.2×3e-06
GPCR downstream signalling515.5×4e-05

GO biological processes:

GO termPartnersFoldFDR
eosinophil chemotaxis5244.2×2e-10
monocyte chemotaxis5193.7×7e-10
chemokine-mediated signaling pathway7151.2×4e-13
neutrophil chemotaxis6114.2×2e-10
antimicrobial humoral immune response mediated by antimicrobial peptide997.2×4e-15
chemotaxis981.5×1e-14
cell chemotaxis561.7×2e-07
cell-cell signaling732.5×1e-08

Disease & clinical

Clinical variants and AI predictions

ClinVar

21 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance16
Likely benign3
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

152 predictions. Top by Δscore:

VariantEffectΔscore
1:168541116:TAAAA:Tacceptor_gain1.0000
1:168541121:C:CCacceptor_gain1.0000
1:168541988:CTCA:Cdonor_loss1.0000
1:168541991:A:ACdonor_gain1.0000
1:168541992:C:Adonor_loss1.0000
1:168541992:C:CCdonor_gain1.0000
1:168541992:CATT:Cdonor_gain1.0000
1:168541992:CATTA:Cdonor_gain1.0000
1:168541996:A:ACdonor_gain1.0000
1:168541997:C:CCdonor_gain1.0000
1:168541997:CTG:Cdonor_gain1.0000
1:168541997:CTGCT:Cdonor_gain1.0000
1:168542014:T:TAdonor_gain1.0000
1:168542103:TACAC:Tacceptor_gain1.0000
1:168542104:ACAC:Aacceptor_gain1.0000
1:168542105:CAC:Cacceptor_gain1.0000
1:168542105:CACC:Cacceptor_gain1.0000
1:168543899:CTTA:Cdonor_loss1.0000
1:168543900:TTAC:Tdonor_loss1.0000
1:168543902:A:ACdonor_gain1.0000
1:168543902:ACCTT:Adonor_gain1.0000
1:168543903:C:CAdonor_loss1.0000
1:168543903:C:CCdonor_gain1.0000
1:168543903:CCTT:Cdonor_gain1.0000
1:168543903:CCTTC:Cdonor_gain1.0000
1:168541117:AAAA:Aacceptor_gain0.9900
1:168541118:AAA:Aacceptor_gain0.9900
1:168541118:AAAC:Aacceptor_loss0.9900
1:168541119:AA:Aacceptor_gain0.9900
1:168541121:C:Gacceptor_loss0.9900

AlphaMissense

729 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:168541069:C:AW76C0.998
1:168541069:C:GW76C0.998
1:168541118:A:GF60S0.996
1:168541071:A:GW76R0.995
1:168541071:A:TW76R0.995
1:168541091:C:GC69S0.982
1:168541092:A:TC69S0.982
1:168542027:A:CY48D0.977
1:168541112:G:AT62I0.976
1:168542035:A:CI45S0.975
1:168541118:A:CF60C0.974
1:168542035:A:GI45T0.972
1:168541088:G:TA70D0.971
1:168541089:C:GA70P0.971
1:168541092:A:GC69R0.971
1:168541091:C:TC69Y0.967
1:168542074:C:GC32S0.958
1:168542075:A:GC32R0.958
1:168542075:A:TC32S0.958
1:168541070:C:GW76S0.955
1:168542035:A:TI45N0.954
1:168541070:C:AW76L0.952
1:168541090:A:CC69W0.952
1:168541071:A:CW76G0.951
1:168541106:C:GR64P0.948
1:168541103:C:AG65V0.946
1:168542074:C:TC32Y0.941
1:168541068:C:AV77L0.939
1:168541068:C:GV77L0.939
1:168541996:A:TV58E0.939

dbSNP variants (sampled 300 via entrez): RS1000316518 (1:168540317 C>T), RS1000352527 (1:168544963 A>G), RS1000807092 (1:168544821 A>C), RS1001918384 (1:168544349 A>C), RS1001970622 (1:168544098 T>A), RS1002926599 (1:168543084 C>T), RS1002977227 (1:168542795 G>A), RS1004433099 (1:168542556 C>A,T), RS1004832223 (1:168542747 A>C,T), RS1005429752 (1:168541844 T>C), RS1005897724 (1:168541694 A>G), RS1006260357 (1:168545570 G>C), RS1006327446 (1:168545393 C>A), RS1006719656 (1:168541309 T>C,G), RS1006847552 (1:168540897 G>A,C,T)

Disease associations

OMIM: gene MIM:604828 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

4 associations (top):

StudyTraitp-value
GCST002945_1Emphysema imaging phenotypes3.000000e-07
GCST002945_21Emphysema imaging phenotypes1.000000e-06
GCST004748_62Lung cancer2.000000e-07
GCST004750_93Squamous cell lung carcinoma3.000000e-06

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0007626emphysema imaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

17 total (human), top 17 by PubMed support.

ChemicalActions (top 5)PubMed papers
GSK-J4decreases expression1
triphenyl phosphateaffects expression1
decabromobiphenyl etheraffects expression1
sodium arseniteincreases expression1
3-chlorophenolincreases expression1
di-n-butylphosphoric acidaffects expression1
MT19c compounddecreases expression1
Panobinostataffects cotreatment, affects expression1
Benzo(a)pyreneincreases methylation1
Calcitriolincreases expression1
Cisplatinaffects cotreatment, affects expression1
Diurondecreases expression1
Estradioldecreases expression, affects cotreatment1
Pentachlorophenoldecreases expression1
Progesteroneaffects cotreatment, decreases expression1
Valproic Aciddecreases methylation1
Copper Sulfatedecreases expression1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.