XCL2
geneOn this page
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
| Field | Value |
|---|---|
| HGNC ID | HGNC:10646 |
| Approved symbol | XCL2 |
| Name | X-C motif chemokine ligand 2 |
| Location | 1q24.2 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | SCM-1b |
| Ensembl gene | ENSG00000143185 |
| Ensembl biotype | protein_coding |
| OMIM | 604828 |
| Entrez | 6846 |
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
| Exon | Start | End |
|---|---|---|
| ENSE00001445685 | 168540768 | 168541120 |
| ENSE00001445686 | 168543904 | 168543997 |
| ENSE00002347798 | 168541993 | 168542107 |
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 ID | TPM avg | Samples expressed |
|---|---|---|
| 15822 | 1.2395 | 124 |
Top tissues by expression
148 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| granulocyte | CL:0000094 | 91.02 | gold quality |
| spleen | UBERON:0002106 | 80.83 | gold quality |
| blood | UBERON:0000178 | 78.06 | gold quality |
| vastus lateralis | UBERON:0001379 | 75.92 | gold quality |
| lymph node | UBERON:0000029 | 75.38 | gold quality |
| thymus | UBERON:0002370 | 75.04 | gold quality |
| quadriceps femoris | UBERON:0001377 | 71.94 | gold quality |
| bone marrow | UBERON:0002371 | 71.85 | gold quality |
| cerebellar vermis | UBERON:0004720 | 71.14 | gold quality |
| duodenum | UBERON:0002114 | 71.05 | gold quality |
| vermiform appendix | UBERON:0001154 | 70.91 | gold quality |
| colonic epithelium | UBERON:0000397 | 68.83 | gold quality |
| placenta | UBERON:0001987 | 67.77 | gold quality |
| right lobe of liver | UBERON:0001114 | 67.26 | gold quality |
| smooth muscle tissue | UBERON:0001135 | 66.05 | gold quality |
| gall bladder | UBERON:0002110 | 64.98 | gold quality |
| mucosa of transverse colon | UBERON:0004991 | 64.92 | gold quality |
| liver | UBERON:0002107 | 64.68 | gold quality |
| right uterine tube | UBERON:0001302 | 64.03 | gold quality |
| rectum | UBERON:0001052 | 63.70 | gold quality |
| bone marrow cell | CL:0002092 | 62.73 | silver quality |
| upper lobe of left lung | UBERON:0008952 | 62.55 | gold quality |
| lung | UBERON:0002048 | 61.70 | gold quality |
| endometrium | UBERON:0001295 | 61.25 | gold quality |
| fallopian tube | UBERON:0003889 | 61.23 | gold quality |
| small intestine Peyer’s patch | UBERON:0003454 | 61.22 | gold quality |
| small intestine | UBERON:0002108 | 60.44 | gold quality |
| olfactory segment of nasal mucosa | UBERON:0005386 | 59.91 | gold quality |
| trachea | UBERON:0003126 | 59.07 | gold quality |
| dorsal plus ventral thalamus | UBERON:0001897 | 59.03 | gold quality |
Single-cell (SCXA)
Detected in 24 experiment(s), a significant marker in 23.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-HCAD-36 | yes | 4998.77 |
| E-MTAB-6701 | yes | 4607.50 |
| E-HCAD-24 | yes | 3313.67 |
| E-MTAB-8142 | yes | 2735.83 |
| E-MTAB-10042 | yes | 2310.92 |
| E-CURD-79 | yes | 976.86 |
| E-CURD-84 | yes | 802.81 |
| E-HCAD-32 | yes | 794.77 |
| E-GEOD-70580 | yes | 645.83 |
| E-HCAD-1 | yes | 110.56 |
| E-HCAD-4 | yes | 109.31 |
| E-CURD-122 | yes | 62.49 |
| E-MTAB-10287 | yes | 34.65 |
| E-MTAB-9467 | yes | 29.43 |
| E-MTAB-6678 | yes | 27.78 |
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):
| miRNA | Max score | Avg score | miRNA target_count |
|---|---|---|---|
| HSA-MIR-5692A | 100.00 | 74.40 | 6850 |
| HSA-MIR-548N | 99.98 | 71.94 | 4170 |
| HSA-MIR-4775 | 99.98 | 75.00 | 6394 |
| HSA-MIR-590-3P | 99.96 | 74.34 | 6478 |
| HSA-MIR-548AB | 99.95 | 71.31 | 3488 |
| HSA-MIR-559 | 99.95 | 72.28 | 3609 |
| HSA-MIR-6772-5P | 99.94 | 67.01 | 577 |
| HSA-MIR-548A-5P | 99.94 | 71.27 | 3482 |
| HSA-MIR-548AD-5P | 99.94 | 71.23 | 3502 |
| HSA-MIR-548AE-5P | 99.94 | 71.23 | 3502 |
| HSA-MIR-548AK | 99.94 | 71.24 | 3488 |
| HSA-MIR-548AM-5P | 99.94 | 71.24 | 3488 |
| HSA-MIR-548AP-5P | 99.94 | 71.14 | 3489 |
| HSA-MIR-548AQ-5P | 99.94 | 71.34 | 3426 |
| HSA-MIR-548AR-5P | 99.94 | 71.28 | 3515 |
| HSA-MIR-548AS-5P | 99.94 | 71.22 | 3482 |
| HSA-MIR-548AU-5P | 99.94 | 71.24 | 3488 |
| HSA-MIR-548AY-5P | 99.94 | 71.23 | 3502 |
| HSA-MIR-548B-5P | 99.94 | 71.23 | 3502 |
| HSA-MIR-548BB-5P | 99.94 | 71.27 | 3509 |
| HSA-MIR-548C-5P | 99.94 | 71.24 | 3488 |
| HSA-MIR-548D-5P | 99.94 | 71.23 | 3502 |
| HSA-MIR-548H-5P | 99.94 | 71.24 | 3488 |
| HSA-MIR-548I | 99.94 | 71.25 | 3481 |
| HSA-MIR-548J-5P | 99.94 | 71.14 | 3489 |
| HSA-MIR-548O-5P | 99.94 | 71.24 | 3488 |
| HSA-MIR-548W | 99.94 | 71.24 | 3488 |
| HSA-MIR-548Y | 99.94 | 71.28 | 3514 |
| HSA-MIR-3617-5P | 99.75 | 69.41 | 1968 |
| HSA-MIR-641 | 99.75 | 69.35 | 1975 |
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
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | cxcl32b.1 | ENSDARG00000071499 |
| mus_musculus | Xcl1 | ENSMUSG00000026573 |
| rattus_norvegicus | Xcl1 | ENSRNOG00000002964 |
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 beta — Q9UBD3 (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)
| ID | Name | Type |
|---|---|---|
| IPR001811 | Chemokine_IL8-like_dom | Domain |
| IPR008105 | Chemokine_XCL1/XCL2 | Family |
| IPR036048 | Interleukin_8-like_sf | Homologous_superfamily |
| IPR039809 | Chemokine_b/g/d | Family |
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)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q9UBD3-F1 | 81.47 | 0.50 |
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
| ID | Pathway |
|---|---|
| R-HSA-380108 | Chemokine receptors bind chemokines |
| R-HSA-416476 | G 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:
| Category | Pathways |
|---|---|
| Peptide ligand-binding receptors | 1 |
| GPCR downstream signalling | 1 |
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| cell migration | 2 |
| chemokine receptor binding | 2 |
| defense response | 1 |
| cell communication | 1 |
| cellular process | 1 |
| signaling | 1 |
| regulation of cellular process | 1 |
| cellular response to stimulus | 1 |
| circulatory system process | 1 |
| regulation of cell migration | 1 |
| positive regulation of cell motility | 1 |
| chemotaxis | 1 |
| cellular response to chemical stimulus | 1 |
| antimicrobial humoral response | 1 |
| G protein-coupled receptor signaling pathway | 1 |
| cytokine-mediated signaling pathway | 1 |
| cellular response to chemokine | 1 |
| response to chemical | 1 |
| taxis | 1 |
| immune system process | 1 |
| response to stimulus | 1 |
| cytokine activity | 1 |
| cell chemotaxis | 1 |
| receptor ligand activity | 1 |
| binding | 1 |
| cellular anatomical structure | 1 |
Protein interactions and networks
STRING
1094 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| XCL2 | XCR1 | P46094 | 997 |
| XCL2 | CCL3 | P10147 | 751 |
| XCL2 | CCR7 | P32248 | 594 |
| XCL2 | CCL19 | Q99731 | 591 |
| XCL2 | CCL21 | O00585 | 582 |
| XCL2 | CD8A | P01732 | 574 |
| XCL2 | CCR5 | P51681 | 566 |
| XCL2 | CCL25 | O15444 | 563 |
| XCL2 | CCR2 | P41597 | 552 |
| XCL2 | CD160 | O95971 | 507 |
| XCL2 | CXCR3 | P49682 | 480 |
| XCL2 | CXCL10 | P02778 | 469 |
| XCL2 | CCL4 | P13236 | 468 |
| XCL2 | CXCL8 | P10145 | 467 |
| XCL2 | PROK2 | Q9HC23 | 456 |
IntAct
26 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| XCL2 | KRTAP10-9 | psi-mi:“MI:0915”(physical association) | 0.560 |
| XCL2 | NOTCH2NLA | psi-mi:“MI:0915”(physical association) | 0.560 |
| XCL2 | CCL5 | psi-mi:“MI:0407”(direct interaction) | 0.560 |
| XCL2 | CXCL12 | psi-mi:“MI:0407”(direct interaction) | 0.560 |
| CCL5 | XCL2 | psi-mi:“MI:0407”(direct interaction) | 0.560 |
| CXCL12 | XCL2 | psi-mi:“MI:0407”(direct interaction) | 0.560 |
| KRTAP1-3 | XCL2 | psi-mi:“MI:0915”(physical association) | 0.560 |
| CCL7 | XCL2 | psi-mi:“MI:0407”(direct interaction) | 0.440 |
| CCL8 | XCL2 | psi-mi:“MI:0407”(direct interaction) | 0.440 |
| CCL20 | XCL2 | psi-mi:“MI:0407”(direct interaction) | 0.440 |
| CCL21 | XCL2 | psi-mi:“MI:0407”(direct interaction) | 0.440 |
| CCL26 | XCL2 | psi-mi:“MI:0407”(direct interaction) | 0.440 |
| CCL28 | XCL2 | psi-mi:“MI:0407”(direct interaction) | 0.440 |
| CXCL2 | XCL2 | psi-mi:“MI:0407”(direct interaction) | 0.440 |
| CXCL3 | XCL2 | psi-mi:“MI:0407”(direct interaction) | 0.440 |
| PF4 | XCL2 | psi-mi:“MI:0407”(direct interaction) | 0.440 |
| PF4V1 | XCL2 | psi-mi:“MI:0407”(direct interaction) | 0.440 |
| CXCL5 | XCL2 | psi-mi:“MI:0407”(direct interaction) | 0.440 |
| CXCL17 | XCL2 | psi-mi:“MI:0407”(direct interaction) | 0.440 |
| XCL2 | KRTAP1-3 | psi-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:
| Pathway | Partners | Fold | FDR |
|---|---|---|---|
| Chemokine receptors bind chemokines | 10 | 133.7× | 2e-19 |
| Class A/1 (Rhodopsin-like receptors) | 6 | 31.8× | 1e-07 |
| Peptide ligand-binding receptors | 6 | 31.8× | 1e-07 |
| GPCR ligand binding | 6 | 27.5× | 2e-07 |
| G alpha (i) signalling events | 9 | 25.1× | 1e-10 |
| Signaling by GPCR | 6 | 17.2× | 3e-06 |
| GPCR downstream signalling | 5 | 15.5× | 4e-05 |
GO biological processes:
| GO term | Partners | Fold | FDR |
|---|---|---|---|
| eosinophil chemotaxis | 5 | 244.2× | 2e-10 |
| monocyte chemotaxis | 5 | 193.7× | 7e-10 |
| chemokine-mediated signaling pathway | 7 | 151.2× | 4e-13 |
| neutrophil chemotaxis | 6 | 114.2× | 2e-10 |
| antimicrobial humoral immune response mediated by antimicrobial peptide | 9 | 97.2× | 4e-15 |
| chemotaxis | 9 | 81.5× | 1e-14 |
| cell chemotaxis | 5 | 61.7× | 2e-07 |
| cell-cell signaling | 7 | 32.5× | 1e-08 |
Disease & clinical
Clinical variants and AI predictions
ClinVar
21 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 0 |
| Uncertain significance | 16 |
| Likely benign | 3 |
| Benign | 0 |
Top pathogenic / likely-pathogenic (0)
SpliceAI
152 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 1:168541116:TAAAA:T | acceptor_gain | 1.0000 |
| 1:168541121:C:CC | acceptor_gain | 1.0000 |
| 1:168541988:CTCA:C | donor_loss | 1.0000 |
| 1:168541991:A:AC | donor_gain | 1.0000 |
| 1:168541992:C:A | donor_loss | 1.0000 |
| 1:168541992:C:CC | donor_gain | 1.0000 |
| 1:168541992:CATT:C | donor_gain | 1.0000 |
| 1:168541992:CATTA:C | donor_gain | 1.0000 |
| 1:168541996:A:AC | donor_gain | 1.0000 |
| 1:168541997:C:CC | donor_gain | 1.0000 |
| 1:168541997:CTG:C | donor_gain | 1.0000 |
| 1:168541997:CTGCT:C | donor_gain | 1.0000 |
| 1:168542014:T:TA | donor_gain | 1.0000 |
| 1:168542103:TACAC:T | acceptor_gain | 1.0000 |
| 1:168542104:ACAC:A | acceptor_gain | 1.0000 |
| 1:168542105:CAC:C | acceptor_gain | 1.0000 |
| 1:168542105:CACC:C | acceptor_gain | 1.0000 |
| 1:168543899:CTTA:C | donor_loss | 1.0000 |
| 1:168543900:TTAC:T | donor_loss | 1.0000 |
| 1:168543902:A:AC | donor_gain | 1.0000 |
| 1:168543902:ACCTT:A | donor_gain | 1.0000 |
| 1:168543903:C:CA | donor_loss | 1.0000 |
| 1:168543903:C:CC | donor_gain | 1.0000 |
| 1:168543903:CCTT:C | donor_gain | 1.0000 |
| 1:168543903:CCTTC:C | donor_gain | 1.0000 |
| 1:168541117:AAAA:A | acceptor_gain | 0.9900 |
| 1:168541118:AAA:A | acceptor_gain | 0.9900 |
| 1:168541118:AAAC:A | acceptor_loss | 0.9900 |
| 1:168541119:AA:A | acceptor_gain | 0.9900 |
| 1:168541121:C:G | acceptor_loss | 0.9900 |
AlphaMissense
729 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 1:168541069:C:A | W76C | 0.998 |
| 1:168541069:C:G | W76C | 0.998 |
| 1:168541118:A:G | F60S | 0.996 |
| 1:168541071:A:G | W76R | 0.995 |
| 1:168541071:A:T | W76R | 0.995 |
| 1:168541091:C:G | C69S | 0.982 |
| 1:168541092:A:T | C69S | 0.982 |
| 1:168542027:A:C | Y48D | 0.977 |
| 1:168541112:G:A | T62I | 0.976 |
| 1:168542035:A:C | I45S | 0.975 |
| 1:168541118:A:C | F60C | 0.974 |
| 1:168542035:A:G | I45T | 0.972 |
| 1:168541088:G:T | A70D | 0.971 |
| 1:168541089:C:G | A70P | 0.971 |
| 1:168541092:A:G | C69R | 0.971 |
| 1:168541091:C:T | C69Y | 0.967 |
| 1:168542074:C:G | C32S | 0.958 |
| 1:168542075:A:G | C32R | 0.958 |
| 1:168542075:A:T | C32S | 0.958 |
| 1:168541070:C:G | W76S | 0.955 |
| 1:168542035:A:T | I45N | 0.954 |
| 1:168541070:C:A | W76L | 0.952 |
| 1:168541090:A:C | C69W | 0.952 |
| 1:168541071:A:C | W76G | 0.951 |
| 1:168541106:C:G | R64P | 0.948 |
| 1:168541103:C:A | G65V | 0.946 |
| 1:168542074:C:T | C32Y | 0.941 |
| 1:168541068:C:A | V77L | 0.939 |
| 1:168541068:C:G | V77L | 0.939 |
| 1:168541996:A:T | V58E | 0.939 |
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):
| Study | Trait | p-value |
|---|---|---|
| GCST002945_1 | Emphysema imaging phenotypes | 3.000000e-07 |
| GCST002945_21 | Emphysema imaging phenotypes | 1.000000e-06 |
| GCST004748_62 | Lung cancer | 2.000000e-07 |
| GCST004750_93 | Squamous cell lung carcinoma | 3.000000e-06 |
EFO canonical traits (1, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0007626 | emphysema 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.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| GSK-J4 | decreases expression | 1 |
| triphenyl phosphate | affects expression | 1 |
| decabromobiphenyl ether | affects expression | 1 |
| sodium arsenite | increases expression | 1 |
| 3-chlorophenol | increases expression | 1 |
| di-n-butylphosphoric acid | affects expression | 1 |
| MT19c compound | decreases expression | 1 |
| Panobinostat | affects cotreatment, affects expression | 1 |
| Benzo(a)pyrene | increases methylation | 1 |
| Calcitriol | increases expression | 1 |
| Cisplatin | affects cotreatment, affects expression | 1 |
| Diuron | decreases expression | 1 |
| Estradiol | decreases expression, affects cotreatment | 1 |
| Pentachlorophenol | decreases expression | 1 |
| Progesterone | affects cotreatment, decreases expression | 1 |
| Valproic Acid | decreases methylation | 1 |
| Copper Sulfate | decreases expression | 1 |
Clinical trials (associated diseases)
0 trials via MONDO — disease-level, not drug-specific.
Related Atlas pages
- Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): lung carcinoma, squamous cell lung carcinoma