XCL1 (X-C motif chemokine ligand 1)

Gene

• Entrez ID: 6375
• Gene name: X-C motif chemokine ligand 1
• Gene symbol: XCL1
• Synonyms (NCBI Gene): ATAC, LPTN, LTN, SCM-1, SCM-1a, SCM1, SCM1A, SCYC1
• Chromosome: 1
• Chromosome location: 1q24.2
• Summary: This antimicrobial gene encodes a member of the chemokine superfamily. Chemokines function in inflammatory and immunological responses, inducing leukocyte migration and activation. The encoded protein is a member of the C-chemokine subfamily, retaining on

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT1495287	hsa-miR-548ag	CLIP-seq
MIRT1495288	hsa-miR-548ai	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001916	Process	Positive regulation of T cell mediated cytotoxicity	IDA	18832695
GO:0002690	Process	Positive regulation of leukocyte chemotaxis	ISS
GO:0002725	Process	Negative regulation of T cell cytokine production	IDA	10887101
GO:0002726	Process	Positive regulation of T cell cytokine production	ISS
GO:0002826	Process	Negative regulation of T-helper 1 type immune response	IC	10887101
GO:0005125	Function	Cytokine activity	IEA
GO:0005515	Function	Protein binding	IPI	28381538
GO:0005576	Component	Extracellular region	IEA
GO:0005576	Component	Extracellular region	TAS
GO:0005615	Component	Extracellular space	IBA
GO:0005615	Component	Extracellular space	IEA
GO:0005615	Component	Extracellular space	ISS
GO:0006935	Process	Chemotaxis	IEA
GO:0006954	Process	Inflammatory response	IBA
GO:0006955	Process	Immune response	IEA
GO:0007165	Process	Signal transduction	IC	9632725
GO:0007165	Process	Signal transduction	IEA
GO:0007267	Process	Cell-cell signaling	IDA	7602097
GO:0008009	Function	Chemokine activity	IBA
GO:0008009	Function	Chemokine activity	IDA	7602097
GO:0008009	Function	Chemokine activity	IEA
GO:0009615	Process	Response to virus	IDA	14734774
GO:0010820	Process	Positive regulation of T cell chemotaxis	IDA	7602097
GO:0030335	Process	Positive regulation of cell migration	IBA
GO:0030593	Process	Neutrophil chemotaxis	TAS	11889129
GO:0031640	Process	Killing of cells of another organism	IDA	12949249
GO:0032689	Process	Negative regulation of type II interferon production	IDA	10887101
GO:0032703	Process	Negative regulation of interleukin-2 production	IDA	10887101
GO:0032733	Process	Positive regulation of interleukin-10 production	IDA	18832695
GO:0035782	Process	Mature natural killer cell chemotaxis	IDA	9029087
GO:0042379	Function	Chemokine receptor binding	IDA	9632725
GO:0042379	Function	Chemokine receptor binding	NAS	7602097
GO:0042803	Function	Protein homodimerization activity	IDA	11889129
GO:0045892	Process	Negative regulation of DNA-templated transcription	IDA	10887101
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IDA	10887101
GO:0048020	Function	CCR chemokine receptor binding	IBA
GO:0050727	Process	Regulation of inflammatory response	IDA	18832695
GO:0051209	Process	Release of sequestered calcium ion into cytosol	ISS
GO:0051281	Process	Positive regulation of release of sequestered calcium ion into cytosol	IDA	7602097
GO:0060326	Process	Cell chemotaxis	IBA
GO:0061844	Process	Antimicrobial humoral immune response mediated by antimicrobial peptide	IBA
GO:0061844	Process	Antimicrobial humoral immune response mediated by antimicrobial peptide	IDA	12949249
GO:0070098	Process	Chemokine-mediated signaling pathway	IBA
GO:0071353	Process	Cellular response to interleukin-4	ISS
GO:0071560	Process	Cellular response to transforming growth factor beta stimulus	ISS
GO:0071636	Process	Positive regulation of transforming growth factor beta production	IDA	18832695
GO:0071663	Process	Positive regulation of granzyme B production	IDA	18832695
GO:0090023	Process	Positive regulation of neutrophil chemotaxis	ISS
GO:2000412	Process	Positive regulation of thymocyte migration	ISS
GO:2000503	Process	Positive regulation of natural killer cell chemotaxis	IDA	9029087
GO:2000513	Process	Positive regulation of granzyme A production	IDA	18832695
GO:2000518	Process	Negative regulation of T-helper 1 cell activation	IDA	10887101
GO:2000538	Process	Positive regulation of B cell chemotaxis	ISS
GO:2000553	Process	Positive regulation of T-helper 2 cell cytokine production	ISS
GO:2000556	Process	Positive regulation of T-helper 1 cell cytokine production	ISS
GO:2000558	Process	Positive regulation of immunoglobulin production in mucosal tissue	ISS
GO:2000562	Process	Negative regulation of CD4-positive, alpha-beta T cell proliferation	IDA	10887101
GO:2000563	Process	Positive regulation of CD4-positive, alpha-beta T cell proliferation	ISS
GO:2000566	Process	Positive regulation of CD8-positive, alpha-beta T cell proliferation	IDA	10887101

Other IDs

• MIM: 600250
• HGNC: 10645
• e!Ensembl: ENSG00000143184

Protein

• UniProt ID: P47992
• Protein name: Lymphotactin (ATAC) (C motif chemokine 1) (Cytokine SCM-1) (Lymphotaxin) (SCM-1-alpha) (Small-inducible cytokine C1) (XC chemokine ligand 1)
• Protein function: Chemotactic activity for lymphocytes but not for monocytes or neutrophils. In thymus, mediates medullary accumulation of thymic dendritic cells and contributes to regulatoy T cell development, playing a role in self-tolerance establishment. {ECO
• PDB: 1J8I, 1J9O, 2HDM, 2JP1, 2N54, 2NYZ, 9AST
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00048	IL8	30 → 84	Small cytokines (intecrine/chemokine), interleukin-8 like	Domain

• Tissue specificity: TISSUE SPECIFICITY: Highest level in spleen, lower in peripheral leukocytes and very low levels in lung, colon and small intestine.
• Sequence:

  MRLLILALLGICSLTAYIVEGVGSEVSDKRTCVSLTTQRLPVSRIKTYTITEGSLRAVIF
  ITKRGLKVCADPQATWVRDVVRSMDRKSNTRNNMIQTKPTGTQQSTNTAVTLTG

• Sequence length: 114

Pathways

KEGG:

Cytokine-cytokine receptor interaction
Viral protein interaction with cytokine and cytokine receptor
Chemokine signaling pathway

Reactome:

Chemokine receptors bind chemokines
G alpha (q) signalling events

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
BREAST CARCINOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ESTROGEN-RECEPTOR POSITIVE BREAST CANCER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCOLIOSIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
VENOUS THROMBOEMBOLISM	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Acute lymphocytic leukemia	Lymphocytic Leukemia	BEFREE	29027574		★☆☆☆☆ Found in Text Mining only
Adult Acute Lymphocytic Leukemia	Lymphocytic Leukemia	BEFREE	29027574		★☆☆☆☆ Found in Text Mining only
Age related macular degeneration	Age-related macular degeneration	BEFREE	29636475		★☆☆☆☆ Found in Text Mining only
Allergic sensitization	Allergic Sensitization	BEFREE	29067999		★☆☆☆☆ Found in Text Mining only
Arthritis Rheumatoid	Rheumatoid arthritis	Pubtator	12847680, 20709179	Associate	★☆☆☆☆ Found in Text Mining only
Asthma	Asthma	LHGDN	18832695		★☆☆☆☆ Found in Text Mining only
Asthma	Asthma	Pubtator	18832695	Associate	★☆☆☆☆ Found in Text Mining only
Asthma	Asthma	BEFREE	29474842		★☆☆☆☆ Found in Text Mining only
Autoimmune Diseases	Autoimmune Diseases	BEFREE	28550205		★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	11999142, 23852223, 28369967		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Breast Neoplasms	Breast neoplasm	Pubtator	15662126, 33374849, 36046784, 37684436	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma Renal Cell	Renal cell carcinoma	Pubtator	37006314, 37762031	Associate	★☆☆☆☆ Found in Text Mining only
Cerebral Aneurysm	Cerebral Aneurysm	BEFREE	25922506		★☆☆☆☆ Found in Text Mining only
Childhood Acute Lymphoblastic Leukemia	Lymphoblastic Leukemia	BEFREE	29027574		★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	34185431	Associate	★☆☆☆☆ Found in Text Mining only
Common Variable Immunodeficiency	Common Variable Immunodeficiency	BEFREE	19162554		★☆☆☆☆ Found in Text Mining only
Common Variable Immunodeficiency	Common variable immunodeficiency	Pubtator	19162554	Associate	★☆☆☆☆ Found in Text Mining only
Coronary Artery Disease	Coronary artery disease	Pubtator	35263363	Associate	★☆☆☆☆ Found in Text Mining only
Crohn Disease	Crohn Disease	BEFREE	11696436		★☆☆☆☆ Found in Text Mining only
Crohn Disease	Crohn disease	Pubtator	11696436	Stimulate	★☆☆☆☆ Found in Text Mining only
Degenerative polyarthritis	Arthritis	BEFREE	12847680, 30341348		★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus, Non-Insulin-Dependent	Diabetes Mellitus	BEFREE	27353450		★☆☆☆☆ Found in Text Mining only
Diffuse Intrinsic Pontine Glioma	Diffuse Intrinsic Pontine Glioma	BEFREE	31227500		★☆☆☆☆ Found in Text Mining only
Fatty Liver Disease	Fatty Liver	BEFREE	29603380		★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	BEFREE	21062501		★☆☆☆☆ Found in Text Mining only
Granulomatosis with polyangiitis	Granulomatosis With Polyangiitis	BEFREE	19797511		★☆☆☆☆ Found in Text Mining only
Heart Failure	Heart failure	Pubtator	37684436	Associate	★☆☆☆☆ Found in Text Mining only
IGA Glomerulonephritis	Glomerulonephritis	BEFREE	12053063		★☆☆☆☆ Found in Text Mining only
IGA Glomerulonephritis	Glomerulonephritis	LHGDN	12053063		★☆☆☆☆ Found in Text Mining only
Immunologic Deficiency Syndromes	Immunologic Deficiency Syndromes	BEFREE	30389682		★☆☆☆☆ Found in Text Mining only
Leukemia Myeloid Acute	Myeloid leukemia	Pubtator	33223444	Associate	★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	BEFREE	15149162, 29603380, 31615295, 31666238		★☆☆☆☆ Found in Text Mining only
Lupus Erythematosus, Systemic	Lupus Erythematosus	BEFREE	27249108		★☆☆☆☆ Found in Text Mining only
Lymphopenia	Lymphopenia	LHGDN	16923584		★☆☆☆☆ Found in Text Mining only
Lymphoproliferative Disorders	Lymphoproliferative Disorder	LHGDN	16923584		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	11999142, 23852223, 28369967		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of liver	Liver Cancer	BEFREE	31666238		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of pancreas	Pancreatic cancer	BEFREE	28986391		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	15547752, 25515795, 30361341, 30712429, 30863405		★☆☆☆☆ Found in Text Mining only
Melanoma Cutaneous Malignant	Melanoma	Pubtator	31983065	Associate	★☆☆☆☆ Found in Text Mining only
Memory Disorders	Memory disorders	Pubtator	37522383	Associate	★☆☆☆☆ Found in Text Mining only
Mouth Neoplasms	Mouth neoplasm	Pubtator	32562323	Associate	★☆☆☆☆ Found in Text Mining only
Myeloid Leukemia, Chronic	Myeloid Leukemia	BEFREE	30712429		★☆☆☆☆ Found in Text Mining only
Myopathy	Myopathy	BEFREE	27434589		★☆☆☆☆ Found in Text Mining only
Myositis	Myositis	Pubtator	37522383	Associate	★☆☆☆☆ Found in Text Mining only
Nasopharyngeal carcinoma	Nasopharyngeal Carcinoma	BEFREE	9422524		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	10340547, 16144939, 25515795, 25679813, 31628300, 31801909		★☆☆☆☆ Found in Text Mining only
Neuroblastoma	Neuroblastoma	BEFREE	12406881		★☆☆☆☆ Found in Text Mining only
Neuroblastoma	Neuroblastoma	Pubtator	12406881	Associate	★☆☆☆☆ Found in Text Mining only
Obesity	Obesity	Pubtator	27919438	Associate	★☆☆☆☆ Found in Text Mining only
Osteoporosis	Osteoporosis	Pubtator	36755691	Associate	★☆☆☆☆ Found in Text Mining only
Ovarian Neoplasms	Ovarian neoplasm	Pubtator	38527595	Associate	★☆☆☆☆ Found in Text Mining only
Pancreatic carcinoma	Pancreatic carcinoma	BEFREE	28986391		★☆☆☆☆ Found in Text Mining only
Pauci-immune Glomerulonephritis associated with Granulomatosis with Polyangiitis	Granulomatosis with polyangiitis	BEFREE	19797511		★☆☆☆☆ Found in Text Mining only
Pemphigoid Benign Mucous Membrane	Benign mucous membrane pemphigoid	Pubtator	37690517	Associate	★☆☆☆☆ Found in Text Mining only
Pulmonary Disease Chronic Obstructive	Chronic obstructive pulmonary disease	Pubtator	35263363, 38203236	Associate	★☆☆☆☆ Found in Text Mining only
Pulmonary Fibrosis	Pulmonary fibrosis	Pubtator	12449175	Associate	★☆☆☆☆ Found in Text Mining only
Rheumatoid Arthritis	Rheumatoid arthritis	BEFREE	12847680		★☆☆☆☆ Found in Text Mining only
Rheumatoid Arthritis	Rheumatoid arthritis	LHGDN	12847680		★☆☆☆☆ Found in Text Mining only
Sarcoidosis	Sarcoidosis	Pubtator	12449175	Stimulate	★☆☆☆☆ Found in Text Mining only
Small cell carcinoma of lung	Lung carcinoma	BEFREE	30712429		★☆☆☆☆ Found in Text Mining only
Spinal Muscular Atrophy	Spinal Muscular Atrophy	BEFREE	27146274		★☆☆☆☆ Found in Text Mining only
Synovitis	Synovitis	BEFREE	25724256		★☆☆☆☆ Found in Text Mining only
Synovitis	Synovitis	Pubtator	25724256	Associate	★☆☆☆☆ Found in Text Mining only
Systemic Scleroderma	Scleroderma	LHGDN	18322986		★☆☆☆☆ Found in Text Mining only
Triple Negative Breast Neoplasms	Triple negative breast cancer	Pubtator	37762493	Associate	★☆☆☆☆ Found in Text Mining only