XCL1

X-C motif chemokine ligand 1, the group of Chemokine ligands

Basic information

Region (hg38): 1:168576604-168582069

Previous symbols: [ "LTN", "SCYC1" ]

Links

ENSG00000143184 ∙ NCBI:6375 ∙ OMIM:600250 ∙ HGNC:10645 ∙ Uniprot:P47992 ∙ 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 XCL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the XCL1 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			7		1	8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	1

Variants in XCL1

This is a list of pathogenic ClinVar variants found in the XCL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-168576660-T-C		not specified	Uncertain significance (Dec 08, 2023)
1-168580069-G-C		not specified	Uncertain significance (Jul 05, 2023)
1-168580143-T-C		not specified	Uncertain significance (Sep 26, 2023)
1-168581065-C-T		not specified	Uncertain significance (Jul 06, 2021)
1-168581101-T-C		not specified	Uncertain significance (Mar 07, 2023)
1-168581159-T-C		not specified	Uncertain significance (Mar 01, 2024)
1-168581191-A-T			Benign (Dec 04, 2017)
1-168581198-C-T		not specified	Uncertain significance (Aug 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
XCL1	protein_coding	protein_coding	ENST00000367818	3	5605

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00130	0.429	125700	0	10	125710	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.129	64	61.2	1.05	0.00000313	708
Missense in Polyphen		22	15.76	1.3959		202
Synonymous	0.858	19	24.4	0.779	0.00000130	239
Loss of Function	-0.156	4	3.68	1.09	2.40e-7	35

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000580	0.0000580
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.0000544	0.0000544
South Asian	0.000163	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: 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:0000250|UniProtKB:P47993}.
• Pathway: Chemokine signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);Chemokine 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 (q) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.205

Intolerance Scores

• loftool: 0.611
• rvis_EVS: 0.73
• rvis_percentile_EVS: 85.98

Haploinsufficiency Scores

• pHI: 0.0931
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.120

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Xcl1
• Phenotype: vision/eye phenotype; digestive/alimentary phenotype; immune system phenotype; liver/biliary system phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); endocrine/exocrine gland phenotype

Gene ontology

• Biological process: positive regulation of T cell mediated cytotoxicity;monocyte chemotaxis;positive regulation of leukocyte chemotaxis;negative regulation of T cell cytokine production;positive regulation of T cell cytokine production;negative regulation of T-helper 1 type immune response;inflammatory response;signal transduction;G protein-coupled receptor signaling pathway;cell-cell signaling;response to virus;regulation of signaling receptor activity;positive regulation of T cell chemotaxis;neutrophil chemotaxis;negative regulation of interferon-gamma production;negative regulation of interleukin-2 production;positive regulation of interleukin-10 production;mature natural killer cell chemotaxis;negative regulation of DNA-binding transcription factor activity;positive regulation of GTPase activity;negative regulation of transcription, DNA-templated;lymphocyte chemotaxis;regulation of inflammatory response;release of sequestered calcium ion into cytosol;positive regulation of release of sequestered calcium ion into cytosol;chemokine-mediated signaling pathway;positive regulation of ERK1 and ERK2 cascade;cellular response to interferon-gamma;cellular response to interleukin-1;cellular response to interleukin-4;cellular response to tumor necrosis factor;cellular response to transforming growth factor beta stimulus;positive regulation of transforming growth factor beta production;positive regulation of granzyme B production;positive regulation of neutrophil chemotaxis;positive regulation of thymocyte migration;positive regulation of natural killer cell chemotaxis;positive regulation of granzyme A production;negative regulation of T-helper 1 cell activation;positive regulation of B cell chemotaxis;positive regulation of T-helper 2 cell cytokine production;positive regulation of T-helper 1 cell cytokine production;positive regulation of immunoglobulin production in mucosal tissue;negative regulation of CD4-positive, alpha-beta T cell proliferation;positive regulation of CD4-positive, alpha-beta T cell proliferation;positive regulation of CD8-positive, alpha-beta T cell proliferation
• Cellular component: extracellular region;extracellular space;cell
• Molecular function: protein binding;chemokine activity;chemokine receptor binding;protein homodimerization activity;CCR chemokine receptor binding