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XCL1

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

Basic information

Region (hg38): 1:168576604-168582069

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

Links

ENSG00000143184NCBI:6375OMIM:600250HGNC:10645Uniprot:P47992AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the XCL1 gene.

  • Inborn genetic diseases (4 variants)
  • not provided (1 variants)

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
4
clinvar
1
clinvar
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 4 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)3190954
1-168580069-G-C not specified Uncertain significance (Jul 05, 2023)2609513
1-168580143-T-C not specified Uncertain significance (Sep 26, 2023)3190953
1-168581065-C-T not specified Uncertain significance (Jul 06, 2021)2407211
1-168581101-T-C not specified Uncertain significance (Mar 07, 2023)2495496
1-168581159-T-C not specified Uncertain significance (Mar 01, 2024)3190955
1-168581191-A-T Benign (Dec 04, 2017)780276
1-168581198-C-T not specified Uncertain significance (Aug 26, 2022)2308879

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
XCL1protein_codingprotein_codingENST00000367818 35605
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.001300.4291257000101257100.0000398
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.1296461.21.050.00000313708
Missense in Polyphen2215.761.3959202
Synonymous0.8581924.40.7790.00000130239
Loss of Function-0.15643.681.092.40e-735

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00005800.0000580
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.000.00
European (Non-Finnish)0.00001760.0000176
Middle Eastern0.00005440.0000544
South Asian0.0001630.000163
Other0.000.00

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
ghis

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.120

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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