XCL1
X-C motif chemokine ligand 1, the group of Chemokine ligands
Basic information
Region (hg38): 1:168576605-168582069
Previous symbols: [ "LTN", "SCYC1" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
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 | 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) | ||
| 1-168581165-C-A | not specified | Uncertain significance (May 16, 2024) | ||
| 1-168581191-A-T | Benign (Dec 04, 2017) | |||
| 1-168581198-C-T | not specified | Uncertain significance (Aug 26, 2022) |
GnomAD
Source:
| 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:
- 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
| 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