XCL2
Basic information
Region (hg38): 1:168540767-168543997
Previous symbols: [ "SCYC2" ]
Links
Phenotypes
GenCC
Source:
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 XCL2 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 | 1 | |||||
missense | 10 | |||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region ? | 0 | |||||
non coding ? | 0 | |||||
Total | 0 | 0 | 9 | 2 | 0 |
Variants in XCL2
This is a list of pathogenic ClinVar variants found in the XCL2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
1-168540975-T-A | not specified | Uncertain significance (May 26, 2022) | ||
1-168541046-A-G | not specified | Uncertain significance (Jan 30, 2024) | ||
1-168541059-C-T | not specified | Uncertain significance (Dec 18, 2023) | ||
1-168541076-G-C | not specified | Uncertain significance (Feb 14, 2023) | ||
1-168541076-G-T | not specified | Uncertain significance (Nov 02, 2023) | ||
1-168541103-C-A | not specified | Uncertain significance (Sep 20, 2023) | ||
1-168542040-G-T | not specified | Uncertain significance (Apr 26, 2023) | ||
1-168542079-C-A | not specified | Likely benign (Apr 17, 2023) | ||
1-168542091-G-A | Likely benign (Nov 01, 2022) | |||
1-168542093-C-T | not specified | Uncertain significance (Oct 18, 2021) | ||
1-168543916-A-G | not specified | Uncertain significance (May 30, 2024) | ||
1-168543937-C-T | not specified | Uncertain significance (Apr 25, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
XCL2 | protein_coding | protein_coding | ENST00000367819 | 3 | 3233 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.00907 | 0.600 | 125575 | 0 | 4 | 125579 | 0.0000159 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.321 | 69 | 61.9 | 1.11 | 0.00000325 | 711 |
Missense in Polyphen | 15 | 13.816 | 1.0857 | 183 | ||
Synonymous | -0.716 | 29 | 24.5 | 1.18 | 0.00000130 | 239 |
Loss of Function | 0.279 | 3 | 3.57 | 0.841 | 2.36e-7 | 35 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00 | 0.00 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.00000887 | 0.00000881 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.000113 | 0.0000980 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Chemotactic activity for lymphocytes but not for monocytes or neutrophils. {ECO:0000250}.;
- Pathway
- Chemokine signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);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
- 0.0759
Intolerance Scores
- loftool
- 0.693
- rvis_EVS
- 0.28
- rvis_percentile_EVS
- 71.08
Haploinsufficiency Scores
- pHI
- 0.255
- hipred
- N
- hipred_score
- 0.112
- ghis
- 0.393
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.0820
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
- monocyte chemotaxis;inflammatory response;signal transduction;G protein-coupled receptor signaling pathway;blood circulation;regulation of signaling receptor activity;positive regulation of T cell chemotaxis;neutrophil chemotaxis;positive regulation of GTPase activity;lymphocyte chemotaxis;chemokine-mediated signaling pathway;positive regulation of ERK1 and ERK2 cascade;cellular response to interferon-gamma;cellular response to interleukin-1;cellular response to tumor necrosis factor
- Cellular component
- extracellular region;extracellular space
- Molecular function
- protein binding;chemokine activity;CCR chemokine receptor binding