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GeneBe

XCL2

X-C motif chemokine ligand 2, the group of Chemokine ligands

Basic information

Region (hg38): 1:168540767-168543997

Previous symbols: [ "SCYC2" ]

Links

ENSG00000143185NCBI:6846OMIM:604828HGNC:10646Uniprot:Q9UBD3AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the XCL2 gene.

  • Inborn genetic diseases (6 variants)
  • not provided (1 variants)

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
clinvar
1
missense
5
clinvar
1
clinvar
6
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 5 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 Inborn genetic diseases Uncertain significance (May 26, 2022)2367690
1-168541076-G-C Inborn genetic diseases Uncertain significance (Feb 14, 2023)2461811
1-168542040-G-T Inborn genetic diseases Uncertain significance (Apr 26, 2023)2541341
1-168542079-C-A Inborn genetic diseases Likely benign (Apr 17, 2023)2537286
1-168542091-G-A Likely benign (Nov 01, 2022)2639533
1-168542093-C-T Inborn genetic diseases Uncertain significance (Oct 18, 2021)2387232
1-168543937-C-T Inborn genetic diseases Uncertain significance (Apr 25, 2022)2285795

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
XCL2protein_codingprotein_codingENST00000367819 33233
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.009070.600125575041255790.0000159
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.3216961.91.110.00000325711
Missense in Polyphen1513.8161.0857183
Synonymous-0.7162924.51.180.00000130239
Loss of Function0.27933.570.8412.36e-735

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000008870.00000881
Middle Eastern0.000.00
South Asian0.0001130.0000980
Other0.000.00

dbNSFP

Source: dbNSFP

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

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
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