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GeneBe

CCL22

C-C motif chemokine ligand 22, the group of Chemokine ligands

Basic information

Region (hg38): 16:57358782-57366189

Previous symbols: [ "SCYA22" ]

Links

ENSG00000102962NCBI:6367OMIM:602957HGNC:10621Uniprot:O00626AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CCL22 gene.

  • Inborn genetic diseases (3 variants)
  • not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCL22 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
3
clinvar
1
clinvar
4
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 3 1 0

Variants in CCL22

This is a list of pathogenic ClinVar variants found in the CCL22 region.

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

Position Type Phenotype Significance ClinVar
16-57360475-C-T Inborn genetic diseases Uncertain significance (Nov 18, 2022)2228457
16-57360481-T-C Likely benign (Jul 31, 2018)769900
16-57360505-C-T Inborn genetic diseases Uncertain significance (Sep 28, 2022)2362545
16-57360506-G-A Inborn genetic diseases Uncertain significance (Sep 07, 2022)2370722

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CCL22protein_codingprotein_codingENST00000219235 37419
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.008400.5841257250181257430.0000716
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.4505363.10.8410.00000440590
Missense in Polyphen1623.8450.67099222
Synonymous-1.683625.21.430.00000174187
Loss of Function0.21933.440.8731.47e-736

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002890.000289
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.000.00
European (Non-Finnish)0.00004400.0000440
Middle Eastern0.00005440.0000544
South Asian0.000.00
Other0.0003260.000326

dbNSFP

Source: dbNSFP

Function
FUNCTION: May play a role in the trafficking of activated/effector T-lymphocytes to inflammatory sites and other aspects of activated T-lymphocyte physiology. Chemotactic for monocytes, dendritic cells and natural killer cells. Mild chemoattractant for primary activated T-lymphocytes and a potent chemoattractant for chronically activated T-lymphocytes but has no chemoattractant activity for neutrophils, eosinophils, and resting T-lymphocytes. Binds to CCR4. Processed forms MDC(3-69), MDC(5-69) and MDC(7-69) seem not be active.;
Pathway
Chemokine signaling pathway - Homo sapiens (human);C-type lectin receptor signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);C-type lectin receptors (CLRs);Chemokine signaling pathway;Interleukin-10 signaling;Interleukin-4 and 13 signaling (Consensus)

Intolerance Scores

loftool
0.501
rvis_EVS
0.26
rvis_percentile_EVS
70.26

Haploinsufficiency Scores

pHI
0.101
hipred
N
hipred_score
0.123
ghis
0.484

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.752

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Ccl22
Phenotype
mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); immune system phenotype;

Gene ontology

Biological process
monocyte chemotaxis;chemotaxis;inflammatory response;immune response;signal transduction;G protein-coupled receptor signaling pathway;cell-cell signaling;response to virus;regulation of signaling receptor activity;cytokine-mediated signaling pathway;neutrophil chemotaxis;positive regulation of GTPase activity;eosinophil chemotaxis;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
chemokine activity;CCR chemokine receptor binding