CCL22

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

Basic information

Region (hg38): 16:57358783-57366189

Previous symbols: [ "SCYA22" ]

Links

ENSG00000102962

∙ NCBI:6367 ∙ OMIM:602957 ∙ HGNC:10621 ∙ Uniprot:O00626 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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			4 clinvar	2 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	4	2	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	Phenotype	Significance	ClinVar
16-57358853-G-A	not specified	Likely benign (Dec 08, 2023)	3139727
16-57360475-C-T	not specified	Uncertain significance (Nov 18, 2022)	2228457
16-57360476-G-A	not specified	Uncertain significance (Dec 22, 2023)	3139726
16-57360481-T-C		Likely benign (Jul 31, 2018)	769900
16-57360488-G-A	not specified	Uncertain significance (May 13, 2024)	3264474
16-57360494-G-A	not specified	Uncertain significance (Apr 23, 2024)	3264473
16-57360505-C-T	not specified	Uncertain significance (Sep 28, 2022)	2362545
16-57360506-G-A	not specified	Uncertain significance (Sep 07, 2022)	2370722

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCL22	protein_coding	protein_coding	ENST00000219235	3	7419

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00840	0.584	125725	0	18	125743	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.450	53	63.1	0.841	0.00000440	590
Missense in Polyphen		16	23.845	0.67099		222
Synonymous	-1.68	36	25.2	1.43	0.00000174	187
Loss of Function	0.219	3	3.44	0.873	1.47e-7	36

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000289	0.000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000440	0.0000440
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.000326	0.000326

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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

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