Menu
GeneBe

CCL21

C-C motif chemokine ligand 21, the group of Chemokine ligands

Basic information

Region (hg38): 9:34709004-34710136

Previous symbols: [ "SCYA21" ]

Links

ENSG00000137077NCBI:6366OMIM:602737HGNC:10620Uniprot:O00585AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CCL21 gene.

  • Inborn genetic diseases (5 variants)
  • not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCL21 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
4
clinvar
1
clinvar
5
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 1 1

Variants in CCL21

This is a list of pathogenic ClinVar variants found in the CCL21 region.

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

Position Type Phenotype Significance ClinVar
9-34709419-C-T Inborn genetic diseases Likely benign (Nov 12, 2021)2398484
9-34709423-C-T Inborn genetic diseases Uncertain significance (Apr 06, 2022)2221802
9-34709583-T-C Benign (Apr 28, 2018)792124
9-34709594-T-C Inborn genetic diseases Uncertain significance (Dec 02, 2021)2402630
9-34709674-G-T Inborn genetic diseases Uncertain significance (Dec 14, 2022)2334921
9-34709841-C-A Inborn genetic diseases Uncertain significance (Mar 21, 2022)2279117

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CCL21protein_codingprotein_codingENST00000259607 41120
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.03620.842125739031257420.0000119
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.1187375.90.9620.00000419855
Missense in Polyphen2228.8470.76263332
Synonymous0.06252828.40.9850.00000131271
Loss of Function1.2436.370.4712.70e-774

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00006150.0000615
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00001760.0000176
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Inhibits hemopoiesis and stimulates chemotaxis. Chemotactic in vitro for thymocytes and activated T-cells, but not for B-cells, macrophages, or neutrophils. Shows preferential activity towards naive T-cells. May play a role in mediating homing of lymphocytes to secondary lymphoid organs. Binds to atypical chemokine receptor ACKR4 and mediates the recruitment of beta-arrestin (ARRB1/2) to ACKR4.;
Pathway
Chemokine signaling pathway - Homo sapiens (human);NF-kappa B signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);Allograft Rejection;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 (i) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

pRec
0.598

Intolerance Scores

loftool
0.442
rvis_EVS
-0.08
rvis_percentile_EVS
47.79

Haploinsufficiency Scores

pHI
0.0448
hipred
N
hipred_score
0.146
ghis
0.552

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.539

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumLowLow
Primary ImmunodeficiencyMediumLowMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Gm21541
Phenotype

Gene ontology

Biological process
establishment of T cell polarity;immunological synapse formation;positive regulation of cell-matrix adhesion;dendritic cell chemotaxis;monocyte chemotaxis;positive regulation of dendritic cell antigen processing and presentation;inflammatory response;immune response;G protein-coupled receptor signaling pathway;cell-cell signaling;regulation of signaling receptor activity;positive regulation of glycoprotein biosynthetic process;positive regulation of T cell chemotaxis;neutrophil chemotaxis;positive regulation of actin filament polymerization;positive regulation of pseudopodium assembly;T cell costimulation;ruffle organization;positive regulation of cell adhesion mediated by integrin;response to prostaglandin E;mesangial cell-matrix adhesion;chemokine (C-C motif) ligand 21 signaling pathway;positive regulation of I-kappaB kinase/NF-kappaB signaling;positive regulation of GTPase activity;positive regulation of phosphatidylinositol 3-kinase activity;positive regulation of protein kinase activity;positive regulation of JNK cascade;lymphocyte chemotaxis;positive regulation of receptor-mediated endocytosis;cell maturation;positive regulation of chemotaxis;release of sequestered calcium ion into cytosol;positive regulation of filopodium assembly;positive regulation of protein kinase B signaling;cell 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;positive regulation of neutrophil chemotaxis;activation of GTPase activity;dendritic cell dendrite assembly;negative regulation of leukocyte tethering or rolling;cellular response to chemokine;positive regulation of cell motility;positive regulation of T cell migration;positive regulation of myeloid dendritic cell chemotaxis;negative regulation of dendritic cell dendrite assembly;negative regulation of dendritic cell apoptotic process
Cellular component
extracellular region;extracellular space;cell
Molecular function
protein binding;chemokine activity;CCR7 chemokine receptor binding;chemokine receptor binding;CCR chemokine receptor binding