CCL21

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

Basic information

Region (hg38): 9:34709004-34710136

Previous symbols: [ "SCYA21" ]

Links

ENSG00000137077 ∙ NCBI:6366 ∙ OMIM:602737 ∙ HGNC:10620 ∙ Uniprot:O00585 ∙ 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 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	1
missense			4	1		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		not specified	Likely benign (Nov 12, 2021)
9-34709423-C-T		not specified	Uncertain significance (Apr 06, 2022)
9-34709509-C-A		not specified	Uncertain significance (Dec 09, 2023)
9-34709583-T-C			Benign (Apr 28, 2018)
9-34709587-G-T		not specified	Uncertain significance (Jan 03, 2024)
9-34709594-T-C		not specified	Uncertain significance (Jan 31, 2024)
9-34709674-G-T		not specified	Uncertain significance (Dec 14, 2022)
9-34709841-C-A		not specified	Uncertain significance (Mar 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCL21	protein_coding	protein_coding	ENST00000259607	4	1120

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0362	0.842	125739	0	3	125742	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.118	73	75.9	0.962	0.00000419	855
Missense in Polyphen		22	28.847	0.76263		332
Synonymous	0.0625	28	28.4	0.985	0.00000131	271
Loss of Function	1.24	3	6.37	0.471	2.70e-7	74

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

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

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

Mouse Genome Informatics

• Gene name: Gm21541

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