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GeneBe

CCL25

C-C motif chemokine ligand 25, the group of Chemokine ligands

Basic information

Region (hg38): 19:8052317-8062660

Previous symbols: [ "SCYA25" ]

Links

ENSG00000131142NCBI:6370OMIM:602565HGNC:10624Uniprot:O15444AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CCL25 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 CCL25 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 0 1

Variants in CCL25

This is a list of pathogenic ClinVar variants found in the CCL25 region.

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

Position Type Phenotype Significance ClinVar
19-8053061-G-T Inborn genetic diseases Uncertain significance (Aug 02, 2021)2375775
19-8056190-A-G Inborn genetic diseases Uncertain significance (Apr 10, 2023)2570417
19-8056191-T-C Inborn genetic diseases Uncertain significance (Sep 22, 2022)2313152
19-8056208-C-T Benign (May 31, 2018)782620

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CCL25protein_codingprotein_codingENST00000390669 59884
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.01520.8881247650101247750.0000401
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.9805478.40.6890.00000404950
Missense in Polyphen1120.6540.53258267
Synonymous0.2583132.90.9430.00000183286
Loss of Function1.3948.320.4814.21e-791

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00002920.0000292
Ashkenazi Jewish0.000.00
East Asian0.00005830.0000556
Finnish0.000.00
European (Non-Finnish)0.00005500.0000530
Middle Eastern0.00005830.0000556
South Asian0.00008160.0000654
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Potentially involved in T-cell development. Recombinant protein shows chemotactic activity on thymocytes, macrophages, THP-1 cells, and dendritics cells but is inactive on peripheral blood lymphocytes and neutrophils. Binds to CCR9. Isoform 2 is an antagonist of isoform 1. Binds to atypical chemokine receptor ACKR4 and mediates the recruitment of beta-arrestin (ARRB1/2) to ACKR4.;
Pathway
Chemokine signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);Intestinal immune network for IgA production - Homo sapiens (human);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
0.194

Intolerance Scores

loftool
0.428
rvis_EVS
1.04
rvis_percentile_EVS
91.21

Haploinsufficiency Scores

pHI
0.0624
hipred
N
hipred_score
0.203
ghis

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.154

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Ccl25
Phenotype
growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); immune system phenotype; digestive/alimentary phenotype; hematopoietic system phenotype;

Zebrafish Information Network

Gene name
ccl25b
Affected structure
caudal hematopoietic tissue
Phenotype tag
abnormal
Phenotype quality
decreased occurrence

Gene ontology

Biological process
positive regulation of cell-matrix adhesion;monocyte chemotaxis;chemotaxis;inflammatory response;immune response;cell surface receptor signaling pathway;G protein-coupled receptor signaling pathway;regulation of signaling receptor activity;neutrophil chemotaxis;positive regulation of GTPase activity;lymphocyte chemotaxis;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;negative regulation of leukocyte tethering or rolling
Cellular component
extracellular region;extracellular space
Molecular function
hormone activity;protein binding;chemokine activity;CCR10 chemokine receptor binding;chemokine receptor binding;CCR chemokine receptor binding