CCL25

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

Basic information

Region (hg38): 19:8052317-8062660

Previous symbols: [ "SCYA25" ]

Links

ENSG00000131142 ∙ NCBI:6370 ∙ OMIM:602565 ∙ HGNC:10624 ∙ Uniprot:O15444 ∙ 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 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		1	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		not specified	Uncertain significance (Aug 02, 2021)
19-8053102-C-T		not specified	Uncertain significance (Oct 17, 2023)
19-8056190-A-G		not specified	Uncertain significance (Apr 10, 2023)
19-8056191-T-C		not specified	Uncertain significance (Sep 22, 2022)
19-8056208-C-T			Benign (May 31, 2018)
19-8056209-G-A		not specified	Uncertain significance (Sep 21, 2023)
19-8056224-A-T		not specified	Uncertain significance (Jan 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCL25	protein_coding	protein_coding	ENST00000390669	5	9884

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0152	0.888	124765	0	10	124775	0.0000401

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.980	54	78.4	0.689	0.00000404	950
Missense in Polyphen		11	20.654	0.53258		267
Synonymous	0.258	31	32.9	0.943	0.00000183	286
Loss of Function	1.39	4	8.32	0.481	4.21e-7	91

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000292	0.0000292
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000583	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.0000550	0.0000530
Middle Eastern	0.0000583	0.0000556
South Asian	0.0000816	0.0000654
Other	0.00	0.00

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

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

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

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