CCL25

protein-coding

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

Gene summary

This antimicrobial gene belongs to the subfamily of small cytokine CC genes. Cytokines are a family of secreted proteins involved in immunoregulatory and inflammatory processes. The CC cytokines are proteins characterized by two adjacent cysteines. The cytokine encoded by this gene displays chemotactic activity for dendritic cells, thymocytes, and activated macrophages but is inactive on peripheral blood lymphocytes and neutrophils. The product of this gene binds to chemokine receptor CCR9. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2014]

Previous symbols:

SCYA25

MANE transcript

NM_005624.4

Inheritance

—

ClinVar variants

U:10B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.48

Max pathogenic AF

—

Genomic locus

chr19:8,052,318-8,062,660

External References & Databases

Ensembl (ENSG00000131142)

Transcript & Mutation Effects

hg38 • Region Span ~10.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CCL25 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 12

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005624.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			9 clinvar	3 clinvar	1 clinvar	13
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	10	3	1	14

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 35 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005624.4	RefSeq	NP_005615.2	5	MANE Select
ENST00000315626.6	Ensembl	ENSP00000324756.6	5	MANE Select
NM_001201359.2	RefSeq	NP_001188288.1	5	Standard
NM_001394634.1	RefSeq	NP_001381563.1	5	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
ccl25b	Danio rerio	Structure: caudal hematopoietic tissue Quality: decreased occurrence abnormal

Gene / Model

Organism

Observed Phenotype

ccl25b

Danio rerio

Structure: caudal hematopoietic tissue

Quality: decreased occurrence

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Biological Process

positive regulation of cell-matrix adhesion
monocyte chemotaxis
chemotaxis
inflammatory response
immune response

Molecular Function

hormone activity
protein binding
chemokine activity
CCR10 chemokine receptor binding
chemokine receptor binding

Cellular Component

extracellular region
extracellular space

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000390669
Coding exons: 5
Length: 9884
Individuals with no LoFs: 124765
Homozygous LoFs: 0
Heterozygous LoFs: 10
Defined: 124775
p: 0.0000401

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.980	54	78.4	0.689	0.00000404	950
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000058	0.000056	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000055	0.000053	rare
South Asian	0.000082	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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.;

Recessive Scores

pRec: 0.194

Intolerance Scores

LoFtool: 0.428
RVIS EVS: 1.04
RVIS percentile EVS: 91.21

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.154

Gene Damage Prediction

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