ACKR4

atypical chemokine receptor 4, the group of Atypical chemokine receptors

Basic information

Region (hg38): 3:132597270-132618967

Previous symbols: [ "CCRL1" ]

Links

ENSG00000129048 ∙ NCBI:51554 ∙ OMIM:606065 ∙ HGNC:1611 ∙ Uniprot:Q9NPB9 ∙ 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 ACKR4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ACKR4 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			4			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	4	0	0

Variants in ACKR4

This is a list of pathogenic ClinVar variants found in the ACKR4 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-132601200-T-C		not specified	Uncertain significance (Aug 13, 2021)
3-132601238-A-G		not specified	Uncertain significance (Sep 17, 2021)
3-132601239-T-C		not specified	Uncertain significance (Jun 18, 2021)
3-132601286-T-C		not specified	Uncertain significance (Jul 06, 2021)
3-132603242-T-A		not specified	Uncertain significance (Oct 29, 2021)
3-132603276-C-T		not specified	Uncertain significance (Jun 10, 2024)
3-132603303-G-A		not specified	Uncertain significance (May 05, 2023)
3-132605177-C-T			Uncertain significance (Nov 11, 2013)
3-132605194-T-C		not specified	Uncertain significance (May 13, 2024)
3-132618681-G-C		not specified	Uncertain significance (Dec 26, 2023)
3-132618708-A-C		not specified	Uncertain significance (Jan 18, 2023)
3-132618709-C-G		not specified	Uncertain significance (Mar 18, 2024)
3-132618709-C-T		not specified	Uncertain significance (Aug 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ACKR4	protein_coding	protein_coding	ENST00000249887	1	21731

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.00e-9	0.0480	125433	1	140	125574	0.000562

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.844	147	179	0.822	0.00000851	2275
Missense in Polyphen		45	57.851	0.77786		761
Synonymous	0.0455	61	61.5	0.993	0.00000285	669
Loss of Function	-0.551	12	10.1	1.19	5.75e-7	131

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00151	0.00151
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000550	0.0000544
Finnish	0.000325	0.000323
European (Non-Finnish)	0.000407	0.000406
Middle Eastern	0.0000550	0.0000544
South Asian	0.00112	0.00108
Other	0.000494	0.000490

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Atypical chemokine receptor that controls chemokine levels and localization via high-affinity chemokine binding that is uncoupled from classic ligand-driven signal transduction cascades, resulting instead in chemokine sequestration, degradation, or transcytosis. Also known as interceptor (internalizing receptor) or chemokine-scavenging receptor or chemokine decoy receptor. Acts as a receptor for chemokines CCL2, CCL8, CCL13, CCL19, CCL21 and CCL25. Chemokine-binding does not activate G-protein-mediated signal transduction but instead induces beta-arrestin recruitment, leading to ligand internalization. Plays an important role in controlling the migration of immune and cancer cells that express chemokine receptors CCR7 and CCR9, by reducing the availability of CCL19, CCL21, and CCL25 through internalization. Negatively regulates CXCR3-induced chemotaxis. Regulates T-cell development in the thymus. {ECO:0000269|PubMed:10706668, ECO:0000269|PubMed:23121557, ECO:0000269|PubMed:23341447}.
• Pathway: GPCRs, Class A Rhodopsin-like;Signaling by GPCR;Signal Transduction;Chemokine receptors bind chemokines;Peptide ligand-binding receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding (Consensus)

Recessive Scores

• pRec: 0.0861

Intolerance Scores

• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.73

Haploinsufficiency Scores

• pHI: 0.201
• hipred: N
• hipred_score: 0.354
• ghis: 0.395

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ackr4
• Phenotype: immune system phenotype; homeostasis/metabolism phenotype; hematopoietic system phenotype; normal phenotype

Gene ontology

• Biological process: receptor-mediated endocytosis;chemotaxis;immune response;G protein-coupled receptor signaling pathway;positive regulation of cytosolic calcium ion concentration;calcium-mediated signaling;cell chemotaxis;chemokine-mediated signaling pathway
• Cellular component: early endosome;plasma membrane;integral component of plasma membrane;external side of plasma membrane;recycling endosome
• Molecular function: chemokine receptor activity;scavenger receptor activity;protein binding;C-C chemokine receptor activity;chemokine binding;C-C chemokine binding