CCRL2

C-C motif chemokine receptor like 2, the group of Atypical chemokine receptors

Basic information

Region (hg38): 3:46407166-46412997

Links

ENSG00000121797 ∙ NCBI:9034 ∙ OMIM:608379 ∙ HGNC:1612 ∙ Uniprot:O00421 ∙ 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 CCRL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCRL2 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			17	1		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	1	0

Variants in CCRL2

This is a list of pathogenic ClinVar variants found in the CCRL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-46407683-C-T		not specified	Uncertain significance (Oct 03, 2022)
3-46408126-T-C		not specified	Uncertain significance (Jun 11, 2024)
3-46408236-G-A		not specified	Uncertain significance (Apr 20, 2024)
3-46408237-T-C		not specified	Uncertain significance (Feb 28, 2024)
3-46408269-G-A		not specified	Uncertain significance (Sep 27, 2022)
3-46408291-G-T		not specified	Uncertain significance (May 06, 2024)
3-46408383-A-G		not specified	Uncertain significance (Mar 24, 2023)
3-46408395-C-A		not specified	Uncertain significance (Jul 20, 2021)
3-46408399-T-C		not specified	Uncertain significance (Jun 10, 2024)
3-46408510-G-A		not specified	Uncertain significance (Nov 18, 2022)
3-46408585-T-C		not specified	Uncertain significance (May 27, 2022)
3-46408618-A-C		not specified	Uncertain significance (Oct 14, 2023)
3-46408638-C-T		not specified	Uncertain significance (May 18, 2023)
3-46408641-T-A		not specified	Uncertain significance (Aug 10, 2021)
3-46408671-C-A		not specified	Uncertain significance (May 15, 2024)
3-46408738-A-G		not specified	Uncertain significance (Nov 17, 2023)
3-46408794-C-G		not specified	Uncertain significance (Dec 07, 2023)
3-46408815-G-A		not specified	Uncertain significance (Jun 29, 2023)
3-46408845-A-G		not specified	Uncertain significance (May 10, 2024)
3-46408908-A-T		not specified	Uncertain significance (Jun 11, 2021)
3-46408951-C-T		not specified	Uncertain significance (Jan 24, 2024)
3-46408981-C-T		not specified	Likely benign (Oct 06, 2022)
3-46409095-A-G		not specified	Uncertain significance (Aug 30, 2021)
3-46409113-A-C			Benign (Jul 23, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCRL2	protein_coding	protein_coding	ENST00000357392	2	5835

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.369	0.490	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.406	203	187	1.08	0.00000969	2332
Missense in Polyphen		35	43.404	0.80638		638
Synonymous	0.120	77	78.3	0.983	0.00000436	702
Loss of Function	0.822	0	0.788	0.00	3.32e-8	12

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for CCL19 and chemerin/RARRES2. Does not appear to be a signaling receptor, but may have a role in modulating chemokine-triggered immune responses by capturing and internalizing CCL19 or by presenting RARRES2 ligand to CMKLR1, a functional signaling receptors. Plays a critical role for the development of Th2 responses.
• 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: 0.0893

Intolerance Scores

• loftool: 0.654
• rvis_EVS: 1.26
• rvis_percentile_EVS: 93.58

Haploinsufficiency Scores

• pHI: 0.0773
• hipred: N
• hipred_score: 0.153

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.126

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccrl2
• Phenotype: cellular phenotype; normal phenotype; hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: chemotaxis;inflammatory response;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: cytoplasm;plasma membrane;integral component of plasma membrane;external side of plasma membrane
• Molecular function: chemokine receptor activity;C-C chemokine receptor activity;chemokine binding;C-C chemokine binding;chemokine receptor binding;CCR chemokine receptor binding