CCR10

C-C motif chemokine receptor 10, the group of C-C motif chemokine receptors

Basic information

Region (hg38): 17:42678889-42683917

Previous symbols: [ "GPR2" ]

Links

ENSG00000184451 ∙ NCBI:2826 ∙ OMIM:600240 ∙ HGNC:4474 ∙ Uniprot:P46092 ∙ 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 CCR10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCR10 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					1	1
missense			18	1	1	20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	1	2

Variants in CCR10

This is a list of pathogenic ClinVar variants found in the CCR10 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-42679593-G-A		not specified	Uncertain significance (May 27, 2022)
17-42679645-C-T		not specified	Uncertain significance (Oct 17, 2023)
17-42679657-T-C		not specified	Likely benign (Jan 04, 2022)
17-42679665-C-T		not specified	Uncertain significance (Mar 02, 2023)
17-42679707-A-T		not specified	Uncertain significance (Aug 07, 2024)
17-42679710-G-C		not specified	Uncertain significance (Sep 27, 2021)
17-42679791-G-T		not specified	Uncertain significance (Nov 21, 2022)
17-42679843-G-T		not specified	Uncertain significance (Aug 19, 2024)
17-42679893-A-G		not specified	Uncertain significance (Jul 02, 2024)
17-42680152-T-C		not specified	Uncertain significance (Nov 15, 2021)
17-42680177-G-C			Benign (Dec 31, 2019)
17-42680197-C-A		not specified	Uncertain significance (Feb 23, 2023)
17-42680215-C-T		not specified	Uncertain significance (Nov 30, 2022)
17-42680224-C-A		not specified	Uncertain significance (Nov 17, 2022)
17-42680307-G-A		not specified	Uncertain significance (Feb 28, 2024)
17-42680401-G-C		not specified	Uncertain significance (Apr 09, 2024)
17-42680409-G-A		not specified	Uncertain significance (Sep 20, 2023)
17-42680466-T-C		not specified	Uncertain significance (Sep 22, 2022)
17-42680491-C-T		not specified	Uncertain significance (Jul 11, 2023)
17-42680497-G-C		not specified	Uncertain significance (Nov 10, 2022)
17-42680559-G-C		not specified	Uncertain significance (May 17, 2023)
17-42680565-G-A		not specified	Uncertain significance (Dec 08, 2023)
17-42680574-G-A		not specified	Uncertain significance (Oct 25, 2022)
17-42681816-G-A			Benign (Feb 08, 2018)
17-42682613-G-C			Benign (Sep 04, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCR10	protein_coding	protein_coding	ENST00000332438	2	5029

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000505	0.701	125593	0	12	125605	0.0000478

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.89	130	206	0.630	0.0000111	2192
Missense in Polyphen		48	79.869	0.60098		949
Synonymous	2.82	69	106	0.651	0.00000580	889
Loss of Function	0.838	6	8.66	0.693	4.70e-7	79

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000606	0.0000606
Ashkenazi Jewish	0.000114	0.0000994
East Asian	0.0000645	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000203	0.0000176
Middle Eastern	0.0000645	0.0000544
South Asian	0.000199	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for chemokines SCYA27 and SCYA28. Subsequently transduces a signal by increasing the intracellular calcium ions level and stimulates chemotaxis in a pre-B cell line.
• Pathway: Chemokine signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);Intestinal immune network for IgA production - Homo sapiens (human);Peptide GPCRs;Chemokine signaling 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;G alpha (i) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.119

Intolerance Scores

• loftool: 0.481
• rvis_EVS: 0.3
• rvis_percentile_EVS: 72.01

Haploinsufficiency Scores

• pHI: 0.224
• hipred: N
• hipred_score: 0.375
• ghis: 0.501

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.898

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccr10
• Phenotype: muscle phenotype; cellular phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); skeleton phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: 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: endoplasmic reticulum;plasma membrane;integral component of plasma membrane;external side of plasma membrane;cell surface
• Molecular function: G protein-coupled receptor activity;protein binding;C-C chemokine receptor activity;chemokine binding;C-C chemokine binding