CCR10
protein-codingC-C motif chemokine receptor 10, the group of C-C motif chemokine receptors
Gene summary
Chemokines are a group of small (approximately 8 to 14 kD), mostly basic, structurally related molecules that regulate cell trafficking of various types of leukocytes through interactions with a subset of 7-transmembrane, G protein-coupled receptors. Chemokines also play fundamental roles in the development, homeostasis, and function of the immune system, and they have effects on cells of the central nervous system as well as on endothelial cells involved in angiogenesis or angiostasis. Chemokines are divided into 2 major subfamilies, CXC and CC, based on the arrangement of the first 2 of the 4 conserved cysteine residues; the 2 cysteines are separated by a single amino acid in CXC chemokines and are adjacent in CC chemokines. CCR10 is the receptor for CCL27 (SCYA27; MIM 604833); CCR10-CCL27 interactions are involved in T cell-mediated skin inflammation (Homey et al., 2002 [PubMed 11821900]).[supplied by OMIM, Mar 2008]
- GPR2
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~5.0 kbGenCC 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 CCR10 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_016602.3. 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 | 1 | 1 | ||||
| missense | 40 | 2 | 1 | 43 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 40 | 2 | 2 | 44 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_057686.2 | 2 | MANE Select | |
| Ensembl | ENSP00000332504.4 | 2 | MANE Select | |
| Ensembl | ENSP00000467331.1 | 1 | Standard | |
| Ensembl | ENSP00000468135.1 | 1 | Standard |
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)
- Peptide GPCRs
- Chemokine signaling pathway
Biological Process
- chemotaxis
- immune response
- G protein-coupled receptor signaling pathway
- positive regulation of cytosolic calcium ion concentration
- calcium-mediated signaling
Molecular Function
- G protein-coupled receptor activity
- protein binding
- C-C chemokine receptor activity
- chemokine binding
- C-C chemokine binding
Cellular Component
- endoplasmic reticulum
- plasma membrane
- integral component of plasma membrane
- external side of plasma membrane
- cell surface
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000332438
- Coding exons
- 2
- Length
- 5029
- Individuals with no LoFs
- 125593
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 12
- Defined
- 125605
- p
- 0.0000478
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.89 | 130 | 206 | 0.630 | 0.0000111 | 2192 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000061 | 0.000058 | rare |
| Ashkenazi Jewish | 0.00011 | 0.000099 | rare |
| East Asian | 0.000065 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000020 | 0.000018 | rare |
| South Asian | 0.00020 | 0.00020 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- 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.;
Recessive Scores
- pRec
- 0.119
Intolerance Scores
- LoFtool
- 0.481
- RVIS EVS
- 0.3
- RVIS percentile EVS
- 72.01
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.898
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |