CCR7
C-C motif chemokine receptor 7, the group of CD molecules|C-C motif chemokine receptors
Basic information
Region (hg38): 17:40551081-40565472
Previous symbols: [ "CMKBR7", "EBI1" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCR7 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 | |||||
| missense | 13 | 13 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 13 | 0 | 1 |
Variants in CCR7
This is a list of pathogenic ClinVar variants found in the CCR7 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 17-40554783-T-C | not specified | Uncertain significance (Sep 16, 2021) | ||
| 17-40554791-C-T | not specified | Uncertain significance (Apr 18, 2023) | ||
| 17-40554795-G-A | not specified | Uncertain significance (Jul 21, 2022) | ||
| 17-40554816-A-G | not specified | Uncertain significance (Nov 05, 2021) | ||
| 17-40554863-T-C | not specified | Uncertain significance (Nov 30, 2022) | ||
| 17-40554900-C-T | not specified | Uncertain significance (Feb 07, 2023) | ||
| 17-40554926-C-T | not specified | Uncertain significance (Nov 01, 2022) | ||
| 17-40555098-C-A | not specified | Uncertain significance (Dec 21, 2021) | ||
| 17-40555102-G-T | not specified | Uncertain significance (Jul 14, 2022) | ||
| 17-40555200-G-C | not specified | Uncertain significance (Nov 14, 2023) | ||
| 17-40555417-G-T | Benign (Jun 12, 2018) | |||
| 17-40555641-C-T | not specified | Uncertain significance (Dec 19, 2023) | ||
| 17-40555689-T-C | not specified | Uncertain significance (Aug 13, 2021) | ||
| 17-40558927-C-T | not specified | Uncertain significance (Feb 05, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CCR7 | protein_coding | protein_coding | ENST00000246657 | 3 | 11704 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0576 | 0.926 | 125742 | 0 | 6 | 125748 | 0.0000239 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.18 | 149 | 245 | 0.608 | 0.0000155 | 2487 |
| Missense in Polyphen | 48 | 98.78 | 0.48593 | 973 | ||
| Synonymous | -0.0566 | 105 | 104 | 1.01 | 0.00000705 | 771 |
| Loss of Function | 2.10 | 4 | 11.8 | 0.340 | 5.86e-7 | 126 |
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 | 0.0000466 | 0.0000462 |
| European (Non-Finnish) | 0.0000352 | 0.0000352 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Receptor for the MIP-3-beta chemokine. Probable mediator of EBV effects on B-lymphocytes or of normal lymphocyte functions.;
- Pathway
- Chemokine signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - 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
- 0.622
Intolerance Scores
- loftool
- 0.174
- rvis_EVS
- -0.51
- rvis_percentile_EVS
- 21.41
Haploinsufficiency Scores
- pHI
- 0.212
- hipred
- Y
- hipred_score
- 0.592
- ghis
- 0.606
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.941
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ccr7
- Phenotype
- hematopoietic system phenotype; immune system phenotype; 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); digestive/alimentary phenotype; vision/eye phenotype; endocrine/exocrine gland phenotype; cellular phenotype; homeostasis/metabolism phenotype;
Zebrafish Information Network
- Gene name
- ccr7
- Affected structure
- blood cell
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- establishment of T cell polarity;positive regulation of cell-matrix adhesion;dendritic cell chemotaxis;myeloid dendritic cell chemotaxis;positive regulation of dendritic cell antigen processing and presentation;positive regulation of hypersensitivity;positive regulation of humoral immune response;chemotaxis;inflammatory response;immune response;G protein-coupled receptor signaling pathway;positive regulation of cytosolic calcium ion concentration;calcium-mediated signaling;positive regulation of actin filament polymerization;positive regulation of pseudopodium assembly;ruffle organization;response to lipopolysaccharide;regulation of interferon-gamma production;positive regulation of interleukin-12 production;response to prostaglandin E;chemokine (C-C motif) ligand 19 signaling pathway;chemokine (C-C motif) ligand 21 signaling pathway;positive regulation of I-kappaB kinase/NF-kappaB signaling;positive regulation of phosphatidylinositol 3-kinase activity;negative thymic T cell selection;positive regulation of cell adhesion;positive regulation of protein kinase activity;positive regulation of JNK cascade;homeostasis of number of cells;regulation of interleukin-1 beta secretion;positive regulation of T cell receptor signaling pathway;release of sequestered calcium ion into cytosol;positive regulation of filopodium assembly;positive regulation of protein kinase B signaling;cell chemotaxis;positive regulation of ERK1 and ERK2 cascade;cellular response to cytokine stimulus;response to nitric oxide;interleukin-12 secretion;positive regulation of neutrophil chemotaxis;activation of GTPase activity;lymphocyte migration into lymph node;mature conventional dendritic cell differentiation;positive regulation of cell motility;positive regulation of dendritic cell chemotaxis;positive regulation of immunological synapse formation;positive regulation of T cell costimulation;positive regulation of glycoprotein biosynthetic process involved in immunological synapse formation;regulation of dendritic cell dendrite assembly;negative regulation of dendritic cell apoptotic process
- Cellular component
- mitochondrion;plasma membrane;external side of plasma membrane;cell surface;integral component of membrane
- Molecular function
- G protein-coupled receptor activity;C-C chemokine receptor activity;chemokine binding;C-C chemokine binding;chemokine (C-C motif) ligand 19 binding;chemokine (C-C motif) ligand 21 binding;C-C motif chemokine 19 receptor activity;C-C motif chemokine 21 receptor activity