CCL28
Basic information
Region (hg38): 5:43376645-43412391
Links
Phenotypes
GenCC
Source:
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 CCL28 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 | 5 | |||||
| nonsense | 0 | |||||
| start loss | 1 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 1 | |||||
| Total | 0 | 0 | 7 | 0 | 0 |
Variants in CCL28
This is a list of pathogenic ClinVar variants found in the CCL28 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-43381903-T-C | not specified | Uncertain significance (Oct 26, 2022) | ||
| 5-43381927-C-A | not specified | Uncertain significance (Jun 24, 2022) | ||
| 5-43382038-C-A | not specified | Uncertain significance (May 03, 2023) | ||
| 5-43388366-C-T | not specified | Uncertain significance (Nov 09, 2021) | ||
| 5-43388398-A-T | not specified | Uncertain significance (Aug 01, 2022) | ||
| 5-43388405-C-G | not specified | Uncertain significance (Dec 13, 2022) | ||
| 5-43412279-A-T | not specified | Uncertain significance (Feb 05, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CCL28 | protein_coding | protein_coding | ENST00000361115 | 3 | 35747 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0516 | 0.709 | 124958 | 0 | 2 | 124960 | 0.00000800 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.451 | 65 | 76.1 | 0.855 | 0.00000414 | 840 |
| Missense in Polyphen | 18 | 23.886 | 0.75358 | 281 | ||
| Synonymous | 0.481 | 25 | 28.3 | 0.885 | 0.00000181 | 232 |
| Loss of Function | 0.688 | 2 | 3.36 | 0.595 | 1.41e-7 | 48 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000545 | 0.0000545 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.0000545 | 0.0000545 |
| South Asian | 0.0000332 | 0.0000330 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Chemotactic activity for resting CD4, CD8 T-cells and eosinophils. Binds to CCR3 and CCR10 and induces calcium mobilization in a dose-dependent manner.;
- Pathway
- Chemokine signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);Intestinal immune network for IgA production - Homo sapiens (human);Chemokine signaling pathway;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
- 0.102
Intolerance Scores
- loftool
- 0.539
- rvis_EVS
- 0.26
- rvis_percentile_EVS
- 70.06
Haploinsufficiency Scores
- pHI
- 0.149
- hipred
- N
- hipred_score
- 0.112
- ghis
- 0.401
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.231
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ccl28
- Phenotype
Gene ontology
- Biological process
- positive regulation of cell-matrix adhesion;chemotaxis;immune response;G protein-coupled receptor signaling pathway;positive regulation of cytosolic calcium ion concentration;response to nutrient;regulation of signaling receptor activity;cell chemotaxis;negative regulation of leukocyte tethering or rolling
- Cellular component
- extracellular region;cell;extracellular exosome
- Molecular function
- protein binding;chemokine activity