CCL17
Basic information
Region (hg38): 16:57404767-57416063
Previous symbols: [ "SCYA17" ]
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 CCL17 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 | 5 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 5 | 0 | 1 |
Variants in CCL17
This is a list of pathogenic ClinVar variants found in the CCL17 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 16-57413960-G-T | not specified | Uncertain significance (Jun 05, 2024) | ||
| 16-57413978-G-A | not specified | Uncertain significance (Feb 13, 2024) | ||
| 16-57415087-G-T | not specified | Uncertain significance (Jun 16, 2024) | ||
| 16-57415094-T-C | Benign (Apr 23, 2018) | |||
| 16-57415102-G-A | not specified | Uncertain significance (May 18, 2022) | ||
| 16-57415129-G-A | not specified | Uncertain significance (Nov 30, 2021) | ||
| 16-57415131-G-A | not specified | Uncertain significance (Jun 29, 2023) | ||
| 16-57415192-C-T | not specified | Uncertain significance (Mar 28, 2024) | ||
| 16-57415781-G-A | not specified | Uncertain significance (Oct 06, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CCL17 | protein_coding | protein_coding | ENST00000219244 | 3 | 11296 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000139 | 0.249 | 125728 | 0 | 17 | 125745 | 0.0000676 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.476 | 42 | 51.6 | 0.814 | 0.00000279 | 595 |
| Missense in Polyphen | 14 | 16.837 | 0.8315 | 188 | ||
| Synonymous | 1.12 | 15 | 21.6 | 0.694 | 0.00000121 | 190 |
| Loss of Function | -0.697 | 5 | 3.58 | 1.40 | 2.18e-7 | 37 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000148 | 0.000148 |
| Ashkenazi Jewish | 0.000101 | 0.0000992 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000484 | 0.0000462 |
| European (Non-Finnish) | 0.0000443 | 0.0000439 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000196 | 0.000196 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Chemotactic factor for T-lymphocytes but not monocytes or granulocytes. May play a role in T-cell development in thymus and in trafficking and activation of mature T-cells. Binds to CCR4. {ECO:0000269|PubMed:10540332}.;
- Pathway
- Chemokine signaling pathway - Homo sapiens (human);C-type lectin receptor signaling pathway - Homo sapiens (human);IL-17 signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);C-type lectin receptors (CLRs);Chemokine signaling pathway;IL4-mediated signaling events
(Consensus)
Recessive Scores
- pRec
- 0.239
Intolerance Scores
- loftool
- 0.651
- rvis_EVS
- 0.44
- rvis_percentile_EVS
- 77.45
Haploinsufficiency Scores
- pHI
- 0.0800
- hipred
- N
- hipred_score
- 0.146
- ghis
- 0.390
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.871
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ccl17
- Phenotype
- hematopoietic system phenotype; immune system phenotype; cellular phenotype;
Gene ontology
- Biological process
- monocyte chemotaxis;chemotaxis;inflammatory response;G protein-coupled receptor signaling pathway;cell-cell signaling;multicellular organism development;regulation of signaling receptor activity;neutrophil chemotaxis;positive regulation of GTPase activity;negative regulation of myoblast differentiation;lymphocyte chemotaxis;chemokine-mediated signaling pathway;positive regulation of ERK1 and ERK2 cascade;cellular response to interferon-gamma;cellular response to interleukin-1;cellular response to tumor necrosis factor
- Cellular component
- extracellular space
- Molecular function
- signaling receptor binding;protein binding;chemokine activity;CCR4 chemokine receptor binding;CCR chemokine receptor binding