CXCL17
protein-codingC-X-C motif chemokine ligand 17, the group of Chemokine ligands
Gene summary
The protein encoded by this gene is a mucosal chemokine that attracts immature dendritic cells and blood monocytes to the lungs. The encoded protein also promotes tumorigenesis through an angiogenic activity. Finally, this protein exhibits strong antimicrobial activity against E. coli, S. aureus, Salmonella, P. aeruginosa, and C. albicans. Two transcript variants, one protein-coding and the other non-protein coding, have been found for this gene. [provided by RefSeq, Dec 2015]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~14.7 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 CXCL17 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_198477.3. 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 | 9 | 9 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 12 | 0 | 1 | 13 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_940879.1 | 4 | MANE Select | |
| Ensembl | ENSP00000472467.1 | 4 | MANE Select | |
| Ensembl | ENSP00000345317.4 | 3 | Standard | |
| Ensembl | ENSP00000539387.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- activation of MAPK activity
- angiogenesis
- positive regulation of vascular endothelial growth factor production
- positive regulation of macrophage chemotaxis
- cell differentiation
Molecular Function
- protein binding
Cellular Component
- extracellular space
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000601181
- Coding exons
- 4
- Length
- 14761
- Individuals with no LoFs
- 125738
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 4
- Defined
- 125742
- p
- 0.0000159
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.398 | 52 | 60.7 | 0.856 | 0.00000270 | 779 |
| Missense (PolyPhen) | 11 | 13.719 | 0.80183 | 184 | ||
| Synonymous | 0.519 | 21 | 24.3 | 0.866 | 0.00000116 | 220 |
| Loss of Function | 0.710 | 4 | 5.85 | 0.683 | 2.52e-7 | 68 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.000018 | 0.000018 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Chemokine that acts as chemoattractant for monocytes, macrophages and dendritic cells (PubMed:16455961, PubMed:23115081). Plays a role in angiogenesis and possibly in the development of tumors (PubMed:16989774, PubMed:23115081). Acts as an anti-inflammatory in the stomach (PubMed:23115081). May play a role in the innate defense against infections (PubMed:17307946). Activates the C-X-C chemokine receptor GPR35 to induce a rapid and transient rise in the level of intracellular calcium ions (PubMed:25411203). {ECO:0000269|PubMed:16455961, ECO:0000269|PubMed:16989774, ECO:0000269|PubMed:17307946, ECO:0000269|PubMed:23115081, ECO:0000269|PubMed:25411203}.;
Recessive Scores
- pRec
- 0.0866
Intolerance Scores
- LoFtool
- 0.535
- RVIS EVS
- -0.12
- RVIS percentile EVS
- 44.54
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.228
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |