CXCL17
Basic information
Region (hg38): 19:42428278-42442946
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 CXCL17 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 | 4 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 4 | 0 | 1 |
Variants in CXCL17
This is a list of pathogenic ClinVar variants found in the CXCL17 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 19-42428981-C-T | not specified | Uncertain significance (May 11, 2022) | ||
| 19-42433032-C-T | not specified | Uncertain significance (Feb 14, 2025) | ||
| 19-42433787-C-G | not specified | Uncertain significance (May 31, 2022) | ||
| 19-42433851-C-T | not specified | Uncertain significance (Oct 13, 2023) | ||
| 19-42442768-C-G | not specified | Uncertain significance (Oct 05, 2023) | ||
| 19-42442779-G-A | Benign (Dec 10, 2018) | |||
| 19-42442788-C-T | not specified | Uncertain significance (Dec 15, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CXCL17 | protein_coding | protein_coding | ENST00000601181 | 4 | 14761 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00481 | 0.705 | 125738 | 0 | 4 | 125742 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.398 | 52 | 60.7 | 0.856 | 0.00000270 | 779 |
| Missense in 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 |
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 | 0.0000463 | 0.0000462 |
| European (Non-Finnish) | 0.0000176 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
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
Haploinsufficiency Scores
- pHI
- 0.133
- hipred
- N
- hipred_score
- 0.123
- ghis
- 0.400
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.228
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cxcl17
- Phenotype
- integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); pigmentation phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan);
Gene ontology
- Biological process
- activation of MAPK activity;angiogenesis;positive regulation of vascular endothelial growth factor production;positive regulation of macrophage chemotaxis;cell differentiation;macrophage chemotaxis;negative regulation of inflammatory response;positive regulation of monocyte chemotaxis
- Cellular component
- extracellular space
- Molecular function
- protein binding