CXCL17

C-X-C motif chemokine ligand 17, the group of Chemokine ligands

Basic information

Region (hg38): 19:42428278-42442946

Links

ENSG00000189377 ∙ NCBI:284340 ∙ OMIM:611387 ∙ HGNC:19232 ∙ Uniprot:Q6UXB2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CXCL17 gene.

• not_specified (9 variants)
• not_provided (1 variants)

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. These statistics are base on transcript: NM_000198477.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			9			9
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	9	0	1

GnomAD

Source: gnomAD

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: dbNSFP

• 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