CXCL5

C-X-C motif chemokine ligand 5, the group of Chemokine ligands

Basic information

Region (hg38): 4:73995641-73998677

Previous symbols: [ "SCYB5" ]

Links

ENSG00000163735 ∙ NCBI:6374 ∙ OMIM:600324 ∙ HGNC:10642 ∙ Uniprot:P42830 ∙ 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 CXCL5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CXCL5 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			7	1		8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	1	0

Variants in CXCL5

This is a list of pathogenic ClinVar variants found in the CXCL5 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
4-73997644-T-C		not specified	Uncertain significance (Jan 03, 2024)
4-73998034-C-T		not specified	Likely benign (Jun 09, 2022)
4-73998035-T-A		not specified	Uncertain significance (Apr 25, 2022)
4-73998224-C-T		not specified	Uncertain significance (Feb 28, 2024)
4-73998240-C-T		not specified	Uncertain significance (Jul 25, 2023)
4-73998547-G-C		not specified	Uncertain significance (Oct 10, 2023)
4-73998559-G-A		not specified	Uncertain significance (Aug 20, 2023)
4-73998577-C-T		not specified	Uncertain significance (Dec 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CXCL5	protein_coding	protein_coding	ENST00000296027	4	3138

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000504	0.138	125717	0	30	125747	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.125	65	62.2	1.04	0.00000292	714
Missense in Polyphen		20	16.824	1.1888		223
Synonymous	-0.622	31	26.9	1.15	0.00000137	239
Loss of Function	-0.782	7	5.09	1.37	2.16e-7	60

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000687	0.000684
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000441	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.000132	0.000131
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in neutrophil activation. In vitro, ENA-78(8- 78) and ENA-78(9-78) show a threefold higher chemotactic activity for neutrophil granulocytes. {ECO:0000269|PubMed:10095777}.
• Pathway: Pertussis - Homo sapiens (human);TNF signaling pathway - Homo sapiens (human);Chemokine signaling pathway - Homo sapiens (human);IL-17 signaling pathway - Homo sapiens (human);Rheumatoid arthritis - Homo sapiens (human);Cytokine-cytokine receptor interaction - 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: 0.203

Intolerance Scores

• loftool: 0.441
• rvis_EVS: 0.21
• rvis_percentile_EVS: 67.72

Haploinsufficiency Scores

• pHI: 0.285
• hipred: N
• hipred_score: 0.112
• ghis: 0.389

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.242

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Gene ontology

• Biological process: chemotaxis;inflammatory response;immune response;signal transduction;G protein-coupled receptor signaling pathway;cell-cell signaling;positive regulation of cell population proliferation;regulation of signaling receptor activity;neutrophil chemotaxis;leukocyte chemotaxis;antimicrobial humoral immune response mediated by antimicrobial peptide;chemokine-mediated signaling pathway;cellular response to lipopolysaccharide
• Cellular component: extracellular region;extracellular space
• Molecular function: chemokine activity;identical protein binding