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GeneBe

CXCL5

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

Basic information

Region (hg38): 4:73995641-73998677

Previous symbols: [ "SCYB5" ]

Links

ENSG00000163735NCBI:6374OMIM:600324HGNC:10642Uniprot:P42830AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CXCL5 gene.

  • Inborn genetic diseases (4 variants)

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
3
clinvar
1
clinvar
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 3 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
4-73998034-C-T Inborn genetic diseases Likely benign (Jun 09, 2022)2384120
4-73998035-T-A Inborn genetic diseases Uncertain significance (Apr 25, 2022)2395362
4-73998240-C-T Inborn genetic diseases Uncertain significance (Jul 25, 2023)2599528
4-73998559-G-A Inborn genetic diseases Uncertain significance (Aug 20, 2023)2619733

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CXCL5protein_codingprotein_codingENST00000296027 43138
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.000005040.1381257170301257470.000119
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.1256562.21.040.00000292714
Missense in Polyphen2016.8241.1888223
Synonymous-0.6223126.91.150.00000137239
Loss of Function-0.78275.091.372.16e-760

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0006870.000684
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.00004620.0000462
European (Non-Finnish)0.00004410.0000439
Middle Eastern0.000.00
South Asian0.0001320.000131
Other0.0001640.000163

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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