CXCL1

C-X-C motif chemokine ligand 1, the group of Chemokine ligands

Basic information

Region (hg38): 4:73869393-73871308

Previous symbols: [ "MGSA", "GRO1", "FSP" ]

Links

ENSG00000163739 ∙ NCBI:2919 ∙ OMIM:155730 ∙ HGNC:4602 ∙ Uniprot:P09341 ∙ 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 CXCL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CXCL1 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			9	1	1	11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	1	1

Variants in CXCL1

This is a list of pathogenic ClinVar variants found in the CXCL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-73869495-G-A		not specified	Uncertain significance (Oct 24, 2024)
4-73869498-C-T		not specified	Uncertain significance (Aug 22, 2022)
4-73869567-G-A		not specified	Uncertain significance (Feb 24, 2025)
4-73869698-C-G		not specified	Uncertain significance (Mar 22, 2023)
4-73869716-C-A		not specified	Uncertain significance (Nov 23, 2022)
4-73869719-G-A		not specified	Uncertain significance (Mar 29, 2024)
4-73869738-T-C		not specified	Uncertain significance (Dec 19, 2022)
4-73869751-C-G		not specified	Likely benign (Sep 06, 2022)
4-73869752-G-A		not specified	Uncertain significance (Jan 08, 2024)
4-73869761-C-T		not specified	Uncertain significance (Oct 07, 2024)
4-73869777-C-T			Benign (Dec 31, 2019)
4-73869977-A-T		not specified	Uncertain significance (May 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CXCL1	protein_coding	protein_coding	ENST00000395761	4	1850

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.118	0.788	125734	0	6	125740	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0153	61	61.3	0.995	0.00000294	663
Missense in Polyphen		9	16.558	0.54354		203
Synonymous	-2.67	45	27.3	1.65	0.00000130	235
Loss of Function	1.33	2	5.30	0.377	2.26e-7	56

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	0.0000462	0.0000462
European (Non-Finnish)	0.0000440	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has chemotactic activity for neutrophils. May play a role in inflammation and exerts its effects on endothelial cells in an autocrine fashion. In vitro, the processed forms GRO- alpha(4-73), GRO-alpha(5-73) and GRO-alpha(6-73) show a 30-fold higher chemotactic activity. {ECO:0000269|PubMed:10095777}.
• Pathway: Kaposi,s sarcoma-associated herpesvirus infection - Homo sapiens (human);Salmonella infection - Homo sapiens (human);Legionellosis - Homo sapiens (human);TNF signaling pathway - Homo sapiens (human);Chemokine signaling pathway - Homo sapiens (human);Amoebiasis - Homo sapiens (human);Epithelial cell signaling in Helicobacter pylori infection - Homo sapiens (human);NOD-like receptor signaling pathway - Homo sapiens (human);IL-17 signaling pathway - Homo sapiens (human);Rheumatoid arthritis - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);Spinal Cord Injury;Interleukin-10 signaling;Cytokines and Inflammatory Response;Senescence and Autophagy in Cancer;Signaling by GPCR;Neutrophil degranulation;Signal Transduction;Innate Immune System;Immune System;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;IL23-mediated signaling events (Consensus)

Recessive Scores

• pRec: 0.575

Intolerance Scores

• loftool: 0.601
• rvis_EVS: 0.44
• rvis_percentile_EVS: 77.45

Haploinsufficiency Scores

• pHI: 0.266
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.753

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;nervous system development;cell population proliferation;negative regulation of cell population proliferation;regulation of signaling receptor activity;cytokine-mediated signaling pathway;actin cytoskeleton organization;neutrophil chemotaxis;leukocyte chemotaxis;intracellular signal transduction;positive regulation of catalytic activity;neutrophil degranulation;antimicrobial humoral immune response mediated by antimicrobial peptide;chemokine-mediated signaling pathway;cellular response to lipopolysaccharide
• Cellular component: extracellular region;extracellular space;specific granule lumen;tertiary granule lumen
• Molecular function: signaling receptor binding;chemokine activity;enzyme activator activity;growth factor activity