CXCL10
protein-codingC-X-C motif chemokine ligand 10, the group of Chemokine ligands
Gene summary
This antimicrobial gene encodes a chemokine of the CXC subfamily and ligand for the receptor CXCR3. Binding of this protein to CXCR3 results in pleiotropic effects, including stimulation of monocytes, natural killer and T-cell migration, and modulation of adhesion molecule expression. This gene may also be a key regulator of the 'cytokine storm' immune response to SARS-CoV-2 infection. [provided by RefSeq, Sep 2020]
- INP10
- SCYB10
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~2.4 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CXCL10 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001565.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 14 | 2 | 1 | 17 | ||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 15 | 2 | 2 | 19 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001556.2 | 4 | MANE Select | |
| Ensembl | ENSP00000305651.1 | 4 | MANE Select | |
| Ensembl | ENSP00000805775.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Influenza A - Homo sapiens (human)
- TNF signaling pathway - Homo sapiens (human)
- Chemokine signaling pathway - Homo sapiens (human)
- Cytosolic DNA-sensing pathway - Homo sapiens (human)
- Toll-like receptor signaling pathway - Homo sapiens (human)
Biological Process
- chemotaxis
- inflammatory response
- immune response
- signal transduction
- cell surface receptor signaling pathway
Molecular Function
- signaling receptor binding
- protein binding
- chemokine activity
- heparin binding
- cAMP-dependent protein kinase regulator activity
Cellular Component
- extracellular region
- extracellular space
- external side of plasma membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000306602
- Coding exons
- 4
- Length
- 2378
- Individuals with no LoFs
- 124538
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 1
- Defined
- 124539
- p
- 0.00000401
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.335 | 45 | 51.8 | 0.869 | 0.00000253 | 636 |
| Missense (PolyPhen) | 13 | 11.13 | 1.168 | 147 | ||
| Synonymous | 0.588 | 13 | 16.0 | 0.813 | 7.44e-7 | 185 |
| Loss of Function | 1.59 | 1 | 4.72 | 0.212 | 1.98e-7 | 60 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0 | 0.0 | absent |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Chemotactic for monocytes and T-lymphocytes. Binds to CXCR3.;
Recessive Scores
- pRec
- 0.588
Intolerance Scores
- RVIS EVS
- 0.3
- RVIS percentile EVS
- 71.81
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.716
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |