CXCL16
protein-codingC-X-C motif chemokine ligand 16, the group of Chemokine ligands|Scavenger receptors
Gene summary
Enables chemokine activity. Involved in several processes, including positive regulation of cell growth; response to tumor necrosis factor; and response to type II interferon. Located in obsolete extracellular space. Biomarker of COVID-19 and systemic scleroderma. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~6.4 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 CXCL16 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001386809.1. 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 | 0 | |||||
| missense | 21 | 6 | 1 | 28 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 21 | 6 | 1 | 28 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001373738.1 | 5 | MANE Select | |
| Ensembl | ENSP00000293778.7 | 5 | MANE Select | |
| RefSeq | NP_001094282.2 | 5 | Standard | |
| Ensembl | ENSP00000460145.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Chemokine signaling pathway - Homo sapiens (human)
- Cytokine-cytokine receptor interaction - Homo sapiens (human)
- Chemokine signaling pathway
- TYROBP Causal Network
- Signaling by GPCR
Biological Process
- receptor-mediated endocytosis
- chemotaxis
- G protein-coupled receptor signaling pathway
- regulation of signaling receptor activity
- T cell chemotaxis
Molecular Function
- low-density lipoprotein particle receptor activity
- scavenger receptor activity
- chemokine activity
Cellular Component
- extracellular region
- extracellular space
- plasma membrane
- membrane
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000293778
- Coding exons
- 5
- Length
- 6397
- Individuals with no LoFs
- 125740
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 8
- Defined
- 125748
- p
- 0.0000318
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.346 | 140 | 152 | 0.921 | 0.00000752 | 1731 |
| Missense (PolyPhen) | 30 | 37.974 | 0.79002 | 426 | ||
| Synonymous | 0.985 | 55 | 65.1 | 0.845 | 0.00000341 | 591 |
| Loss of Function | 0.768 | 8 | 10.7 | 0.747 | 4.53e-7 | 135 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000058 | 0.000058 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000018 | 0.000018 | rare |
| South Asian | 0.000065 | 0.000065 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Acts as a scavenger receptor on macrophages, which specifically binds to OxLDL (oxidized low density lipoprotein), suggesting that it may be involved in pathophysiology such as atherogenesis (By similarity). Induces a strong chemotactic response. Induces calcium mobilization. Binds to CXCR6/Bonzo. {ECO:0000250}.;
Recessive Scores
- pRec
- 0.0345
Intolerance Scores
- LoFtool
- 0.606
- RVIS EVS
- 0.6
- RVIS percentile EVS
- 82.66
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.000625
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |