CXCL16

Chr 17

C-X-C motif chemokine ligand 16

Also known as: CXCLG16, SR-PSOX, SRPSOX

NCBI Gene: 58191ENSG00000161921UniProt: Q9H2A7OMIM: 605398

The CXCL16 protein functions as a chemokine that induces chemotactic responses and calcium mobilization, and also acts as a scavenger receptor on macrophages that binds oxidized low-density lipoprotein. This gene is extremely tolerant to loss-of-function variants in the general population (very low constraint), and no established Mendelian diseases have been definitively linked to CXCL16 mutations in current medical literature.

OMIMResearchSummary from RefSeq, UniProt
DNmechanismLOEUF 1.34
Clinical Summary— CXCL16
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
22 unique Pathogenic / Likely Pathogenic· 36 VUS of 77 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.34LOEUF
pLI 0.000
Z-score 0.77
OE 0.75 (0.44–1.34)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
0.35Z-score
OE missense 0.92 (0.80–1.06)
140 obs / 152.0 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.75 (0.44–1.34)
0≤0.351.4
Missense OE0.92 (0.80–1.06)
0≤0.61.4
Synonymous OE0.84
0≤1.21.6
LoF obs/exp: 8 / 10.7Missense obs/exp: 140 / 152.0Syn Z: 0.98
DN
0.75top 25%
GOF
0.6053th %ile
LOF
0.1994th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

77 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic21
Likely Pathogenic1
VUS36
Likely Benign7
Benign2
21
Pathogenic
1
Likely Pathogenic
36
VUS
7
Likely Benign
2
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
21
0
21
Likely Pathogenic
0
0
1
0
1
VUS
0
16
20
0
36
Likely Benign
0
6
1
0
7
Benign
0
1
1
0
2
Total02344067

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

CXCL16 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients