CX3CL1

Chr 16

C-X3-C motif chemokine ligand 1

Also known as: ABCD-3, C3Xkine, CXC3, CXC3C, NTN, NTT, SCYD1, fractalkine

This gene belongs to the CX3C subgroup of chemokines, characterized by the number of amino acids located between the conserved cysteine residues. This is the only member of the CX3C subgroup, which contains three amino acids between cysteine residues, resulting in a Cys-X-X-X-Cys configuration. The encoded protein contains an extended mucin-like stalk with a chemokine domain on top, and exists in both a membrane-anchored form where it acts as a binding molecule, or, in soluble form, as a chemotactic cytokine. The mature form of this protein can be cleaved at the cell surface, yielding different soluble forms that can interact with the G-protein coupled receptor, C-X3-C motif chemokine receptor 1 gene product. This gene plays a role in a wide range of diseases, including cancer, vasculitis, neuropathies, atherosclerosis, inflammatory diseases, and in human immunodeficiency virus infections. [provided by RefSeq, Sep 2017]

GeneReviewsResearchGenerating clinical summary…

Clinical highlights

Interpreting a novel variant
This gene is strongly intolerant of loss-of-function variation in the population, so LoF variants warrant close attention. No curated mechanism annotation is available — see the mechanism card for the computational prediction and its caveats.Based on population constraint only.
6
Active trials
310
Pubs (1 yr)
P/LP submissions
P/LP missense
0.55
LOEUF
Mechanism
📖
GeneReview available — CX3CL1
Authoritative clinical overview · Recommended first read
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Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Moderate LoF intolerance
LoF Constraint?
0.55LOEUF
pLI 0.608
Z-score 2.61
OE 0.17 (0.070.55)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?
0.84Z-score
OE missense 0.85 (0.760.95)
211 obs / 248.4 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?
LoF OE?0.17 (0.070.55)
00.351.4
Missense OE?0.85 (0.760.95)
00.61.4
Synonymous OE?1.23
01.21.6
LoF obs/exp: 2 / 11.6Missense obs/exp: 211 / 248.4Syn Z: -1.95

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

CX3CL1 · protein map & ClinVar variants

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