PF4V1

gene
On this page

Also known as SCYB4V1CXCL4V1CXCL4L1

Summary

PF4V1 (platelet factor 4 variant 1, HGNC:8862) is a protein-coding gene on chromosome 4q13.3, encoding Platelet factor 4 variant (P10720). Inhibitor of angiogenesis.

The protein encoded by this gene is a chemokine that is highly similar to platelet factor 4. The encoded protein displays a strong antiangiogenic function and is regulated by chemokine (C-X-C motif) receptor 3. This protein also impairs tumor growth and can protect against blood-retinal barrier breakdown in diabetes patients.

Source: NCBI Gene 5197 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 26 total
  • MANE Select transcript: NM_002620

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:8862
Approved symbolPF4V1
Nameplatelet factor 4 variant 1
Location4q13.3
Locus typegene with protein product
StatusApproved
AliasesSCYB4V1, CXCL4V1, CXCL4L1
Ensembl geneENSG00000109272
Ensembl biotypeprotein_coding
OMIM173461
Entrez5197

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000226524

RefSeq mRNA: 1 — MANE Select: NM_002620 NM_002620

CCDS: CCDS3561

Canonical transcript exons

ENST00000226524 — 3 exons

ExonStartEnd
ENSE000007219417385329673853462
ENSE000010778277385403573854483
ENSE000024624277385378373853909

Expression profiles

Bgee: expression breadth ubiquitous, 117 present calls, max score 96.31.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 2.1402 / max 527.0811, expressed in 116 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
482252.1402116

Top tissues by expression

261 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
monocyteCL:000057696.31gold quality
mononuclear cellCL:000084295.83gold quality
leukocyteCL:000073894.42gold quality
bloodUBERON:000017878.53gold quality
granulocyteCL:000009473.00gold quality
palpebral conjunctivaUBERON:000181268.10gold quality
bone marrowUBERON:000237165.64gold quality
spleenUBERON:000210665.55gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099163.11gold quality
trabecular bone tissueUBERON:000248362.51silver quality
bone marrow cellCL:000209261.80gold quality
olfactory segment of nasal mucosaUBERON:000538659.16gold quality
bronchial epithelial cellCL:000232857.93silver quality
epithelium of bronchusUBERON:000203157.14silver quality
deciduaUBERON:000245056.55gold quality
bronchusUBERON:000218556.53silver quality
lower lobe of lungUBERON:000894955.90silver quality
metanephros cortexUBERON:001053354.06gold quality
jejunal mucosaUBERON:000039953.94gold quality
duodenumUBERON:000211453.22gold quality
hair follicleUBERON:000207352.43gold quality
metanephrosUBERON:000008151.71gold quality
adult mammalian kidneyUBERON:000008251.04gold quality
cranial nerve IIUBERON:000094150.93silver quality
right lungUBERON:000216750.57gold quality
cortex of kidneyUBERON:000122550.45gold quality
frontal poleUBERON:000279550.41gold quality
middle frontal gyrusUBERON:000270250.30gold quality
quadriceps femorisUBERON:000137750.18gold quality
nasal cavity mucosaUBERON:000182650.18gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

ExperimentMarker?Max mean expression
E-MTAB-9221yes19.90
E-HCAD-1yes8.39
E-ANND-3no0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): RUNX1

miRNA regulators (miRDB)

48 targeting PF4V1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-5692B100.0071.322622
HSA-MIR-5692C100.0071.322622
HSA-MIR-126-5P100.0072.713180
HSA-MIR-4262100.0073.263931
HSA-MIR-3646100.0073.565283
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-181A-5P99.9972.962995
HSA-MIR-181B-5P99.9972.972996
HSA-MIR-181C-5P99.9972.952996
HSA-MIR-181D-5P99.9973.042997
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939
HSA-MIR-365899.9673.874379
HSA-MIR-590-3P99.9674.346478
HSA-MIR-141-3P99.9472.792421
HSA-MIR-200A-3P99.9472.682420
HSA-MIR-9983-3P99.9471.483631
HSA-MIR-7-1-3P99.9171.534384
HSA-MIR-7-2-3P99.9171.404394
HSA-MIR-806399.9169.763146
HSA-MIR-374A-5P99.9071.342923
HSA-MIR-374B-5P99.9069.982734
HSA-MIR-129-5P99.8870.263273
HSA-MIR-369-3P99.8570.522264
HSA-MIR-205-5P99.8170.051557
HSA-MIR-129999.7771.242389
HSA-MIR-548AG99.7769.251492
HSA-MIR-451799.7669.191867
HSA-MIR-6885-3P99.7570.363187

Literature-anchored findings (GeneRIF, showing 13)

  • The study determines the binding parameters of CXCL4 and CXCL4L1 for heparin, heparan sulfate, and chondroitin sulfate B. (PMID:20688960)
  • CXCL4L1 may act angiostatically causing random endothelial cell locomotion, disturbing directed migration towards angiogenic chemokines, serving as a homeostatic chemokine with moderate structural distinction yet different functional profile from CXCL4. (PMID:20961394)
  • both CXCR3A and CXCR3B are implicated in the chemotactic and vascular effects of CXCL4L1. (PMID:20980681)
  • Current knowledge on the role of CXCL4/PF-4 and CXCL4L1/PF-4var in physiological and pathological processes. (PMID:21111666)
  • PF-4var/CXCL4L1 predicts outcome in stable coronary artery disease patients with preserved left ventricular function (PMID:22384011)
  • Structural insight into the novel functional properties of human CXCL4L1. (PMID:23536183)
  • Fibstatin and CXCL4L1 cooperate to inhibit endothelial cell proliferation, migration and tubulogenesis in vitro. (PMID:23747987)
  • fibstatin and CXCL4L1 have cooperative roles in inhibition of tumor invasion in lymph nodes (PMID:23747987)
  • CXCL4 and CXCL4L1 activated p38 MAPK, as well as Src kinase within 30 and 5 min, respectively. Extracellular signal-regulated kinase (ERK) phosphorylation occurred in activated lymphocytes. (PMID:24469069)
  • CXCL4 and CXCL4L1 shift the angiogenic/angiostatic balance in favor of angiostasis. CXCL4L1 in particular was found to be a more potent angiostatic, anti-tumoral and anti-metastatic chemokine, which was verified in different in vivo models. (PMID:29903575)
  • CXCL4L1 promoter variants may protect against the development of renal inflammation in diabetes by increasing CXCL4L1 expression, which in turn activates the anti-inflammatory SMAD7 and IkappaBalpha factors in mesangial cells. (PMID:30593538)
  • Differential Effects of Platelet Factor 4 (CXCL4) and Its Non-Allelic Variant (CXCL4L1) on Cultured Human Vascular Smooth Muscle Cells. (PMID:35054772)
  • Heterocomplexes between the atypical chemokine MIF and the CXC-motif chemokine CXCL4L1 regulate inflammation and thrombus formation. (PMID:36094626)

Cross-species orthologs

0 orthologs

Paralogs (12): CXCL2 (ENSG00000081041), CXCL6 (ENSG00000124875), CXCL9 (ENSG00000138755), CXCL13 (ENSG00000156234), CXCL3 (ENSG00000163734), CXCL5 (ENSG00000163735), PPBP (ENSG00000163736), PF4 (ENSG00000163737), CXCL1 (ENSG00000163739), CXCL10 (ENSG00000169245), CXCL11 (ENSG00000169248), CXCL8 (ENSG00000169429)

Protein

Protein identifiers

Platelet factor 4 variantP10720 (reviewed: P10720)

Alternative names: C-X-C motif chemokine 4 variant, CXCL4L1, PF4alt, PF4var1

All UniProt accessions (1): P10720

UniProt curated annotations — full annotation on UniProt →

Function. Inhibitor of angiogenesis. Inhibitor of endothelial cell chemotaxis (in vitro).

Subunit / interactions. Homotetramer.

Subcellular location. Secreted.

Post-translational modifications. The N-terminal processed forms of platelet factor 4 variant seems to be produced by proteolytic cleavage. The most abundant form is Platelet factor 4 variant(5-74).

Miscellaneous. Binding to heparin is much weaker than in the close homolog PF4/CXCL4.

Similarity. Belongs to the intercrine alpha (chemokine CxC) family.

RefSeq proteins (1): NP_002611* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001089Chemokine_CXCFamily
IPR001811Chemokine_IL8-like_domDomain
IPR018048Chemokine_CXC_CSConserved_site
IPR033899CXC_Chemokine_domainDomain
IPR036048Interleukin_8-like_sfHomologous_superfamily
IPR039809Chemokine_b/g/dFamily

Pfam: PF00048

UniProt features (17 total): strand 5, chain 4, helix 2, disulfide bond 2, signal peptide 1, turn 1, binding site 1, sequence conflict 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
4HSVX-RAY DIFFRACTION2.08

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P10720-F177.180.24

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (1): 95–101

Disulfide bonds (2): 44–70, 46–86

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

IDPathway
R-HSA-202733Cell surface interactions at the vascular wall
R-HSA-9769739Regulation of clotting cascade
R-HSA-140875

MSigDB gene sets: 96 (showing top): GOBP_ANTIMICROBIAL_HUMORAL_RESPONSE, GOBP_MYELOID_LEUKOCYTE_MIGRATION, GOBP_CELL_CHEMOTAXIS, GOBP_INFLAMMATORY_RESPONSE, GOBP_CELLULAR_RESPONSE_TO_LIPID, GOBP_CELLULAR_RESPONSE_TO_BIOTIC_STIMULUS, GOBP_CELLULAR_RESPONSE_TO_OXYGEN_CONTAINING_COMPOUND, GOBP_LEUKOCYTE_CHEMOTAXIS, chr4q13, GOBP_TAXIS, GOBP_LEUKOCYTE_MIGRATION, GOBP_DEFENSE_RESPONSE_TO_OTHER_ORGANISM, GOBP_GRANULOCYTE_MIGRATION, GOBP_RESPONSE_TO_OXYGEN_CONTAINING_COMPOUND, GOBP_HUMORAL_IMMUNE_RESPONSE

GO Biological Process (8): inflammatory response (GO:0006954), neutrophil chemotaxis (GO:0030593), antimicrobial humoral immune response mediated by antimicrobial peptide (GO:0061844), cellular response to lipopolysaccharide (GO:0071222), chemotaxis (GO:0006935), defense response (GO:0006952), immune response (GO:0006955), signal transduction (GO:0007165)

GO Molecular Function (5): chemokine activity (GO:0008009), heparin binding (GO:0008201), CXCR chemokine receptor binding (GO:0045236), cytokine activity (GO:0005125), protein binding (GO:0005515)

GO Cellular Component (2): obsolete extracellular space (GO:0005615), extracellular region (GO:0005576)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
Hemostasis1
Coagulation pathway1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
chemokine receptor binding2
defense response1
granulocyte chemotaxis1
neutrophil migration1
antimicrobial humoral response1
response to lipopolysaccharide1
cellular response to molecule of bacterial origin1
cellular response to lipid1
cellular response to oxygen-containing compound1
response to chemical1
taxis1
response to stress1
immune system process1
response to stimulus1
cell communication1
cellular process1
signaling1
regulation of cellular process1
cellular response to stimulus1
cytokine activity1
cell chemotaxis1
glycosaminoglycan binding1
sulfur compound binding1
receptor ligand activity1
binding1
cellular anatomical structure1

Protein interactions and networks

STRING

940 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
PF4V1CXCR3P49682977
PF4V1CCL5P13501927
PF4V1SELPP16109890
PF4V1VWFP04275845
PF4V1SERPINC1P01008803
PF4V1FN1P02751770
PF4V1CXCL10P02778751
PF4V1CXCL9Q07325740
PF4V1PLGP00747730
PF4V1CCL1P22362707
PF4V1FCGR2AP12318696
PF4V1THBS1P07996689
PF4V1ITGAMP11215688
PF4V1F3P13726664
PF4V1APOHP02749654

IntAct

28 interactions, top by confidence:

ABTypeScore
PF4V1CXCL12psi-mi:“MI:0407”(direct interaction)0.560
CXCL12PF4V1psi-mi:“MI:0407”(direct interaction)0.560
PF4V1CCL19psi-mi:“MI:0407”(direct interaction)0.440
PF4V1CCL21psi-mi:“MI:0407”(direct interaction)0.440
PF4V1CCL22psi-mi:“MI:0407”(direct interaction)0.440
PF4V1CCL25psi-mi:“MI:0407”(direct interaction)0.440
PF4V1CCL26psi-mi:“MI:0407”(direct interaction)0.440
PF4V1CCL27psi-mi:“MI:0407”(direct interaction)0.440
PF4V1CCL28psi-mi:“MI:0407”(direct interaction)0.440
PF4V1XCL1psi-mi:“MI:0407”(direct interaction)0.440
PF4V1XCL2psi-mi:“MI:0407”(direct interaction)0.440
CCL4L1PF4V1psi-mi:“MI:0407”(direct interaction)0.440
CCL11PF4V1psi-mi:“MI:0407”(direct interaction)0.440
CCL21PF4V1psi-mi:“MI:0407”(direct interaction)0.440
CCL25PF4V1psi-mi:“MI:0407”(direct interaction)0.440
XCL1PF4V1psi-mi:“MI:0407”(direct interaction)0.440
CXCL11PF4V1psi-mi:“MI:0407”(direct interaction)0.440
PF4V1CXCL10psi-mi:“MI:0407”(direct interaction)0.440
PF4V1CXCL11psi-mi:“MI:0407”(direct interaction)0.440
PF4V1CXCL13psi-mi:“MI:0407”(direct interaction)0.440
PF4V1UBA52psi-mi:“MI:0915”(physical association)0.400
PF4V1H2BC9psi-mi:“MI:0915”(physical association)0.400
ALBSH3BP5psi-mi:“MI:0914”(association)0.350
SCN2AIGLL5psi-mi:“MI:0914”(association)0.350
PF4V1ATG9Apsi-mi:“MI:0914”(association)0.350

BioGRID (27): PF4V1 (Affinity Capture-MS), UBA52 (Proximity Label-MS), HIST1H2BH (Proximity Label-MS), PF4V1 (Reconstituted Complex), PF4V1 (Reconstituted Complex), PF4V1 (Reconstituted Complex), PF4V1 (Reconstituted Complex), PF4V1 (Reconstituted Complex), PF4V1 (Reconstituted Complex), CCL19 (Reconstituted Complex), CCL21 (Reconstituted Complex), CCL22 (Reconstituted Complex), CCL25 (Reconstituted Complex), CCL26 (Reconstituted Complex), CCL27 (Reconstituted Complex)

ESM2 similar proteins: A0A0R4INB9, A9QWP9, B0R191, K7XWG4, O43927, O55038, O62812, P02776, P02778, P06765, P10145, P10146, P10720, P17515, P18340, P19874, P22362, P26894, P36925, P41324, P43030, P46653, P48298, P48973, P49113, P67813, P67814, P78556, P79255, P80325, P82943, P97545, P97884, P97885, Q03366, Q07325, Q09141, Q102R3, Q2KIQ8, Q5KSV9

Diamond homologs: A0A0R4INB9, A9QWP9, B0R191, O46675, O46676, O46677, O46678, O55235, O62812, P02775, P02776, P02778, P06765, P08317, P09340, P09341, P10145, P10720, P10889, P12850, P14095, P17515, P18340, P19874, P19875, P19876, P22952, P26894, P30034, P30348, P30782, P36925, P41324, P42830, P43030, P46653, P47854, P48973, P49113, P50228

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 22 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Chemokine receptors bind chemokines13128.1×6e-24
Class A/1 (Rhodopsin-like receptors)831.2×5e-09
Peptide ligand-binding receptors831.2×5e-09
GPCR ligand binding827.0×1e-08
G alpha (i) signalling events1020.5×1e-09
Signaling by GPCR919.0×1e-08
GPCR downstream signalling716.0×6e-06

GO biological processes:

GO termPartnersFoldFDR
eosinophil chemotaxis7233.1×3e-14
chemokine-mediated signaling pathway13191.5×5e-26
antimicrobial humoral immune response mediated by antimicrobial peptide1288.4×1e-19
cell chemotaxis975.8×5e-14
neutrophil chemotaxis564.9×2e-07
chemotaxis955.6×7e-13
response to virus532.7×6e-06
positive regulation of cell migration1028.1×2e-11

Disease & clinical

Clinical variants and AI predictions

ClinVar

26 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance25
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

220 predictions. Top by Δscore:

VariantEffectΔscore
4:73853460:GAG:Gdonor_gain1.0000
4:73853461:AGGT:Adonor_loss1.0000
4:73853463:G:Adonor_loss1.0000
4:73853463:G:GGdonor_gain1.0000
4:73853781:A:AGacceptor_gain1.0000
4:73853781:AGCT:Aacceptor_gain1.0000
4:73853782:G:GTacceptor_gain1.0000
4:73853782:GC:Gacceptor_gain1.0000
4:73853782:GCT:Gacceptor_gain1.0000
4:73853782:GCTG:Gacceptor_gain1.0000
4:73853782:GCTGA:Gacceptor_gain1.0000
4:73853905:CTCAT:Cdonor_gain1.0000
4:73853909:TGT:Tdonor_loss1.0000
4:73853910:G:GAdonor_loss1.0000
4:73853910:G:GGdonor_gain1.0000
4:73853912:GA:Gdonor_loss1.0000
4:73853464:T:Adonor_loss0.9900
4:73853784:T:Aacceptor_gain0.9900
4:73853866:G:GTdonor_gain0.9900
4:73853906:TCAT:Tdonor_gain0.9900
4:73853907:CAT:Cdonor_gain0.9900
4:73853908:AT:Adonor_gain0.9900
4:73853913:AG:Adonor_loss0.9900
4:73853914:G:Cdonor_loss0.9900
4:73854031:CCAG:Cacceptor_gain0.9900
4:73854033:A:AGacceptor_gain0.9900
4:73854034:G:GGacceptor_gain0.9900
4:73854034:GA:Gacceptor_gain0.9900
4:73854034:GAGCC:Gacceptor_gain0.9900
4:73854029:TGCCA:Tacceptor_loss0.9800

AlphaMissense

666 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
4:73854037:C:AA77D0.959
4:73853890:T:AC70S0.937
4:73853891:G:CC70S0.937
4:73854063:T:AC86S0.928
4:73854064:G:CC86S0.928
4:73853818:T:AC46S0.923
4:73853819:G:CC46S0.923
4:73853890:T:CC70R0.916
4:73853812:T:AC44S0.907
4:73853813:G:CC44S0.907
4:73854063:T:CC86R0.907
4:73854067:T:CL87S0.900
4:73853891:G:AC70Y0.878
4:73854065:C:GC86W0.877
4:73853906:T:CL75P0.875
4:73853812:T:CC44R0.874
4:73854064:G:AC86Y0.863
4:73853890:T:GC70G0.862
4:73853818:T:CC46R0.858
4:73854052:G:TG82V0.858
4:73853892:C:GC70W0.854
4:73853855:T:CI58T0.842
4:73853855:T:GI58S0.840
4:73854036:G:CA77P0.839
4:73853819:G:AC46Y0.835
4:73854063:T:GC86G0.812
4:73853904:A:CQ74H0.803
4:73853904:A:TQ74H0.803
4:73853855:T:AI58N0.799
4:73853891:G:TC70F0.788

dbSNP variants (sampled 300 via entrez): RS1000494433 (4:73854948 A>C,G), RS1000633386 (4:73854704 C>T), RS1003176557 (4:73852422 T>C), RS1004772460 (4:73854296 T>C), RS1005140536 (4:73851858 C>A,T), RS1005188210 (4:73854836 A>G), RS1006300099 (4:73851328 C>G,T), RS1006743023 (4:73851533 A>G), RS1007156677 (4:73854381 T>A,C), RS1008121288 (4:73851763 G>A), RS1009262247 (4:73852787 G>T), RS1009314584 (4:73852465 G>A), RS1011900158 (4:73852066 G>T), RS1014763759 (4:73854303 A>G), RS1014813902 (4:73851863 T>C)

Disease associations

OMIM: gene MIM:173461 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

1 associations (top):

StudyTraitp-value
GCST001725_78Inflammatory bowel disease3.000000e-08

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

ChemicalActions (top 5)PubMed papers
Asian ginsengdecreases reaction, increases expression1
triphenyl phosphateaffects expression1
trichostatin Aincreases expression1
arseniteincreases methylation1
chromium hexavalent ionincreases expression1
CGP 52608increases reaction, affects binding1
thrombin receptor-activating peptide SFLLRNPNDKYdecreases reaction, increases secretion1
K 7174increases expression1
Air Pollutantsdecreases expression, increases abundance1
Aspirindecreases reaction, increases secretion1
Benzo(a)pyreneincreases expression1
Diethylhexyl Phthalatedecreases reaction, increases expression1
Malathiondecreases expression1
Tamoxifenaffects expression1
Tobacco Smoke Pollutiondecreases expression1
Valproic Acidincreases expression1
Cyclosporinedecreases expression1
beta-Naphthoflavoneincreases expression1
Particulate Matterdecreases expression, increases abundance1
Coal Ashincreases expression1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.