FBXW4

gene
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Also known as Fbw4dactylin

Summary

FBXW4 (F-box and WD repeat domain containing 4, HGNC:10847) is a protein-coding gene on chromosome 10q24.32, encoding F-box/WD repeat-containing protein 4 (P57775). Probably recognizes and binds to some phosphorylated proteins and promotes their ubiquitination and degradation.

This gene is a member of the F-box/WD-40 gene family, which recruit specific target proteins through their WD-40 protein-protein binding domains for ubiquitin mediated degradation. In mouse, a highly similar protein is thought to be responsible for maintaining the apical ectodermal ridge of developing limb buds; disruption of the mouse gene results in the absence of central digits, underdeveloped or absent metacarpal/metatarsal bones and syndactyly. This phenotype is remarkably similar to split hand-split foot malformation in humans, a clinically heterogeneous condition with a variety of modes of transmission. An autosomal recessive form has been mapped to the chromosomal region where this gene is located, and complex rearrangements involving duplications of this gene and others have been associated with the condition. A pseudogene of this locus has been mapped to one of the introns of the BCR gene on chromosome 22.

Source: NCBI Gene 6468 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): split hand-foot malformation 3 (Limited, GenCC)
  • GWAS associations: 1
  • Clinical variants (ClinVar): 147 total — 1 pathogenic
  • Phenotypes (HPO): 8
  • Dosage sensitivity (ClinGen): haploinsufficiency no evidence, triplosensitivity no evidence
  • MANE Select transcript: NM_022039

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:10847
Approved symbolFBXW4
NameF-box and WD repeat domain containing 4
Location10q24.32
Locus typegene with protein product
StatusApproved
AliasesFbw4, dactylin
Ensembl geneENSG00000107829
Ensembl biotypeprotein_coding
OMIM608071
Entrez6468

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 9 protein_coding, 3 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000331272, ENST00000457105, ENST00000470093, ENST00000482428, ENST00000489578, ENST00000664783, ENST00000919944, ENST00000919945, ENST00000919946, ENST00000945850, ENST00000945851, ENST00000945852, ENST00000945853

RefSeq mRNA: 2 — MANE Select: NM_022039 NM_001323541, NM_022039

CCDS: CCDS31271

Canonical transcript exons

ENST00000331272 — 9 exons

ExonStartEnd
ENSE00001333590101694381101695170
ENSE00002290987101624745101624810
ENSE00003465345101612337101612477
ENSE00003474993101611628101611769
ENSE00003477983101673488101673673
ENSE00003541215101672915101673047
ENSE00003637643101676341101676436
ENSE00003666781101610666101611410
ENSE00003678265101667886101667980

Expression profiles

Bgee: expression breadth ubiquitous, 281 present calls, max score 97.99.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 7.7908 / max 215.6569, expressed in 1707 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
1110947.31711681
1110920.4737188

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
C1 segment of cervical spinal cordUBERON:000646997.99gold quality
spinal cordUBERON:000224097.67gold quality
apex of heartUBERON:000209897.05gold quality
lower esophagus muscularis layerUBERON:003583396.42gold quality
lower esophagusUBERON:001347396.41gold quality
amygdalaUBERON:000187696.34gold quality
putamenUBERON:000187496.23gold quality
inferior vagus X ganglionUBERON:000536396.19gold quality
muscle layer of sigmoid colonUBERON:003580596.06gold quality
gastrocnemiusUBERON:000138896.05gold quality
hindlimb stylopod muscleUBERON:000425295.93gold quality
esophagogastric junction muscularis propriaUBERON:003584195.85gold quality
muscle of legUBERON:000138395.77gold quality
subthalamic nucleusUBERON:000190695.74gold quality
mucosa of stomachUBERON:000119995.64gold quality
ventral tegmental areaUBERON:000269195.64gold quality
substantia nigraUBERON:000203895.58gold quality
right lungUBERON:000216795.52gold quality
sural nerveUBERON:001548895.50gold quality
midbrainUBERON:000189195.46gold quality
nucleus accumbensUBERON:000188295.45gold quality
skin of legUBERON:000151195.43gold quality
fundus of stomachUBERON:000116095.42gold quality
saphenous veinUBERON:000731895.38gold quality
nippleUBERON:000203095.24gold quality
heart left ventricleUBERON:000208495.18gold quality
pituitary glandUBERON:000000795.17gold quality
adenohypophysisUBERON:000219695.15gold quality
right atrium auricular regionUBERON:000663195.07gold quality
hypothalamusUBERON:000189895.03gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

30 targeting FBXW4, 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-4673100.0066.641490
HSA-MIR-3646100.0073.565283
HSA-MIR-366299.9973.825684
HSA-MIR-4645-5P99.9865.811284
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-6783-3P99.8967.922059
HSA-MIR-345-3P99.8970.231421
HSA-MIR-1343-3P99.8966.781815
HSA-MIR-449299.8768.253611
HSA-MIR-3151-5P99.8663.831069
HSA-MIR-431999.7669.832586
HSA-MIR-2681-5P99.7567.641655
HSA-MIR-29B-2-5P99.6768.981726
HSA-MIR-670-5P99.6769.941565
HSA-MIR-486-3P99.5166.821901
HSA-MIR-608099.4369.43373
HSA-MIR-330-3P99.4169.952521
HSA-MIR-125A-5P99.3670.591640
HSA-MIR-125B-5P99.3670.361662
HSA-MIR-6840-3P98.6865.951923
HSA-MIR-6764-3P98.4467.641153
HSA-MIR-6824-3P98.4467.621154
HSA-MIR-4646-5P97.7066.841692
HSA-MIR-393697.6464.47732
HSA-MIR-805797.6466.54897
HSA-MIR-66597.6065.641781
HSA-MIR-4732-3P97.1565.45881
HSA-MIR-6822-3P96.6066.06680
HSA-MIR-7109-3P94.2367.19743

Functional genomics

ClinGen dosage: haploinsufficiency 0 (no evidence), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 5)

  • a complex rearrangement associated with a approximately 0.5 Mb tandem duplication ion containing a disrupted extra copy of the DACTYLIN gene and the entire LBX1 and beta-TRCP genes. (PMID:12913067)
  • results indicate that genomic rearrangement of SHFM3 is rare among non-syndromic SHFM patients and emphasize the importance of screening for genomic rearrangements even in sporadic cases of SHFM (PMID:16235095)
  • Genomic rearrangements involving the SHFM3 locus at chromosome 10q24 is associated with syndromic and non-syndromic split-hand/foot malformation (PMID:16761290)
  • biochemical characterization of the novel F-box and WD40 containing protein, FBXW4 (PMID:23658844)
  • CircFBXW4 Suppresses Colorectal Cancer Progression by Regulating the MiR-338-5p/SLC5A7 Axis. (PMID:38461489)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriofbxw4ENSDARG00000033551
mus_musculusFbxw4ENSMUSG00000040913
rattus_norvegicusFbxw4ENSRNOG00000046211
drosophila_melanogasterCG33969FBGN0053969

Protein

Protein identifiers

F-box/WD repeat-containing protein 4P57775 (reviewed: P57775)

Alternative names: Dactylin, F-box and WD-40 domain-containing protein 4

All UniProt accessions (3): P57775, A0A384P5X9, A0A5F9UQ55

UniProt curated annotations — full annotation on UniProt →

Function. Probably recognizes and binds to some phosphorylated proteins and promotes their ubiquitination and degradation. Likely to be involved in key signaling pathways crucial for normal limb development. May participate in Wnt signaling.

Subunit / interactions. Part of a SCF (SKP1-cullin-F-box) protein ligase complex. Interacts with POUF51.

Tissue specificity. Expressed in brain, kidney, lung and liver.

Disease relevance. Split-hand/foot malformation 3 (SHFM3) [MIM:246560] A limb malformation involving the central rays of the autopod and presenting with syndactyly, median clefts of the hands and feet, and aplasia and/or hypoplasia of the phalanges, metacarpals, and metatarsals. Some patients have been found to have intellectual disability, ectodermal and craniofacial findings, and orofacial clefting. The disease is caused by variants affecting the gene represented in this entry.

RefSeq proteins (2): NP_001310470, NP_071322* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001680WD40_rptRepeat
IPR001810F-box_domDomain
IPR015943WD40/YVTN_repeat-like_dom_sfHomologous_superfamily
IPR036047F-box-like_dom_sfHomologous_superfamily
IPR036322WD40_repeat_dom_sfHomologous_superfamily
IPR052301SCF_F-box/WD-repeatFamily

Pfam: PF00400, PF12937

UniProt features (9 total): repeat 6, chain 1, domain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P57775-F190.910.79

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

IDPathway
R-HSA-390471Association of TriC/CCT with target proteins during biosynthesis
R-HSA-8951664Neddylation
R-HSA-983168Antigen processing: Ubiquitination & Proteasome degradation

MSigDB gene sets: 218 (showing top): PAX4_01, REACTOME_ADAPTIVE_IMMUNE_SYSTEM, MODULE_255, RORA1_01, REACTOME_CLASS_I_MHC_MEDIATED_ANTIGEN_PROCESSING_PRESENTATION, REACTOME_ANTIGEN_PROCESSING_UBIQUITINATION_PROTEASOME_DEGRADATION, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, MODULE_317, TGACCTY_ERR1_Q2, CEBPB_01, TCF4_Q5, KOYAMA_SEMA3B_TARGETS_UP, BLALOCK_ALZHEIMERS_DISEASE_UP

GO Biological Process (8): ubiquitin-dependent protein catabolic process (GO:0006511), Wnt signaling pathway (GO:0016055), embryonic limb morphogenesis (GO:0030326), SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146), positive regulation of mesenchymal cell proliferation (GO:0002053), embryonic digit morphogenesis (GO:0042733), cartilage development (GO:0051216), limb development (GO:0060173)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (3): ubiquitin ligase complex (GO:0000151), cytosol (GO:0005829), SCF ubiquitin ligase complex (GO:0019005)

Reactome top-level categories

Rollup of top-3 pathways:

CategoryPathways
Chaperonin-mediated protein folding1
Post-translational protein modification1
Class I MHC mediated antigen processing & presentation1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
protein ubiquitination1
modification-dependent protein catabolic process1
cell surface receptor signaling pathway1
limb morphogenesis1
embryonic appendage morphogenesis1
proteasome-mediated ubiquitin-dependent protein catabolic process1
positive regulation of cell population proliferation1
mesenchymal cell proliferation1
regulation of mesenchymal cell proliferation1
embryonic limb morphogenesis1
embryonic morphogenesis1
skeletal system development1
animal organ development1
connective tissue development1
appendage development1
binding1
intracellular protein-containing complex1
transferase complex1
cytoplasm1
cellular anatomical structure1
cullin-RING ubiquitin ligase complex1

Protein interactions and networks

STRING

658 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
FBXW4LBX1P52954894
FBXW4POLLQ9UGP5874
FBXW4BTRCQ9Y297794
FBXW4SEM1Q6ZVN7738
FBXW4SUFUQ9UMX1684
FBXW4FBXW2Q9UKT8612
FBXW4FBXW5Q969U6598
FBXW4TLX1P31314577
FBXW4FBXW8Q8N3Y1569
FBXW4FGF8P55075558
FBXW4DLX6P56179552
FBXW4DLX5P56178541
FBXW4FBXW9Q5XUX1532
FBXW4SKP1P34991520
FBXW4FBXW12Q6X9E4488

IntAct

24 interactions, top by confidence:

ABTypeScore
COPS6RHOBTB1psi-mi:“MI:0914”(association)0.730
SKP1FBXW4psi-mi:“MI:0915”(physical association)0.670
PRKNFBXW4psi-mi:“MI:0915”(physical association)0.560
FBXW4TXNDC9psi-mi:“MI:0914”(association)0.530
PFDN2CDC40psi-mi:“MI:0914”(association)0.530
FBXW4TCP1psi-mi:“MI:0914”(association)0.530
SKP1FBXW4psi-mi:“MI:0915”(physical association)0.400
CUL1FBXW4psi-mi:“MI:0915”(physical association)0.400
FBXW4CDC37psi-mi:“MI:0915”(physical association)0.370
ECSITFBXW4psi-mi:“MI:0915”(physical association)0.370
MAST1FBXW4psi-mi:“MI:0915”(physical association)0.370
FBXW4RNF32psi-mi:“MI:0915”(physical association)0.370
SLX4IPRNASEH1psi-mi:“MI:0914”(association)0.350
CUL4ADDX39Apsi-mi:“MI:0914”(association)0.350
ANKRD39UBA6psi-mi:“MI:0914”(association)0.350
SKP1BHLHE40psi-mi:“MI:0914”(association)0.350
SKP1NDC80psi-mi:“MI:0914”(association)0.350
LCORFBXW4psi-mi:“MI:0915”(physical association)0.000

BioGRID (107): CUL1 (Affinity Capture-Western), TCP1 (Affinity Capture-MS), CCT3 (Affinity Capture-MS), CCT7 (Affinity Capture-MS), CCT4 (Affinity Capture-MS), CCT6B (Affinity Capture-MS), CCT6A (Affinity Capture-MS), CCT2 (Affinity Capture-MS), PDCL3 (Affinity Capture-MS), CCT8 (Affinity Capture-MS), CCT5 (Affinity Capture-MS), PFDN5 (Affinity Capture-MS), PDRG1 (Affinity Capture-MS), TXNDC9 (Affinity Capture-MS), PDCL (Affinity Capture-MS)

ESM2 similar proteins: A2AA28, A4FV42, A4FV98, A6NDG6, D3YWP0, D3ZVU9, O15315, O35719, O70277, O75382, O94759, P21964, P57775, P81799, Q2TBS1, Q3UGX3, Q4R3I0, Q5E9V4, Q5H879, Q5RJL2, Q5SUV1, Q6DC64, Q7Z624, Q86WI3, Q86XA0, Q8BNV1, Q8C436, Q8CIW5, Q8IZ69, Q8N8L6, Q8N9F0, Q8VCX6, Q8WXB1, Q96AZ1, Q96FB5, Q96RR1, Q9BQD7, Q9BRQ3, Q9BUU2, Q9CQL0

Diamond homologs: A1C7E4, A1CBP8, A1DDL6, A1DHW6, A2QCU8, A2R3Z3, A4RJV3, A6ZQL5, A6ZZZ8, A7ETB3, A7THX0, A7TNS8, A8PTE4, A8Q2R5, B0XTS1, B6GZA1, B6Q4Z5, B8M7Q5, B8NGT5, C5FP68, D4AM37, D4D8P3, O42937, P0CS44, P0CS45, P25387, P36130, P47025, P57775, Q00659, Q01277, Q0CJD8, Q0CY32, Q0U2T3, Q1DIW7, Q2H139, Q2KJJ5, Q2U5Z8, Q2UFN8, Q4P8R5

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.

GO biological processes:

GO termPartnersFoldFDR
protein ubiquitination510.9×5e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance97
Likely benign22
Benign8

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
625658GRCh37/hg19 10q24.31-24.32(chr10:102822575-103558868)Pathogenic

SpliceAI

1767 predictions. Top by Δscore:

VariantEffectΔscore
10:101611621:CACTT:Cdonor_loss1.0000
10:101611622:ACTTA:Adonor_loss1.0000
10:101611623:CTTA:Cdonor_loss1.0000
10:101611624:TTACG:Tdonor_loss1.0000
10:101611625:TAC:Tdonor_loss1.0000
10:101611626:A:ACdonor_gain1.0000
10:101611626:A:Cdonor_loss1.0000
10:101611626:ACGTG:Adonor_gain1.0000
10:101611627:C:CGdonor_gain1.0000
10:101611627:CG:Cdonor_gain1.0000
10:101611627:CGT:Cdonor_gain1.0000
10:101611627:CGTG:Cdonor_gain1.0000
10:101611627:CGTGC:Cdonor_gain1.0000
10:101611765:ATTTC:Aacceptor_gain1.0000
10:101611766:TTTC:Tacceptor_gain1.0000
10:101611767:TTC:Tacceptor_gain1.0000
10:101611768:TC:Tacceptor_gain1.0000
10:101611769:CC:Cacceptor_gain1.0000
10:101611770:C:CAacceptor_loss1.0000
10:101611770:C:CCacceptor_gain1.0000
10:101611775:C:CTacceptor_gain1.0000
10:101611775:C:Tacceptor_gain1.0000
10:101611776:A:Tacceptor_gain1.0000
10:101612335:A:ACdonor_gain1.0000
10:101612336:C:CCdonor_gain1.0000
10:101612475:CCA:Cacceptor_gain1.0000
10:101612476:CA:Cacceptor_gain1.0000
10:101612476:CAC:Cacceptor_gain1.0000
10:101612478:C:CCacceptor_gain1.0000
10:101670993:C:Adonor_gain1.0000

AlphaMissense

3640 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
10:101624797:C:AG262W1.000
10:101672939:A:CS217R1.000
10:101672939:A:TS217R1.000
10:101672941:T:GS217R1.000
10:101612364:C:GR317P0.999
10:101624796:C:TG262E0.999
10:101611655:C:AW364C0.998
10:101611655:C:GW364C0.998
10:101611657:A:GW364R0.998
10:101611657:A:TW364R0.998
10:101611686:C:TG354D0.998
10:101611753:A:GW332R0.998
10:101611753:A:TW332R0.998
10:101612359:A:GW319R0.998
10:101612359:A:TW319R0.998
10:101624758:A:GW275R0.998
10:101624758:A:TW275R0.998
10:101624797:C:GG262R0.998
10:101624797:C:TG262R0.998
10:101672935:A:GS219P0.998
10:101672937:C:TG218D0.998
10:101672943:A:TV216E0.998
10:101673496:A:CS178R0.998
10:101673496:A:TS178R0.998
10:101673498:T:GS178R0.998
10:101611687:C:GG354R0.997
10:101612376:T:AD313V0.997
10:101667916:A:TV247D0.997
10:101667923:C:GD245H0.997
10:101611337:G:TA398D0.996

dbSNP variants (sampled 300 via entrez): RS1000066042 (10:101628379 C>A), RS1000077450 (10:101628734 C>T), RS1000099322 (10:101649661 A>G), RS1000125423 (10:101677604 A>C), RS1000147375 (10:101655212 G>T), RS1000168739 (10:101662735 C>T), RS1000221409 (10:101662548 T>A), RS1000274341 (10:101613905 G>A), RS1000368716 (10:101614333 C>G), RS1000387131 (10:101662839 C>G), RS1000508028 (10:101691178 T>G), RS1000519903 (10:101677196 A>G,T), RS1000520719 (10:101641054 C>T), RS1000551576 (10:101661238 T>A), RS1000565203 (10:101682703 G>T)

Disease associations

OMIM: gene MIM:608071 | disease phenotypes: MIM:246560

GenCC curated gene-disease

DiseaseClassificationInheritance
split hand-foot malformation 3LimitedAutosomal dominant

Mondo (1): split hand-foot malformation 3 (MONDO:0009525)

Orphanet (1): Distal limb deficiencies-micrognathia syndrome (Orphanet:1307)

HPO phenotypes

8 total (8 of 8 shown, HPO-id order):

HPOTerm
HP:0000407Sensorineural hearing impairment
HP:0000526Aniridia
HP:0001171Split hand
HP:0001839Split foot
HP:0004050Absent hand
HP:0004058Hand monodactyly
HP:0006101Finger syndactyly
HP:0012165Oligodactyly

GWAS associations

1 associations (top):

StudyTraitp-value
GCST006979_603Heel bone mineral density5.000000e-10

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0009270heel bone mineral density

MeSH disease descriptors (1)

DescriptorNameTree numbers
C565437Limb Deficiencies, Distal, with Micrognathia (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression, decreases expression, affects expression7
Cisplatindecreases expression, increases expression2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
1,6-hexamethylene diisocyanateincreases methylation1
sodium arseniteincreases expression1
butyraldehydedecreases expression1
di-n-butylphosphoric acidaffects expression1
perfluorooctane sulfonic acidincreases expression1
2-palmitoylglycerolincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
belinostatdecreases expression1
abrineincreases expression1
dorsomorphinaffects cotreatment, decreases expression1
Vorinostatdecreases expression1
Acetaminophenincreases expression1
Air Pollutantsincreases abundance, increases expression1
Carbamazepineaffects expression1
Dichlorodiphenyl Dichloroethylenedecreases expression1
Hydralazineaffects cotreatment, increases expression1
Silicon Dioxidedecreases expression1
Thiramincreases expression1
Aflatoxin B1decreases methylation1
Okadaic Aciddecreases expression1
Particulate Matterincreases abundance, increases expression1

Clinical trials (associated diseases)

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