FBXO9

gene
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Also known as FBX9NY-REN-57

Summary

FBXO9 (F-box protein 9, HGNC:13588) is a protein-coding gene on chromosome 6p12.1, encoding F-box only protein 9 (Q9UK97). Substrate recognition component of a SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins and plays a role in several biological processes such as cell cycle, cell proliferat….

This gene encodes a member of the F-box protein family which is characterized by an approximately 40 amino acid motif, the F-box. The F-box proteins constitute one of the four subunits of the ubiquitin protein ligase complex called SCFs (SKP1-cullin-F-box), which function in phosphorylation-dependent ubiquitination. The F-box proteins are divided into 3 classes: Fbws containing WD-40 domains, Fbls containing leucine-rich repeats, and Fbxs containing either different protein-protein interaction modules or no recognizable motifs. The protein encoded by this gene belongs to the Fbxs class. Alternative splicing of this gene generates at least 3 transcript variants diverging at the 5’ terminus.

Source: NCBI Gene 26268 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 60 total
  • MANE Select transcript: NM_033480

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:13588
Approved symbolFBXO9
NameF-box protein 9
Location6p12.1
Locus typegene with protein product
StatusApproved
AliasesFBX9, NY-REN-57
Ensembl geneENSG00000112146
Ensembl biotypeprotein_coding
OMIM609091
Entrez26268

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 8 protein_coding, 4 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000244426, ENST00000323557, ENST00000370939, ENST00000459845, ENST00000461222, ENST00000468481, ENST00000473318, ENST00000473337, ENST00000474457, ENST00000480463, ENST00000484436, ENST00000484812, ENST00000498744

RefSeq mRNA: 3 — MANE Select: NM_033480 NM_012347, NM_033480, NM_033481

CCDS: CCDS55022, CCDS55023, CCDS55024

Canonical transcript exons

ENST00000323557 — 13 exons

ExonStartEnd
ENSE000007565215309273453092824
ENSE000007565245309346653093561
ENSE000014365705306540453065792
ENSE000015343015309772253100873
ENSE000034634925307879953078898
ENSE000035194305307648653076543
ENSE000035493815307348153073639
ENSE000035694935307105753071143
ENSE000036805215309242953092547
ENSE000036834365308250453082618
ENSE000037066775309388553093978
ENSE000037097975309551353095664
ENSE000037861945308096853081098

Expression profiles

Bgee: expression breadth ubiquitous, 301 present calls, max score 99.29.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 45.5270 / max 822.0264, expressed in 1824 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
6824842.27491823
682492.39101341
682500.6744357
682470.186769

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
endothelial cellCL:000011599.29gold quality
Brodmann (1909) area 23UBERON:001355499.18gold quality
middle temporal gyrusUBERON:000277199.12gold quality
right adrenal glandUBERON:000123398.92gold quality
right adrenal gland cortexUBERON:003582798.87gold quality
esophagus squamous epitheliumUBERON:000692098.86gold quality
secondary oocyteCL:000065598.85gold quality
left adrenal glandUBERON:000123498.83gold quality
trabecular bone tissueUBERON:000248398.81gold quality
left adrenal gland cortexUBERON:003582598.81gold quality
adrenal cortexUBERON:000123598.76gold quality
tibiaUBERON:000097998.66gold quality
parotid glandUBERON:000183198.66gold quality
Brodmann (1909) area 10UBERON:001354198.63gold quality
germinal epithelium of ovaryUBERON:000130498.45gold quality
adrenal glandUBERON:000236998.42gold quality
ponsUBERON:000098898.35gold quality
lateral nuclear group of thalamusUBERON:000273698.28gold quality
squamous epitheliumUBERON:000691498.17gold quality
choroid plexus epitheliumUBERON:000391198.06gold quality
visceral pleuraUBERON:000240197.97gold quality
renal glomerulusUBERON:000007497.96gold quality
parietal pleuraUBERON:000240097.90gold quality
pleuraUBERON:000097797.88gold quality
gingival epitheliumUBERON:000194997.87gold quality
body of pancreasUBERON:000115097.86gold quality
metanephric glomerulusUBERON:000473697.84gold quality
nephron tubuleUBERON:000123197.83gold quality
palpebral conjunctivaUBERON:000181297.78gold quality
occipital lobeUBERON:000202197.78gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 3.

ExperimentMarker?Max mean expression
E-MTAB-10042yes23.62
E-MTAB-9221yes13.02
E-MTAB-6678no4.06
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

122 targeting FBXO9, 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-190A-3P100.0080.355520
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-5692A100.0074.406850
HSA-MIR-8485100.0077.574731
HSA-MIR-340-5P100.0072.504437
HSA-MIR-4476100.0068.182030
HSA-MIR-6876-5P100.0067.682126
HSA-MIR-548AW99.9972.573559
HSA-MIR-33A-5P99.9968.621055
HSA-MIR-33B-5P99.9968.581062
HSA-MIR-150-5P99.9966.691976
HSA-MIR-1213699.9872.815713
HSA-MIR-480399.9871.993117
HSA-MIR-548P99.9872.253784
HSA-LET-7F-2-3P99.9870.982588
HSA-MIR-1185-1-3P99.9871.042593
HSA-MIR-1185-2-3P99.9871.042593
HSA-MIR-477599.9875.006394
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-60799.9773.625593
HSA-MIR-1229-3P99.9766.49906
HSA-MIR-302C-5P99.9772.563642
HSA-MIR-314899.9775.066478
HSA-MIR-6778-3P99.9667.292693
HSA-MIR-1468-3P99.9672.743797
HSA-MIR-548AA99.9670.643753
HSA-MIR-548AP-3P99.9670.643753
HSA-MIR-548T-3P99.9670.643753
HSA-MIR-4760-3P99.9370.502385

Literature-anchored findings (GeneRIF, showing 2)

  • ICK and FBX9 are divergently transcribed from a bidirectional promoter that is GC-rich and contains a CpG island. (PMID:20459822)
  • F-box only protein 9 and its role in cancer. (PMID:35025031)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriofbxo9ENSDARG00000011055
mus_musculusFbxo9ENSMUSG00000001366
rattus_norvegicusFbxo9ENSRNOG00000008214
drosophila_melanogasterCG5961FBGN0038056

Protein

Protein identifiers

F-box only protein 9Q9UK97 (reviewed: Q9UK97)

Alternative names: Cross-immune reaction antigen 1, Renal carcinoma antigen NY-REN-57

All UniProt accessions (6): Q9UK97, C9IY65, C9J4V1, C9JDZ9, H7C4H6, V9GZ74

UniProt curated annotations — full annotation on UniProt →

Function. Substrate recognition component of a SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins and plays a role in several biological processes such as cell cycle, cell proliferation, or maintenance of chromosome stability. Ubiquitinates mTORC1-bound TTI1 and TELO2 when they are phosphorylated by CK2 following growth factor deprivation, leading to their degradation. In contrast, does not mediate ubiquitination of TTI1 and TELO2 when they are part of the mTORC2 complex. As a consequence, mTORC1 is inactivated to restrain cell growth and protein translation, while mTORC2 is the activated due to the relief of feedback inhibition by mTORC1. Plays a role in maintaining epithelial cell survival by regulating the turn-over of chromatin modulator PRMT4 through ubiquitination and degradation by the proteasomal pathway. Regulates also PPARgamma stability by facilitating PPARgamma/PPARG ubiquitination and thereby plays a role in adipocyte differentiation.

Subunit / interactions. Part of the SCF (SKP1-CUL1-F-box) E3 ubiquitin-protein ligase complex SCF(FBXO9) composed of CUL1, SKP1, RBX1 and FBXO9. Interacts with TTI1 and TELO2; when TTI1 and TELO2 are phosphorylated by CK2.

Subcellular location. Cytoplasm.

Pathway. Protein modification; protein ubiquitination.

Miscellaneous. Overexpressed in multiple myeloma leading to constitutive activation of the PI(3)K/mTORC2/Akt pathway to promote survival.

Isoforms (3)

UniProt IDNamesCanonical?
Q9UK97-11yes
Q9UK97-22
Q9UK97-33

RefSeq proteins (3): NP_036479, NP_258441, NP_258442 (=MANE)

Domains & families (InterPro)

IDNameType
IPR001810F-box_domDomain
IPR036047F-box-like_dom_sfHomologous_superfamily
IPR036181MIT_dom_sfHomologous_superfamily
IPR045464Hrt3/FBXO9_CDomain

Pfam: PF12937, PF19270

UniProt features (8 total): splice variant 2, chain 1, repeat 1, domain 1, region of interest 1, compositionally biased region 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9UK97-F178.070.44

Functional residue map

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

Post-translational modifications (1): 136

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

IDPathway
R-HSA-8951664Neddylation
R-HSA-983168Antigen processing: Ubiquitination & Proteasome degradation

MSigDB gene sets: 196 (showing top): E2F_Q4_01, BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, TGCGCANK_UNKNOWN, REACTOME_ADAPTIVE_IMMUNE_SYSTEM, REACTOME_CLASS_I_MHC_MEDIATED_ANTIGEN_PROCESSING_PRESENTATION, REACTOME_ANTIGEN_PROCESSING_UBIQUITINATION_PROTEASOME_DEGRADATION, MORF_HDAC1, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GGCNKCCATNK_UNKNOWN, BILD_HRAS_ONCOGENIC_SIGNATURE, chr6p12, GOBP_DEFENSE_RESPONSE_TO_OTHER_ORGANISM, YY1_02, BLALOCK_ALZHEIMERS_DISEASE_UP, MORF_CTBP1

GO Biological Process (9): protein ubiquitination (GO:0016567), SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146), regulation of TOR signaling (GO:0032006), proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161), innate immune response (GO:0045087), fat cell differentiation (GO:0045444), protein K48-linked ubiquitination (GO:0070936), apoptotic process (GO:0006915), positive regulation of epithelial cell apoptotic process (GO:1904037)

GO Molecular Function (3): ubiquitin-protein transferase activity (GO:0004842), ubiquitin-like ligase-substrate adaptor activity (GO:1990756), protein binding (GO:0005515)

GO Cellular Component (4): ubiquitin ligase complex (GO:0000151), cytoplasm (GO:0005737), cytosol (GO:0005829), SCF ubiquitin ligase complex (GO:0019005)

Reactome top-level categories

Rollup of top-2 pathways:

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

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure2
protein modification by small protein conjugation1
proteasome-mediated ubiquitin-dependent protein catabolic process1
TOR signaling1
regulation of intracellular signal transduction1
ubiquitin-dependent protein catabolic process1
proteasomal protein catabolic process1
immune response1
defense response to symbiont1
cell differentiation1
protein polyubiquitination1
programmed cell death1
apoptotic signaling pathway1
execution phase of apoptosis1
positive regulation of apoptotic process1
epithelial cell apoptotic process1
regulation of epithelial cell apoptotic process1
ubiquitin-like protein transferase activity1
enzyme-substrate adaptor activity1
binding1
intracellular protein-containing complex1
transferase complex1
intracellular anatomical structure1
cytoplasm1
cullin-RING ubiquitin ligase complex1

Protein interactions and networks

STRING

1058 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
FBXO9CUL1Q13616828
FBXO9SKP1P34991816
FBXO9FBXO4Q9UKT5639
FBXO9TTI1O43156579
FBXO9FBXO11Q86XK2572
FBXO9FBXL3Q9UKT7517
FBXO9FBXO45P0C2W1494
FBXO9RSPRY1Q96DX4490
FBXO9UBE2G1P62253479
FBXO9FBXW8Q8N3Y1477
FBXO9CCDC106Q9BWC9475
FBXO9FBH1Q8NFZ0469
FBXO9FBXO28Q9NVF7468
FBXO9TELO2Q9Y4R8453
FBXO9FBXO10Q9UK96449

IntAct

39 interactions, top by confidence:

ABTypeScore
FBXO9SKP1psi-mi:“MI:0915”(physical association)0.740
SKP1MYCBP2psi-mi:“MI:0914”(association)0.640
FBXO9TELO2psi-mi:“MI:0915”(physical association)0.610
FBXO9TTI1psi-mi:“MI:0914”(association)0.610
FBXO9TTI1psi-mi:“MI:0915”(physical association)0.610
CUL1FBXO21psi-mi:“MI:0914”(association)0.600
GFOD1PER1psi-mi:“MI:0914”(association)0.530
RICTORTTI1psi-mi:“MI:0914”(association)0.460
RPTORTTI1psi-mi:“MI:0914”(association)0.460
SKP1FBXO9psi-mi:“MI:0915”(physical association)0.400
FBXO9EEF2psi-mi:“MI:0915”(physical association)0.400
FBXO9HSP90AB1psi-mi:“MI:0915”(physical association)0.400
SPG11FBXO9psi-mi:“MI:0915”(physical association)0.370
Xpo1IFT56psi-mi:“MI:0914”(association)0.350
FBXO9MTORpsi-mi:“MI:0914”(association)0.350
CUL1LGALS8psi-mi:“MI:0914”(association)0.350
COPS5FBLL1psi-mi:“MI:0914”(association)0.350
Mpsi-mi:“MI:0914”(association)0.350
ATG16L1ESYT2psi-mi:“MI:0914”(association)0.350
S100PPLEKHG3psi-mi:“MI:0914”(association)0.350
SKP1BHLHE40psi-mi:“MI:0914”(association)0.350
RBX1OBSL1psi-mi:“MI:0914”(association)0.350

BioGRID (36): FBXO9 (Affinity Capture-MS), SKP1 (Affinity Capture-Western), FBXO9 (Affinity Capture-MS), FBXO9 (Affinity Capture-MS), FBXO9 (Affinity Capture-MS), FBXO9 (Affinity Capture-MS), EEF2 (Affinity Capture-MS), FBXO9 (Affinity Capture-MS), FBXO9 (Affinity Capture-MS), FBXO9 (Affinity Capture-Western), SKP1 (Two-hybrid), FBXO9 (Affinity Capture-MS), FBXO9 (Affinity Capture-MS), FBXO9 (Affinity Capture-MS), EEF2 (Affinity Capture-MS)

ESM2 similar proteins: A0A1L8GLK3, A0A974CYQ5, A2AHJ4, A5WW08, D2HNY3, D2HWM5, E7F6T8, F1ND48, O75717, O88907, O95071, P59328, Q28DL4, Q3TLR7, Q4V837, Q58WW2, Q5E9J6, Q5FWP4, Q5NVC7, Q5R9B8, Q5RF77, Q5RGA4, Q5RHI5, Q5ZLG9, Q62671, Q66JG1, Q6AXK4, Q6DDH2, Q6NVE8, Q6P1W0, Q6P256, Q6PCD5, Q6PJI9, Q6RI45, Q80TP3, Q80U93, Q810L3, Q8C0M0, Q8CBW4, Q8CIK8

Diamond homologs: F6Y9J3, O74531, Q3ZBT2, Q5U2X1, Q6P3K3, Q8BK06, Q9UK97, Q9XI00

SIGNOR signaling

3 interactions.

AEffectBMechanism
FBXO9“down-regulates quantity by destabilization”TELO2binding
FBXO9“down-regulates quantity by destabilization”TTI1binding
FBXO9“down-regulates activity”“Cullin 1-RBX1-Skp1”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 37 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
Neddylation610.9×5e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance38
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2494 predictions. Top by Δscore:

VariantEffectΔscore
6:53061594:A:ACdonor_gain1.0000
6:53061595:C:CCdonor_gain1.0000
6:53061595:CTGG:Cdonor_gain1.0000
6:53065670:C:Gdonor_gain1.0000
6:53071055:A:AGacceptor_gain1.0000
6:53071056:G:GTacceptor_gain1.0000
6:53071056:GGC:Gacceptor_gain1.0000
6:53071056:GGCA:Gacceptor_gain1.0000
6:53073476:CATA:Cacceptor_loss1.0000
6:53073478:TA:Tacceptor_loss1.0000
6:53073479:A:AGacceptor_gain1.0000
6:53073479:A:ATacceptor_loss1.0000
6:53073480:G:GAacceptor_loss1.0000
6:53073480:G:GGacceptor_gain1.0000
6:53073480:GGC:Gacceptor_gain1.0000
6:53073480:GGCAC:Gacceptor_gain1.0000
6:53073626:C:Tdonor_gain1.0000
6:53073634:GAAAA:Gdonor_gain1.0000
6:53073640:T:TGdonor_gain1.0000
6:53073644:G:GGdonor_gain1.0000
6:53076481:TATAG:Tacceptor_loss1.0000
6:53076483:TAGGC:Tacceptor_loss1.0000
6:53078797:A:AGacceptor_gain1.0000
6:53078798:G:GGacceptor_gain1.0000
6:53078895:GCTA:Gdonor_gain1.0000
6:53078899:G:GGdonor_gain1.0000
6:53080966:A:AGacceptor_gain1.0000
6:53080967:G:GAacceptor_gain1.0000
6:53080967:GC:Gacceptor_gain1.0000
6:53080967:GCATT:Gacceptor_gain1.0000

AlphaMissense

2896 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
6:53076543:G:CA113P1.000
6:53078814:G:CR118P1.000
6:53078819:G:CA120P1.000
6:53078820:C:AA120D1.000
6:53095633:T:AW402R1.000
6:53095633:T:CW402R1.000
6:53076498:T:CF98L0.999
6:53076499:T:CF98S0.999
6:53076500:C:AF98L0.999
6:53076500:C:GF98L0.999
6:53076507:G:CA101P0.999
6:53076508:C:AA101E0.999
6:53078799:C:AA113D0.999
6:53078810:T:GY117D0.999
6:53078829:T:CL123P0.999
6:53078841:T:AI127K0.999
6:53092547:G:CG268R0.999
6:53092734:G:AG268D0.999
6:53092763:C:AR278S0.999
6:53092764:G:CR278P0.999
6:53092769:G:AG280R0.999
6:53092769:G:CG280R0.999
6:53092824:G:TR298M0.999
6:53093534:T:AV321D0.999
6:53093904:G:CG337R0.999
6:53093905:G:AG337D0.999
6:53095589:T:CL387P0.999
6:53095628:T:AL400H0.999
6:53095628:T:CL400P0.999
6:53095645:T:CS406P0.999

dbSNP variants (sampled 300 via entrez): RS1000044763 (6:53056742 A>G), RS1000073603 (6:53063899 C>T), RS1000095883 (6:53080432 C>A,T), RS1000109191 (6:53087362 A>G), RS1000426908 (6:53080725 C>T), RS1000501944 (6:53083159 T>C), RS1000532624 (6:53083662 T>C), RS1000540836 (6:53075657 T>C), RS1000774213 (6:53090512 CAAAG>C), RS1000774305 (6:53095886 T>C), RS1000833318 (6:53068523 TAA>T), RS1000867745 (6:53089942 A>C,G), RS1000875990 (6:53090256 A>G), RS1001201150 (6:53069081 C>A), RS1001209789 (6:53057282 A>G)

Disease associations

OMIM: gene MIM:609091 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

StudyTraitp-value
GCST003181_5Staphylococcus aureus nasal carriage (intermittent)9.000000e-06
GCST90000047_120Age at first sexual intercourse5.000000e-10

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0007758intermittent Staphylococcus aureus carrier status
EFO:0009749age at first sexual intercourse measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

48 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, decreases expression, decreases methylation, increases expression6
mercuric bromidedecreases expression, affects cotreatment2
entinostatdecreases expression, affects cotreatment2
Formaldehydedecreases expression, increases expression2
Phenylmercuric Acetateaffects cotreatment, affects expression2
Silicon Dioxidedecreases expression2
Tretinoinincreases expression2
p-Chloromercuribenzoic Acidaffects cotreatment, decreases expression2
aristolochic acid Iincreases expression1
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamidedecreases expression1
methylmercuric chloridedecreases expression1
bisphenol Adecreases expression, increases methylation1
lead acetatedecreases expression1
trichostatin Adecreases expression, increases expression1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
sodium arsenitedecreases expression1
cobaltous chlorideincreases expression1
nickel sulfatedecreases expression1
CGP 52608affects binding, increases reaction1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression, affects expression1
abrinedecreases expression1
dorsomorphinaffects expression, affects cotreatment, decreases expression1
Resveratrolaffects cotreatment, increases expression1
Sunitinibincreases expression1
Leflunomidedecreases expression1
Panobinostataffects cotreatment, decreases expression1
Acetaminophendecreases expression1
Cisplatindecreases reaction, increases expression1
Dinitrochlorobenzenedecreases expression1
Ethyl Methanesulfonateincreases 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.