FBXO11

gene
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Also known as FBX11UBR6

Summary

FBXO11 (F-box protein 11, HGNC:13590) is a protein-coding gene on chromosome 2p16.3, encoding F-box only protein 11 (Q86XK2). 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, such as DTL/CDT2, BCL6, SNAI1 and PRDM1/BLIMP1. It is a selective cancer dependency (DepMap: 15.3% of cell lines).

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 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. It can function as an arginine methyltransferase that symmetrically dimethylates arginine residues, and it acts as an adaptor protein to mediate the neddylation of p53, which leads to the suppression of p53 function. This gene is known to be down-regulated in melanocytes from patients with vitiligo, a skin disorder that results in depigmentation. Polymorphisms in this gene are associated with chronic otitis media with effusion and recurrent otitis media (COME/ROM), a hearing loss disorder, and the knockout of the homologous mouse gene results in the deaf mouse mutant Jeff (Jf), a single gene model of otitis media. Alternatively spliced transcript variants encoding distinct isoforms have been identified for this gene.

Source: NCBI Gene 80204 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): intellectual developmental disorder with dysmorphic facies and behavioral abnormalities (Definitive, GenCC)
  • GWAS associations: 15
  • Clinical variants (ClinVar): 1,240 total — 54 pathogenic, 93 likely-pathogenic
  • Phenotypes (HPO): 123
  • Druggable target: yes
  • Cancer driver (intOGen): loss-of-function (tumor-suppressor-like) across 3 cancer types
  • Cancer dependency (DepMap): dependent in 15.3% of screened cell lines
  • MANE Select transcript: NM_001190274

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:13590
Approved symbolFBXO11
NameF-box protein 11
Location2p16.3
Locus typegene with protein product
StatusApproved
AliasesFBX11, UBR6
Ensembl geneENSG00000138081
Ensembl biotypeprotein_coding
OMIM607871
Entrez80204

Gene structure

Transcript identifiers

Ensembl transcripts: 21 — 9 protein_coding, 8 retained_intron, 3 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000402508, ENST00000403359, ENST00000405808, ENST00000424163, ENST00000434234, ENST00000465204, ENST00000470899, ENST00000480038, ENST00000492225, ENST00000493962, ENST00000681999, ENST00000682451, ENST00000682484, ENST00000682975, ENST00000683894, ENST00000684085, ENST00000684523, ENST00000684712, ENST00000895446, ENST00000945015, ENST00000945016

RefSeq mRNA: 3 — MANE Select: NM_001190274 NM_001190274, NM_001374325, NM_025133

CCDS: CCDS1837, CCDS54357

Canonical transcript exons

ENST00000403359 — 23 exons

ExonStartEnd
ENSE000015195224790548947906498
ENSE000016439084781379147813867
ENSE000017895944781877947818864
ENSE000034971864783478847834871
ENSE000035089844780915847809266
ENSE000035273744781323447813377
ENSE000035296874783941947839500
ENSE000035299144780832947808427
ENSE000035361084782221847822303
ENSE000035434044783257247832678
ENSE000035524844781031647810426
ENSE000035537504783964247839769
ENSE000035613204783457947834711
ENSE000035632584783296447833070
ENSE000035802964783276947832880
ENSE000035875264781895647819078
ENSE000036036654783885947839003
ENSE000036385664782036247820456
ENSE000036424724782314347823360
ENSE000036463944783234947832486
ENSE000036475404783587247836001
ENSE000036663494780960047809707
ENSE000039024794780692047808247

Expression profiles

Bgee: expression breadth ubiquitous, 287 present calls, max score 97.92.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 32.7701 / max 300.8850, expressed in 1814 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
2824113.63001757
282408.17511735
282397.68801747
282361.7034876
282371.3595690
282380.2141119

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
cortical plateUBERON:000534397.92gold quality
ganglionic eminenceUBERON:000402397.19gold quality
ventricular zoneUBERON:000305396.48gold quality
cerebellar cortexUBERON:000212996.12gold quality
cerebellar hemisphereUBERON:000224596.12gold quality
cerebellumUBERON:000203795.99gold quality
mucosa of paranasal sinusUBERON:000503095.98gold quality
calcaneal tendonUBERON:000370195.96gold quality
right hemisphere of cerebellumUBERON:001489095.82gold quality
superficial temporal arteryUBERON:000161495.00gold quality
ovaryUBERON:000099294.81gold quality
left ovaryUBERON:000211994.77gold quality
trabecular bone tissueUBERON:000248394.74gold quality
monocyteCL:000057694.60gold quality
mononuclear cellCL:000084294.54gold quality
corpus callosumUBERON:000233694.53gold quality
endometriumUBERON:000129594.41gold quality
leukocyteCL:000073894.39gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047394.38gold quality
right ovaryUBERON:000211894.38gold quality
primary visual cortexUBERON:000243694.21gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451194.15gold quality
tendonUBERON:000004394.03gold quality
embryoUBERON:000092293.94gold quality
body of uterusUBERON:000985393.93gold quality
right lungUBERON:000216793.92gold quality
occipital lobeUBERON:000202193.91gold quality
prefrontal cortexUBERON:000045193.87gold quality
dorsolateral prefrontal cortexUBERON:000983493.81gold quality
right testisUBERON:000453493.66gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes5.64

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): GATA3

miRNA regulators (miRDB)

168 targeting FBXO11, 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-4747-5P100.0067.902681
HSA-MIR-5196-5P100.0067.982761
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-1252-5P100.0069.802774
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-3064-3P100.0070.091254
HSA-MIR-4682100.0068.891258
HSA-MIR-4533100.0069.482758
HSA-MIR-6833-3P100.0070.633197
HSA-MIR-4768-5P100.0069.492861
HSA-MIR-4262100.0073.263931
HSA-MIR-4789-3P99.9970.752484
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-1212199.9966.64255
HSA-MIR-513B-5P99.9969.962150
HSA-MIR-806899.9873.852376
HSA-MIR-4715-3P99.9866.03670
HSA-MIR-548AN99.9770.912817
HSA-MIR-60799.9773.625593
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345
HSA-MIR-568899.9673.234504
HSA-MIR-495-3P99.9672.814197
HSA-MIR-551B-5P99.9671.283493
HSA-MIR-9-3P99.9670.882068
HSA-MIR-365899.9673.874379
HSA-MIR-302E99.9670.742669
HSA-MIR-1250-3P99.9670.044038
HSA-MIR-3912-5P99.9566.11925

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 15.3% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 34)

  • A type II protein arginine methyltransferase that forms asymmetric dimethylarginine modifications in proteins. (PMID:16487488)
  • The FBXO11 gene is the human homologue of the gene mutated in the novel deaf mouse mutant jeff (Jf), a single gene model of otitis media. FBXO11 gene for association with chronic otitis media with effusion. (PMID:16847180)
  • FBXO11 promotes the Neddylation (NEDD8) of p53 and inhibits its transcriptional activity (PMID:17098746)
  • Results support the notion that FBXO11 plays an important role in regulating proliferation and apoptosis of melanocytes, and functional export of tyrosinase from ER in vitiligo melanocytes. (PMID:20514423)
  • FBXO11 has a lower expression in skin lesion tissues than in normal tissues from vitiligo patients. (PMID:20646433)
  • these data provide strong evidence for FBXO11 as a susceptibility gene for severe OM. (PMID:21293382)
  • A molecular mechanism controlling BCL6 stability–mutations and deletions in FBXO11 contribute to lymphomagenesis through BCL6 stabilization (PMID:22113614)
  • The functional interaction between FBXO11 and CDT2 is evolutionary conserved from worms to humans and plays an important role in regulating the timing of cell-cycle exit. (PMID:23478441)
  • Migration of epithelial cells is stimulated by CRL1(FBXO11)-mediated downregulation of Cdt2 and the consequent stabilization of Set8. (PMID:23478445)
  • TGF-beta signaling promotes exit from the cell cycle and cellular migration through cullin cross-regulation: SCF-FBXO11 turns off CRL4-Cdt2. (PMID:23892434)
  • study defined eight additional recurrently mutated genes in SMZL; these genes are CREBBP, CBFA2T3, AMOTL1, FAT4, FBXO11, PLA2G4D, TRRAP and USH2A. (PMID:24349473)
  • The PKD1-FBXO11-SNAIL axis is a mechanism of posttranslational regulation of epithelial-mesenchymal transition and cancer metastasis. (PMID:25203322)
  • Our results identify FBXO11 as a novel miR-21 target gene, and demonstrate that the oncogenic miRNA miR-21 decreases the expression of FBXO11, which normally acts as a tumor suppressor, and thereby promotes tumorigenesis. (PMID:25589783)
  • FBXO11 is a direct target of miR-621 in breast cancer cells. (PMID:25867061)
  • UBR3/6 regulate cardiomyocyte Nav 1.5 channel protein levels via the ubiquitin-proteasome pathway. (PMID:26059563)
  • siRNA-mediated knockdown of FBXO11 facilitated HIF-1alpha expression in various cancer cells and HIF-1alpha-driven gene expressions, but the FBXO10 knockdown did not. (PMID:26187670)
  • Chronic otitis media is associated with the TGIF1 and FBXO11 loci that are involved in TGF-beta signaling, suggesting this pathway may be important in the transition from acute to chronic middle ear inflammation, and a potential molecular target. (PMID:28970529)
  • Understanding of the functions of FBXO11. (PMID:29278851)
  • High expression of FBXO11 predicted a poor survival of hepatocellular carcinoma patients. (PMID:29518611)
  • we confirm deleterious de novo mutations in FBXO11 as a cause of Intellectual disability and start the delineation of the associated clinical picture which may also comprise postnatal microcephaly or borderline small head size and behavioural anomalies. (PMID:29796876)
  • Eight missense variants distributed throughout FBXO11. (PMID:30057029)
  • 24 individuals with a de novo disease-causing variant in, or partial deletion of, the F-box only protein 11 gene, are reported. (PMID:30679813)
  • FBXO11 expression was closely related to renal cell carcinoma malignancy and poor prognosis, indicating its potential as a prognostic marker as well as a therapeutic target for renal cell carcinoma. (PMID:31159774)
  • Long non-coding RNA NNT-AS1 regulates proliferation, apoptosis, inflammation and airway remodeling of chronic obstructive pulmonary disease via targeting miR-582-5p/FBXO11 axis. (PMID:32768929)
  • The first familial case of inherited intellectual developmental disorder with dysmorphic facies and behavioral abnormalities (IDDFBA) with a novel FBXO11 variant. (PMID:32902151)
  • FBXO11 is a candidate tumor suppressor in the leukemic transformation of myelodysplastic syndrome. (PMID:33024076)
  • FBXO11-mediated proteolysis of BAHD1 relieves PRC2-dependent transcriptional repression in erythropoiesis. (PMID:33156908)
  • De novo missense variants in FBXO11 alter its protein expression and subcellular localization. (PMID:34505148)
  • Frequent mutations of FBXO11 highlight BCL6 as a therapeutic target in Burkitt lymphoma. (PMID:34625792)
  • Ultrasound-targeted microbubble destruction-mediated silencing of FBXO11 suppresses development of pancreatic cancer. (PMID:35437704)
  • FBXO11 amplifies type I interferon signaling to exert antiviral effects by facilitating the assemble of TRAF3-TBK1-IRF3 complex. (PMID:36897010)
  • FBXO11 governs macrophage cell death and inflammation in response to bacterial toxins. (PMID:36977592)
  • FBXO11 constitutes a major negative regulator of MHC class II through ubiquitin-dependent proteasomal degradation of CIITA. (PMID:37279268)
  • FBXO11 variants are associated with intellectual disability and variable clinical manifestation in Chinese affected individuals. (PMID:38740982)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
mus_musculusFbxo11ENSMUSG00000005371
rattus_norvegicusFbxo11ENSRNOG00000016396
drosophila_melanogasterFBXO11FBGN0037760
caenorhabditis_elegansWBGENE00001089
caenorhabditis_elegansWBGENE00015268

Paralogs (1): FBXO10 (ENSG00000147912)

Protein

Protein identifiers

F-box only protein 11Q86XK2 (reviewed: Q86XK2)

Alternative names: Protein arginine N-methyltransferase 9, Vitiligo-associated protein 1

All UniProt accessions (6): Q86XK2, A0A804HK63, B5MCV6, C9IYF0, E7EP88, H0YAV3

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, such as DTL/CDT2, BCL6, SNAI1 and PRDM1/BLIMP1. The SCF(FBXO11) complex mediates ubiquitination and degradation of BCL6, thereby playing a role in the germinal center B-cells terminal differentiation toward memory B-cells and plasma cells. The SCF(FBXO11) complex also mediates ubiquitination and degradation of DTL, an important step for the regulation of TGF-beta signaling, cell migration and the timing of the cell-cycle progression and exit. The SCF(FBXO11) complex also catalyzes ubiquitination and degradation of GSK3B-phosphorylated SNAI1. Binds to and neddylates phosphorylated p53/TP53, inhibiting its transcriptional activity. Plays a role in the regulatiom of erythropoiesis but not myelopoiesis or megakaryopoiesis. Mechanistically, activates erythroid genes by mediating the degradation of BAHD1, a heterochromatin-associated protein that recruits corepressors to H3K27me3 marks. Participates in macrophage cell death and inflammation in response to bacterial toxins by regulating the expression of complement 5a receptor 1/C5AR1 and IL-1beta. Acts as a critical regulator to determine the level of MHC-II by mediating the recognition of degron at the P/S/T domain of CIITA leading to its ubiquitination and subsequent degradation via the proteasome. Participates in the antiviral repsonse by initiating the activation of TBK1-IRF3-IFN-I axis. Mediates the ‘Lys-63’-linked ubiquitination of TRAF3 to strengthen the interaction between TRAF3 and TBK1.

Subunit / interactions. Component of the SCF(FBXO11) complex consisting of CUL1, RBX1, SKP1 and FBXO11. Interacts with CIITA.

Subcellular location. Nucleus. Chromosome.

Tissue specificity. Isoform 5 is expressed in keratinocytes, fibroblasts and melanocytes.

Disease relevance. Intellectual developmental disorder with dysmorphic facies and behavioral abnormalities (IDDFBA) [MIM:618089] An autosomal dominant developmental disorder with variable manifestations and onset in infancy or first years of life. Clinical features include intellectual disability, speech delay, hyperkinetic disorder, hyperactivity, seizures, pre- and postnatal growth retardation, microcephaly, and facial dysmorphism. The disease is caused by variants affecting the gene represented in this entry. Defects in FBXO11 may be a cause of diffuse large B-cell lymphoma by allowing the accumulation of BCL6, an oncoprotein that has a critical role in lymphomas.

Pathway. Protein modification; protein ubiquitination.

Isoforms (6)

UniProt IDNamesCanonical?
Q86XK2-11yes
Q86XK2-22
Q86XK2-66
Q86XK2-33
Q86XK2-44
Q86XK2-55

RefSeq proteins (3): NP_001177203, NP_001361254, NP_079409 (=MANE)

Domains & families (InterPro)

IDNameType
IPR001810F-box_domDomain
IPR003126Znf_UBRDomain
IPR006626PbH1Repeat
IPR006633Carb-bd_sugar_hydrolysis-domDomain
IPR011050Pectin_lyase_fold/virulenceHomologous_superfamily
IPR012334Pectin_lyas_foldHomologous_superfamily
IPR022441Para_beta_helix_rpt-2Repeat
IPR036047F-box-like_dom_sfHomologous_superfamily
IPR039448Beta_helixDomain
IPR047504FBXO11_UBR-boxDomain
IPR047505F-box_FBXO11Domain
IPR051550SCF-Subunits/Alg-EpimerasesFamily

Pfam: PF02207, PF12937, PF13229

UniProt features (65 total): repeat 19, sequence variant 19, splice variant 8, compositionally biased region 4, sequence conflict 4, strand 3, helix 2, chain 1, domain 1, zinc finger region 1, region of interest 1, mutagenesis site 1, turn 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
5VMDX-RAY DIFFRACTION2.2

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q86XK2-F182.650.69

Functional residue map

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

Mutagenesis-validated functional residues (1):

PositionPhenotype
575greatly reduced ability to bind prdm1 and reduced proteolysis of prdm1.

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

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

MSigDB gene sets: 528 (showing top): RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, REACTOME_ADAPTIVE_IMMUNE_SYSTEM, MODULE_255, REACTOME_CLASS_I_MHC_MEDIATED_ANTIGEN_PROCESSING_PRESENTATION, REACTOME_ANTIGEN_PROCESSING_UBIQUITINATION_PROTEASOME_DEGRADATION, GOBP_SENSORY_PERCEPTION_OF_MECHANICAL_STIMULUS, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, MODULE_317, ATGCAGT_MIR217, GOBP_NEGATIVE_REGULATION_OF_EPITHELIAL_TO_MESENCHYMAL_TRANSITION, FOXD3_01, HERNANDEZ_ABERRANT_MITOSIS_BY_DOCETACEL_2NM_DN, RODRIGUES_NTN1_TARGETS_UP, CTAGGAA_MIR384, OSWALD_HEMATOPOIETIC_STEM_CELL_IN_COLLAGEN_GEL_UP

GO Biological Process (7): ubiquitin-dependent protein catabolic process (GO:0006511), sensory perception of sound (GO:0007605), negative regulation of epithelial to mesenchymal transition (GO:0010719), protein ubiquitination (GO:0016567), regulation of apoptotic process (GO:0042981), proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161), epithelial to mesenchymal transition (GO:0001837)

GO Molecular Function (6): ubiquitin-protein transferase activity (GO:0004842), zinc ion binding (GO:0008270), protein-arginine N-methyltransferase activity (GO:0016274), ubiquitin-like ligase-substrate adaptor activity (GO:1990756), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (7): ubiquitin ligase complex (GO:0000151), nucleus (GO:0005634), nucleoplasm (GO:0005654), chromosome (GO:0005694), nucleolus (GO:0005730), cytoplasm (GO:0005737), cytosol (GO:0005829)

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 structure3
nuclear lumen2
intracellular membraneless organelle2
protein ubiquitination1
modification-dependent protein catabolic process1
sensory perception of mechanical stimulus1
epithelial to mesenchymal transition1
regulation of epithelial to mesenchymal transition1
negative regulation of cell differentiation1
negative regulation of multicellular organismal process1
protein modification by small protein conjugation1
apoptotic process1
regulation of programmed cell death1
ubiquitin-dependent protein catabolic process1
proteasomal protein catabolic process1
mesenchymal cell differentiation1
ubiquitin-like protein transferase activity1
transition metal ion binding1
protein methyltransferase activity1
arginine N-methyltransferase activity1
enzyme-substrate adaptor activity1
binding1
cation binding1
intracellular protein-containing complex1
transferase complex1
intracellular membrane-bounded organelle1
intracellular anatomical structure1
cytoplasm1

Protein interactions and networks

STRING

1606 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
FBXO11SKP1P34991857
FBXO11CUL1Q13616827
FBXO11MSH6P52701788
FBXO11FBXL14Q8N1E6773
FBXO11DTLQ9NZJ0726
FBXO11CUL2Q13617650
FBXO11FBXO45P0C2W1647
FBXO11FBXL5Q9UKA1605
FBXO11PRKD1Q15139589
FBXO11FBXO4Q9UKT5586
FBXO11TP53P04637581
FBXO11FBXO9Q9UK97572
FBXO11GSK3BP49841556
FBXO11UBR3Q6ZT12554
FBXO11UBR7Q8N806529

IntAct

159 interactions, top by confidence:

ABTypeScore
FBXO11SKP1psi-mi:“MI:0915”(physical association)0.930
SKP1FBXO11psi-mi:“MI:0915”(physical association)0.930
CDK13CCNKpsi-mi:“MI:0914”(association)0.830
KHDRBS2KHDRBS3psi-mi:“MI:0914”(association)0.800
CUL4BCOPS2psi-mi:“MI:0914”(association)0.790
COPS6RHOBTB1psi-mi:“MI:0914”(association)0.730
PRPF3PRPF4psi-mi:“MI:0914”(association)0.730
CTBP1CBX4psi-mi:“MI:0914”(association)0.700
SKP1FBXO11psi-mi:“MI:0915”(physical association)0.680
FBXO11SKP1psi-mi:“MI:0915”(physical association)0.680
FBXO11SKP1psi-mi:“MI:0914”(association)0.680
TP53FBXO11psi-mi:“MI:0915”(physical association)0.650
FBXO11TP53psi-mi:“MI:0407”(direct interaction)0.650
FBXO11TP53psi-mi:“MI:0915”(physical association)0.650
FBXO11TP53psi-mi:“MI:0567”(neddylation reaction)0.650
BCL6FBXO11psi-mi:“MI:0407”(direct interaction)0.650
BCL6FBXO11psi-mi:“MI:0915”(physical association)0.650
FBXO11BCL6psi-mi:“MI:0914”(association)0.650
FBXO11RBX1psi-mi:“MI:0914”(association)0.640
SKP1MYCBP2psi-mi:“MI:0914”(association)0.640

BioGRID (235): FBXO11 (Affinity Capture-MS), FBXO11 (Affinity Capture-Western), FBXO11 (Two-hybrid), FBXO11 (Affinity Capture-MS), FBXO11 (Affinity Capture-MS), FBXO11 (Affinity Capture-MS), FBXO11 (Affinity Capture-MS), FBXO11 (Affinity Capture-MS), FBXO11 (Affinity Capture-MS), FBXO11 (Affinity Capture-MS), FBXO11 (Affinity Capture-MS), FBXO11 (Affinity Capture-MS), FBXO11 (Affinity Capture-MS), FBXO11 (Affinity Capture-MS), FBXO11 (Affinity Capture-MS)

ESM2 similar proteins: A0A286ZK88, A1L1L6, A7MB28, A8WGF4, B8BJ39, D0G6S1, O00399, O54956, P11029, P11497, Q13085, Q148G7, Q28007, Q28943, Q28DR7, Q2HJF8, Q2RAK2, Q4R4U1, Q502J7, Q5FVD6, Q5R559, Q5R5F8, Q5R7D8, Q5R8Q7, Q5SWU9, Q5ZIT8, Q5ZM73, Q6AYR2, Q6NVC5, Q6NWV3, Q6P1X5, Q6PC62, Q7TPD1, Q7TSL3, Q86XK2, Q8BG51, Q8BH44, Q8C176, Q8CHR6, Q8IWZ6

Diamond homologs: A2AN08, O95071, P51592, Q29L39, Q2TL32, Q5T4S7, Q62671, Q7TPD1, Q7TSL3, Q80TP3, Q86XK2, Q94251, Q9VLT5, A2VE78, C0HAC0, Q2YDQ5, Q3T0J1, Q58DG6, Q5R6E1, Q5XGI3, Q6INS1, Q8C2S5, Q8IX29, Q96IG2, Q9CZV8, Q9QZH7, Q9QZM9, Q9UKA1, B9G2A8, Q9LG11, Q9SRU2, A1L271, C4JPW9, C5GVJ9, C5JD40, D4AM37, D4D8P3, O08653, O14775, P0CS44

SIGNOR signaling

4 interactions.

AEffectBMechanism
FBXO11down-regulatesTP53neddylation
FBXO11down-regulatesBCL6binding
FBXO11down-regulatesDTLbinding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 187 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
DNA Damage Recognition in GG-NER818.1×9e-06
Recognition of DNA damage by PCNA-containing replication complex515.1×1e-03
FBXL7 down-regulates AURKA during mitotic entry and in early mitosis713.8×9e-05
Formation of TC-NER Pre-Incision Complex813.4×3e-05
GSK3B-mediated proteasomal degradation of PD-L1(CD274)713.2×1e-04
GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2611.8×9e-04
Regulation of TP53 Degradation511.6×2e-03
Regulation of RUNX2 expression and activity811.5×7e-05

GO biological processes:

GO termPartnersFoldFDR
protein neddylation520.6×2e-03
positive regulation of fibroblast proliferation813.9×1e-04

Disease & clinical

Cancer significance

From intOGen — cancer-driver classification: loss-of-function (tumor-suppressor-like) across 3 cancer types — BL, MLYM, NHL.

Clinical variants and AI predictions

ClinVar

1240 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic54
Likely pathogenic93
Uncertain significance418
Likely benign533
Benign57

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1076339NC_000002.11:g.(?47635530)(48035526_?)delPathogenic
1200593NM_001190274.2(FBXO11):c.2744_2745del (p.Ser915fs)Pathogenic
1305954NM_001190274.2(FBXO11):c.1364G>A (p.Arg455His)Pathogenic
1329862NM_001190274.2(FBXO11):c.1797+1G>APathogenic
1329864NM_001190274.2(FBXO11):c.2338+1G>APathogenic
1329865NM_001190274.2(FBXO11):c.588-2A>GPathogenic
1329866NM_001190274.2(FBXO11):c.1696del (p.Ile566fs)Pathogenic
1329869NM_001190274.2(FBXO11):c.500TCT[1] (p.Phe168del)Pathogenic
1329960NM_001190274.2(FBXO11):c.2592_2593del (p.Ile864fs)Pathogenic
1329962NM_001190274.2(FBXO11):c.2570_2572del (p.Asn857del)Pathogenic
1329963NM_001190274.2(FBXO11):c.2520_2521del (p.Ser841fs)Pathogenic
1329964NM_001190274.2(FBXO11):c.552del (p.Lys184fs)Pathogenic
1329965NM_001190274.2(FBXO11):c.2568_2572del (p.Asn857fs)Pathogenic
1329966NM_001190274.2(FBXO11):c.1798-1G>APathogenic
1329972NM_001190274.2(FBXO11):c.668del (p.Pro223fs)Pathogenic
1329974NM_001190274.2(FBXO11):c.1543_1557del (p.Phe515_Lys519del)Pathogenic
1329975NM_001190274.2(FBXO11):c.2392AAC[1] (p.Asn799del)Pathogenic
1329977NM_001190274.2(FBXO11):c.2748_2749del (p.Pro917fs)Pathogenic
1454648NC_000002.11:g.(?47948073)(48035379_?)delPathogenic
1708215NM_001190274.2(FBXO11):c.2732_2738del (p.Thr911fs)Pathogenic
1711499NM_001190274.2(FBXO11):c.1537G>T (p.Gly513Ter)Pathogenic
1804626NM_001190274.2(FBXO11):c.2339-2A>GPathogenic
2134559NM_001190274.2(FBXO11):c.2736dup (p.Tyr913fs)Pathogenic
2288541NM_001190274.2(FBXO11):c.592C>T (p.Arg198Ter)Pathogenic
2756341NM_001190274.2(FBXO11):c.442+3A>GPathogenic
3247085NC_000002.11:g.(?48030569)(48034835_?)delPathogenic
3251130NM_001190274.2(FBXO11):c.2327del (p.Gly776fs)Pathogenic
3364840NM_001190274.2(FBXO11):c.2168GAA[1] (p.Arg724del)Pathogenic
3377013NM_001190274.2(FBXO11):c.1646GAG[1] (p.Gly550del)Pathogenic
3393036NM_001190274.2(FBXO11):c.2138G>A (p.Trp713Ter)Pathogenic

SpliceAI

3871 predictions. Top by Δscore:

VariantEffectΔscore
2:47790918:T:TAacceptor_gain1.0000
2:47790925:A:AGacceptor_gain1.0000
2:47790926:G:GGacceptor_gain1.0000
2:47790926:GTT:Gacceptor_gain1.0000
2:47796049:G:GTdonor_gain1.0000
2:47796061:G:GTdonor_gain1.0000
2:47803682:ACAG:Adonor_loss1.0000
2:47803683:CAGG:Cdonor_loss1.0000
2:47803684:AGGTA:Adonor_loss1.0000
2:47803685:GG:Gdonor_loss1.0000
2:47803686:G:GCdonor_loss1.0000
2:47803687:T:Adonor_loss1.0000
2:47804905:CACA:Cacceptor_loss1.0000
2:47804907:CA:Cacceptor_loss1.0000
2:47804908:AG:Aacceptor_gain1.0000
2:47804908:AGGCT:Aacceptor_gain1.0000
2:47804909:GG:Gacceptor_gain1.0000
2:47804909:GGCT:Gacceptor_gain1.0000
2:47804909:GGCTG:Gacceptor_gain1.0000
2:47805023:GTCAG:Gdonor_gain1.0000
2:47805024:TCAGG:Tdonor_loss1.0000
2:47805025:CAGGT:Cdonor_loss1.0000
2:47805026:AGG:Adonor_loss1.0000
2:47805027:GGT:Gdonor_loss1.0000
2:47805028:G:Tdonor_loss1.0000
2:47805029:T:Gdonor_loss1.0000
2:47805614:TAAG:Tacceptor_loss1.0000
2:47805615:A:AGacceptor_gain1.0000
2:47805615:AAG:Aacceptor_gain1.0000
2:47805615:AAGGT:Aacceptor_gain1.0000

AlphaMissense

6177 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
2:47808205:A:CC899W1.000
2:47808206:C:GC899S1.000
2:47808206:C:TC899Y1.000
2:47808207:A:GC899R1.000
2:47808207:A:TC899S1.000
2:47808230:C:TG891D1.000
2:47808231:C:GG891R1.000
2:47808232:A:CC890W1.000
2:47808233:C:AC890F1.000
2:47808233:C:GC890S1.000
2:47808233:C:TC890Y1.000
2:47808234:A:GC890R1.000
2:47808234:A:TC890S1.000
2:47808236:T:AD889V1.000
2:47808236:T:CD889G1.000
2:47808236:T:GD889A1.000
2:47808237:C:GD889H1.000
2:47808238:A:CC888W1.000
2:47808239:C:AC888F1.000
2:47808239:C:GC888S1.000
2:47808239:C:TC888Y1.000
2:47808240:A:CC888G1.000
2:47808240:A:GC888R1.000
2:47808240:A:TC888S1.000
2:47808241:G:CF887L1.000
2:47808241:G:TF887L1.000
2:47808242:A:CF887C1.000
2:47808242:A:GF887S1.000
2:47808243:A:GF887L1.000
2:47808244:A:CF886L1.000

dbSNP variants (sampled 300 via entrez): RS1000037456 (2:47874935 G>A,C,T), RS1000058174 (2:47900446 G>A), RS1000067880 (2:47878369 T>C,G), RS1000096709 (2:47876371 T>G), RS1000128385 (2:47904927 CG>C,CGG,CGGGG), RS1000140122 (2:47829611 G>C,T), RS1000147193 (2:47824080 A>G), RS1000147911 (2:47859887 C>A,T), RS1000228757 (2:47838504 A>C,T), RS1000229528 (2:47887660 A>G), RS1000258482 (2:47825772 T>C), RS1000283553 (2:47887393 G>A), RS1000291383 (2:47825952 A>G), RS1000299434 (2:47900655 T>A,C), RS1000302168 (2:47887848 T>A)

Disease associations

OMIM: gene MIM:607871 | disease phenotypes: MIM:618089, MIM:614325, MIM:614350

GenCC curated gene-disease

DiseaseClassificationInheritance
intellectual developmental disorder with dysmorphic facies and behavioral abnormalitiesDefinitiveAutosomal dominant

Mondo (11): intellectual disability (MONDO:0001071), intellectual developmental disorder with dysmorphic facies and behavioral abnormalities (MONDO:0060760), neurodevelopmental disorder (MONDO:0700092), Pitt-Hopkins-like syndrome 2 (MONDO:0013690), Lynch syndrome 5 (MONDO:0013710), Lynch syndrome (MONDO:0005835), hereditary neoplastic syndrome (MONDO:0015356), breast cancer (MONDO:0007254), endometrial carcinoma (MONDO:0002447), papillary carcinoma of the corpus uteri (MONDO:0016268), obesity disorder (MONDO:0011122)

Orphanet (8): OBSOLETE: Pitt-Hopkins-like syndrome (Orphanet:221150), NRXN1-related severe neurodevelopmental disorder-motor stereotypies-chronic constipation-sleep-wake cycle disturbance (Orphanet:600663), Lynch syndrome (Orphanet:144), Inherited cancer-predisposing syndrome (Orphanet:140162), Serous carcinoma of the corpus uteri (Orphanet:213726), Obesity due to melanocortin 4 receptor deficiency (Orphanet:71529), NON RARE IN EUROPE: Unexplained intellectual disability (Orphanet:319658), NON RARE IN EUROPE: Non rare obesity (Orphanet:521399)

HPO phenotypes

123 total (30 of 123 shown, HPO-id order):

HPOTerm
HP:0000006Autosomal dominant inheritance
HP:0000028Cryptorchidism
HP:0000098Tall stature
HP:0000154Wide mouth
HP:0000160Narrow mouth
HP:0000175Cleft palate
HP:0000179Thick lower lip vermilion
HP:0000193Bifid uvula
HP:0000218High palate
HP:0000219Thin upper lip vermilion
HP:0000232Everted lower lip vermilion
HP:0000248Brachycephaly
HP:0000252Microcephaly
HP:0000256Macrocephaly
HP:0000276Long face
HP:0000278Retrognathia
HP:0000280Coarse facial features
HP:0000286Epicanthus
HP:0000293Full cheeks
HP:0000303Mandibular prognathia
HP:0000307Pointed chin
HP:0000316Hypertelorism
HP:0000319Smooth philtrum
HP:0000322Short philtrum
HP:0000325Triangular face
HP:0000337Broad forehead
HP:0000343Long philtrum
HP:0000347Micrognathia
HP:0000348High forehead
HP:0000358Posteriorly rotated ears

GWAS associations

15 associations (top):

StudyTraitp-value
GCST001851_12Schizophrenia6.000000e-06
GCST003831_4Asthma3.000000e-06
GCST004861_38Itch intensity from mosquito bite4.000000e-07
GCST004861_40Itch intensity from mosquito bite3.000000e-08
GCST004862_174Itch intensity from mosquito bite adjusted by bite size2.000000e-07
GCST004865_58Itch intensity from mosquito bite adjusted by bite size7.000000e-06
GCST004865_59Itch intensity from mosquito bite adjusted by bite size8.000000e-08
GCST006976_66Macular thickness5.000000e-10
GCST007576_189Chronotype2.000000e-08
GCST010002_391Refractive error6.000000e-09
GCST010320_53PR interval7.000000e-08
GCST010321_190PR interval5.000000e-09
GCST011617_33Cortical surface area2.000000e-16
GCST90000025_742Appendicular lean mass8.000000e-13
GCST90011899_3Aspartate aminotransferase levels5.000000e-12

EFO canonical traits (6, from GWAS)

EFO IDTrait name
EFO:0008377mosquito bite reaction itch intensity measurement
EFO:0008378mosquito bite reaction size measurement
EFO:0008328chronotype measurement
EFO:0004462PR interval
EFO:0004980appendicular lean mass
EFO:0004736aspartate aminotransferase measurement

MeSH disease descriptors (4)

DescriptorNameTree numbers
D008607Intellectual DisabilityC10.597.606.360; C23.888.592.604.646; F01.700.687; F03.625.539
D009386Neoplastic Syndromes, HereditaryC04.700; C16.320.700
D065886Neurodevelopmental DisordersF03.625
C563456Colorectal Cancer, Hereditary Nonpolyposis, Type 5 (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL4879484 (SINGLE PROTEIN)

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

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: enzyme — 2.1.1.- Protein arginine N-methyltransferases

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, decreases expression4
graphene oxideincreases expression2
Estradiolaffects expression, affects cotreatment, increases expression2
Formaldehydedecreases expression2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxidedecreases expression2
Cadmium Chloridedecreases expression2
aristolochic acid Idecreases expression1
GSK-J4increases expression1
sodium arsenitedecreases expression, increases abundance1
di-n-butylphosphoric acidaffects expression1
K 7174increases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
dorsomorphinaffects cotreatment, decreases expression1
jinfukangdecreases expression1
picoxystrobinincreases expression1
Resveratrolaffects cotreatment, increases expression1
Sunitinibincreases expression1
Arbutinincreases expression1
Arsenicincreases abundance, decreases expression1
Aspirinincreases expression1
Atrazineincreases expression1
Caffeinedecreases phosphorylation1
Cisplatindecreases expression1
Bucladesineaffects cotreatment, increases expression1
Endosulfanincreases expression, decreases expression1
Methyl Methanesulfonatedecreases expression1
Paraquatdecreases expression1
Plant Extractsaffects cotreatment, increases expression1
Progesteroneincreases expression1
Rotenoneincreases expression1

ChEMBL screening assays

2 unique, capped per target: 2 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL4833660BindingInhibition of PRMT9 (unknown origin) at 10 uM using SAM as substrate measured up to 960 mins by AlphaScreen microplate reader assay relative to controlDiscovery of IHMT-EZH2-115 as a Potent and Selective Enhancer of Zeste Homolog 2 (EZH2) Inhibitor for the Treatment of B-Cell Lymphomas. — J Med Chem

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_B1S0Abcam HeLa FBXO11 KOCancer cell lineFemale

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT05657860PHASE4COMPLETEDGuanfacine Extended Release for the Reduction of Aggression and Self-injurious Behavior Associated With Prader-Willi Syndrome
NCT05744479PHASE4RECRUITINGMetformin for Antipsychotic-induced Weight Gain in Adults With Intellectual Disability
NCT06107829PHASE4WITHDRAWNValbenazine Treatment of Tardive Dyskinesia in Adults With Intellectual/Developmental Disabilities
NCT06997198PHASE4NOT_YET_RECRUITINGDeutetrabenazine Treatment for Tardive Dyskinesia in Intellectual/Developmental Disabilities
NCT04586348PHASE4UNKNOWNPrenatal Iodine Supplementation and Early Childhood Neurodevelopment
NCT04873115PHASE4UNKNOWNDouble-blind, Placebo-controlled, Randomized Clinical Trial Comparing the Efficacy and Safety of Sialanar Plus orAl rehabiLitation Against Placebo Plus Oral Rehabilitation for chIldren and Adolescents With seVere Sialorrhoea and Neurodisabilties,
NCT02270736PHASE3COMPLETEDClinical Study to Investigate the Efficacy and Safety of NT 201 Compared to Placebo in the Treatment of Chronic Troublesome Drooling Associated With Neurological Disorders and/or Intellectual Disability
NCT02559102PHASE3COMPLETEDDexmedetomidine Sedation Versus General Anaesthesia for Inguinal Hernia Surgery in Infants
NCT02757079PHASE3COMPLETEDStudy of the Efficacy and Safety of NPC-15 for Sleep Disorders of Children With Neurodevelopmental Disorders
NCT06915480PHASE3RECRUITINGReducing Missed Appointments
NCT07377032PHASE3RECRUITINGTAP-GRIN: Interventional Study on Patients With GRIN-related Neurodevelopmental Disorders
NCT02304302PHASE2COMPLETEDDown Syndrome Memantine Follow-up Study
NCT03862950PHASE2COMPLETEDA Trial of Metformin in Individuals With Fragile X Syndrome (Met)
NCT04529226PHASE2UNKNOWNStudy to Compare Clozapine vs Treatment as Usual in People With Intellectual Disability & Treatment-resistant Psychosis
NCT04821856PHASE2COMPLETEDEvaluation of the Effectiveness of Cannabidiol in Treating Severe Behavioural Problems in Children and Adolescents With Intellectual Disability
NCT02909959PHASE2COMPLETEDSulforaphane for the Treatment of Young Men With Autism Spectrum Disorder
NCT06081348PHASE2RECRUITINGSertraline vs. Placebo in the Treatment of Anxiety in Children and AdoLescents With NeurodevelopMental Disorders
NCT06352372PHASE2COMPLETEDSafety and Efficacy of tPBM for Epileptiform Activity in Autism
NCT05273320PHASE1COMPLETEDClinical Trial of Nabilone for Aggression in Adults With Intellectual and Developmental Disabilities
NCT05301361PHASE1ENROLLING_BY_INVITATIONSensitivity of the NIH Toolbox to Stimulant Treatment in Intellectual Disabilities
NCT06016764PHASE1COMPLETEDUse of MRI and cTBS for Catatonia in Autism
NCT06586827PHASE1COMPLETEDImpact of Competency-Based Training and Technical Assistance Employment Outcomes of Individuals With ID/DD
NCT07531940PHASE1NOT_YET_RECRUITINGEscalating Doses of Memantine in Down Syndrome (MEDS-123)
NCT00503191PHASE1COMPLETEDNeuroModulation Technique Treatment of Autism
NCT04475848PHASE1COMPLETEDA Study to Investigate the Safety, Tolerability, Pharmacokinetics, Pharmacodynamics and Food Effect of RO6953958 in Healthy Participants
NCT06300398PHASE1COMPLETEDIAMA-6 Oral Dose Study in Healthy Adults
NCT03479476PHASE2/PHASE3COMPLETEDA Trial of Metformin in Individuals With Fragile X Syndrome
NCT02616796PHASE1/PHASE2COMPLETEDEffects of Social Gaze Training on Brain and Behavior in Fragile X Syndrome
NCT06860672EARLY_PHASE1RECRUITINGClinical Trial of the Dual Vector Base Editor for the Treatment of the CHD3-R1025W Mutation
NCT00597948Not specifiedCOMPLETEDHealthy Lifestyles for People With Intellectual Disabilities
NCT01087320Not specifiedRECRUITINGGenome Medical Sequencing for Gene Discovery
NCT01652963Not specifiedUNKNOWNPicture-based Computerised Assessment and Training of Cognitive Behaviour Therapy Skills
NCT01695395Not specifiedCOMPLETEDMental Health Care Provision for Adults With Intellectual Disability and a Mental Disorder
NCT01867554Not specifiedCOMPLETEDResearch and Characterization of New Genes Involved in Intellectual Disability
NCT01915381Not specifiedCOMPLETEDImproving Adherence Healthy Lifestyle With a Smartphone Application Based on Adults With Intellectual Disabilities
NCT01988623Not specifiedCOMPLETEDPivotal Response Treatment for Individuals With Intellectual Disabilities
NCT02099773Not specifiedCOMPLETEDSupport Staff-client Interactions With Augmentative and Alternative Communication
NCT02136849Not specifiedCOMPLETEDInter-regional Project of the Great Western Exploration Approach for Exome Molecular Causes Severe Intellectual Disability Isolated or Syndromic
NCT02225041Not specifiedCOMPLETEDSedation Strategy and Cognitive Outcome After Critical Illness in Early Childhood
NCT02414438Not specifiedCOMPLETEDEstablishing the Clinical Utility of First StepDx PLUS and NextStepDx PLUS Study