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    FBXO11 F-box protein 11 [ Homo sapiens (human) ]

    Gene ID: 80204, updated on 10-Dec-2024

    Summary

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    Official Symbol
    FBXO11provided by HGNC
    Official Full Name
    F-box protein 11provided by HGNC
    Primary source
    HGNC:HGNC:13590
    See related
    Ensembl:ENSG00000138081 MIM:607871; AllianceGenome:HGNC:13590
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    UBR6; VIT1; FBX11; PRMT9; IDDFBA; UG063H01
    Summary
    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. [provided by RefSeq, Jun 2010]
    Expression
    Ubiquitous expression in testis (RPKM 26.4), brain (RPKM 21.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See FBXO11 in Genome Data Viewer
    Location:
    2p16.3
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (47806920..47906498, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (47812869..47912466, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (48034059..48133637, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374589 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:48008525-48008706 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15741 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11467 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11468 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11469 Neighboring gene mutS homolog 6 Neighboring gene ribosomal protein L36a pseudogene 15 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15742 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15743 Neighboring gene Sharpr-MPRA regulatory region 9679 Neighboring gene RPS27A pseudogene 7 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:48129098-48129367 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:48131440-48132226 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11470 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11471 Neighboring gene uncharacterized LOC100506235 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11472 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11473 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:48133799-48134583 Neighboring gene uncharacterized LOC105374590 Neighboring gene uncharacterized LOC105374592

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. De novo variants in FBXO11 cause a syndromic form of intellectual disability with behavioral problems and dysmorphisms. Jansen S, et al. Eur J Hum Genet, 2019 May. PMID 30679813, Free PMC Article
    2. FBXO11 is a candidate tumor suppressor in the leukemic transformation of myelodysplastic syndrome. Schieber M, et al. Blood Cancer J, 2020 Oct 6. PMID 33024076, Free PMC Article
    3. The first familial case of inherited intellectual developmental disorder with dysmorphic facies and behavioral abnormalities (IDDFBA) with a novel FBXO11 variant. Lee CG, et al. Am J Med Genet A, 2020 Nov. PMID 32902151
    4. FBXO11 variants are associated with intellectual disability and variable clinical manifestation in Chinese affected individuals. Pan X, et al. J Hum Genet, 2024 Aug. PMID 38740982
    5. De novo missense variants in FBXO11 alter its protein expression and subcellular localization. Gregor A, et al. Hum Mol Genet, 2022 Feb 3. PMID 34505148, Free PMC Article

    See all (110) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. FBXO11 variants are associated with intellectual disability and variable clinical manifestation in Chinese affected individuals.
      Title: FBXO11 variants are associated with intellectual disability and variable clinical manifestation in Chinese affected individuals.
    2. FBXO11 constitutes a major negative regulator of MHC class II through ubiquitin-dependent proteasomal degradation of CIITA.
      Title: FBXO11 constitutes a major negative regulator of MHC class II through ubiquitin-dependent proteasomal degradation of CIITA.
    3. FBXO11 governs macrophage cell death and inflammation in response to bacterial toxins.
      Title: FBXO11 governs macrophage cell death and inflammation in response to bacterial toxins.
    4. FBXO11 amplifies type I interferon signaling to exert antiviral effects by facilitating the assemble of TRAF3-TBK1-IRF3 complex.
      Title: FBXO11 amplifies type I interferon signaling to exert antiviral effects by facilitating the assemble of TRAF3-TBK1-IRF3 complex.
    5. Ultrasound-targeted microbubble destruction-mediated silencing of FBXO11 suppresses development of pancreatic cancer.
      Title: Ultrasound-targeted microbubble destruction-mediated silencing of FBXO11 suppresses development of pancreatic cancer.
    6. De novo missense variants in FBXO11 alter its protein expression and subcellular localization.
      Title: De novo missense variants in FBXO11 alter its protein expression and subcellular localization.
    7. Frequent mutations of FBXO11 highlight BCL6 as a therapeutic target in Burkitt lymphoma.
      Title: Frequent mutations of FBXO11 highlight BCL6 as a therapeutic target in Burkitt lymphoma.
    8. The first familial case of inherited intellectual developmental disorder with dysmorphic facies and behavioral abnormalities (IDDFBA) with a novel FBXO11 variant.
      Title: The first familial case of inherited intellectual developmental disorder with dysmorphic facies and behavioral abnormalities (IDDFBA) with a novel FBXO11 variant.
    9. FBXO11 is a candidate tumor suppressor in the leukemic transformation of myelodysplastic syndrome.
      Title: FBXO11 is a candidate tumor suppressor in the leukemic transformation of myelodysplastic syndrome.
    10. FBXO11-mediated proteolysis of BAHD1 relieves PRC2-dependent transcriptional repression in erythropoiesis.
      Title: FBXO11-mediated proteolysis of BAHD1 relieves PRC2-dependent transcriptional repression in erythropoiesis.
    Submit: New GeneRIF Correction See all GeneRIFs (36)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Intellectual developmental disorder with dysmorphic facies and behavioral abnormalities
    MedGen: C4748135 OMIM: 618089 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    A comprehensive family-based replication study of schizophrenia genes.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat Depletion of F-box protein 11 (FBXO11) by siRNA enhances HIV-1 Tat activation of HIV-1 LTR, which is not the results of increased Tat expression and release of CDK9/CCNT1 from 7SK snRNP, and activation of NF-kappaB PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ12673, MGC44383

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein-arginine N-methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables ubiquitin-like ligase-substrate adaptor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables ubiquitin-protein transferase activity NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in negative regulation of epithelial to mesenchymal transition IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in proteasome-mediated ubiquitin-dependent protein catabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in proteasome-mediated ubiquitin-dependent protein catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein modification process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein ubiquitination IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein ubiquitination NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in regulation of apoptotic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in sensory perception of sound IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in ubiquitin-dependent protein catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in ubiquitin-dependent protein catabolic process NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in chromosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of ubiquitin ligase complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    F-box only protein 11
    Names
    protein arginine N-methyltransferase 9
    ubiquitin protein ligase E3 component n-recognin 6
    vitiligo-associated protein 1
    vitiligo-associated protein VIT-1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_008397.1 RefSeqGene

      Range
      4178..103756
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001190274.2 → NP_001177203.1  F-box only protein 11 isoform 4

      See identical proteins and their annotated locations for NP_001177203.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and 5' coding region, and uses an alternate start codon, compared to variant 1. The resulting isoform (4) has a distinct and longer N-terminus, compared to isoform 1.
      Source sequence(s)
      AC006509, AC079807, AI879484, AY827075, DN994547
      Consensus CDS
      CCDS54357.1
      UniProtKB/Swiss-Prot
      A1L491, Q52ZP1, Q53EP7, Q53RT5, Q86XK2, Q8IXG3, Q96E90, Q9H6V8, Q9H9L1, Q9NR14, Q9UFK1, Q9UHI1, Q9UKC2
      UniProtKB/TrEMBL
      B4E272
      Related
      ENSP00000384823.4, ENST00000403359.8
      Conserved Domains (3) summary
      pfam12937
      Location:157 → 200
      F-box-like
      pfam13229
      Location:664 → 823
      Beta_helix; Right handed beta helix region
      cl19744
      Location:850 → 891
      zf-UBR; Putative zinc finger in N-recognin (UBR box)

    2. NM_001374325.1 → NP_001361254.1  F-box only protein 11 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AC006509, AC079807
      Consensus CDS
      CCDS1837.1
      UniProtKB/TrEMBL
      B4E272
      Related
      ENST00000682975.1
      Conserved Domains (3) summary
      pfam12937
      Location:73 → 116
      F-box-like
      pfam13229
      Location:580 → 739
      Beta_helix; Right handed beta helix region
      cl19744
      Location:766 → 807
      zf-UBR; Putative zinc finger in N-recognin (UBR box)

    3. NM_025133.4 → NP_079409.3  F-box only protein 11 isoform 1

      See identical proteins and their annotated locations for NP_079409.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the shorter transcript and encodes the shorter isoform (1).
      Source sequence(s)
      AC006509, AC079807, AI879484, AK315108
      Consensus CDS
      CCDS1837.1
      UniProtKB/TrEMBL
      B4E272
      Related
      ENSP00000385398.1, ENST00000402508.5
      Conserved Domains (3) summary
      pfam12937
      Location:73 → 116
      F-box-like
      pfam13229
      Location:580 → 739
      Beta_helix; Right handed beta helix region
      cl19744
      Location:766 → 807
      zf-UBR; Putative zinc finger in N-recognin (UBR box)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      47806920..47906498 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017005015.2 → XP_016860504.1  F-box only protein 11 isoform X3

      UniProtKB/TrEMBL
      B4E272
      Conserved Domains (3) summary
      pfam12937
      Location:156 → 199
      F-box-like
      pfam13229
      Location:663 → 822
      Beta_helix; Right handed beta helix region
      cl19744
      Location:849 → 890
      zf-UBR; Putative zinc finger in N-recognin (UBR box)

    2. XM_005264573.6 → XP_005264630.1  F-box only protein 11 isoform X2

      UniProtKB/TrEMBL
      B4E272
      Conserved Domains (4) summary
      TIGR03804
      Location:526 → 568
      para_beta_helix; parallel beta-helix repeat (two copies)
      pfam12937
      Location:156 → 201
      F-box-like; F-box-like
      pfam13229
      Location:663 → 822
      Beta_helix; Right handed beta helix region
      cl19744
      Location:849 → 917
      zf-UBR; Putative zinc finger in N-recognin (UBR box)

    3. XM_005264572.6 → XP_005264629.1  F-box only protein 11 isoform X1

      UniProtKB/TrEMBL
      B4E272
      Conserved Domains (4) summary
      TIGR03804
      Location:527 → 569
      para_beta_helix; parallel beta-helix repeat (two copies)
      pfam12937
      Location:157 → 202
      F-box-like; F-box-like
      pfam13229
      Location:664 → 823
      Beta_helix; Right handed beta helix region
      cl19744
      Location:850 → 918
      zf-UBR; Putative zinc finger in N-recognin (UBR box)

    4. XM_047445922.1 → XP_047301878.1  F-box only protein 11 isoform X7

      UniProtKB/TrEMBL
      B4E272

    5. XM_017005016.3 → XP_016860505.1  F-box only protein 11 isoform X4

      UniProtKB/TrEMBL
      A0A804HK63, B4E272
      Conserved Domains (4) summary
      TIGR03804
      Location:443 → 485
      para_beta_helix; parallel beta-helix repeat (two copies)
      pfam12937
      Location:73 → 118
      F-box-like; F-box-like
      pfam13229
      Location:580 → 739
      Beta_helix; Right handed beta helix region
      cl19744
      Location:766 → 834
      zf-UBR; Putative zinc finger in N-recognin (UBR box)

    6. XM_047445921.1 → XP_047301877.1  F-box only protein 11 isoform X6

      UniProtKB/TrEMBL
      B4E272

    7. XM_047445920.1 → XP_047301876.1  F-box only protein 11 isoform X5

      UniProtKB/TrEMBL
      B4E272

    8. XM_047445919.1 → XP_047301875.1  F-box only protein 11 isoform X4

      UniProtKB/TrEMBL
      A0A804HK63, B4E272
      Related
      ENSP00000507789.1, ENST00000683894.1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      47812869..47912466 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054344043.1 → XP_054200018.1  F-box only protein 11 isoform X3

      UniProtKB/TrEMBL
      B4E272

    2. XM_054344042.1 → XP_054200017.1  F-box only protein 11 isoform X2

      UniProtKB/TrEMBL
      B4E272

    3. XM_054344041.1 → XP_054200016.1  F-box only protein 11 isoform X1

      UniProtKB/TrEMBL
      B4E272

    4. XM_054344048.1 → XP_054200023.1  F-box only protein 11 isoform X7

      UniProtKB/TrEMBL
      B4E272

    5. XM_054344044.1 → XP_054200019.1  F-box only protein 11 isoform X4

      UniProtKB/TrEMBL
      A0A804HK63, B4E272

    6. XM_054344047.1 → XP_054200022.1  F-box only protein 11 isoform X6

      UniProtKB/TrEMBL
      B4E272

    7. XM_054344046.1 → XP_054200021.1  F-box only protein 11 isoform X5

      UniProtKB/TrEMBL
      B4E272

    8. XM_054344045.1 → XP_054200020.1  F-box only protein 11 isoform X4

      UniProtKB/TrEMBL
      A0A804HK63, B4E272

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_012167.1: Suppressed sequence

      Description
      NM_012167.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.

    2. NM_018693.2: Suppressed sequence

      Description
      NM_018693.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q86XK2.3 GenPept UniProtKB/Swiss-Prot:Q86XK2

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