U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    RBCK1 RANBP2-type and C3HC4-type zinc finger containing 1 [ Homo sapiens (human) ]

    Gene ID: 10616, updated on 2-May-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    RBCK1provided by HGNC
    Official Full Name
    RANBP2-type and C3HC4-type zinc finger containing 1provided by HGNC
    Primary source
    HGNC:HGNC:15864
    See related
    Ensembl:ENSG00000125826 MIM:610924; AllianceGenome:HGNC:15864
    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
    XAP3; XAP4; HOIL1; PBMEI; PGBM1; RBCK2; RNF54; HOIL-1; ZRANB4; C20orf18; UBCE7IP3
    Summary
    Enables several functions, including identical protein binding activity; protein sequestering activity; and ubiquitin binding activity. Involved in several processes, including T cell receptor signaling pathway; cellular protein metabolic process; and regulation of DNA-binding transcription factor activity. Part of LUBAC complex. Implicated in glycogen storage disease. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in spleen (RPKM 15.0), prostate (RPKM 9.4) and 25 other tissues See more
    Orthologs
    mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    Location:
    20p13
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (408299..432139)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (451838..475908)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (388943..412783)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene serine/arginine repetitive matrix protein 2-like Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:327291-328053 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:328054-328816 Neighboring gene Sharpr-MPRA regulatory region 10349 Neighboring gene Sharpr-MPRA regulatory region 12668 Neighboring gene Sharpr-MPRA regulatory region 10396 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:345627-346226 Neighboring gene neurensin 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12572 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12573 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:362523-363521 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:379646-380146 Neighboring gene tribbles pseudokinase 3 Neighboring gene CRISPRi-validated cis-regulatory element chr20.29 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:386661-386817 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:388888-389530 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12575 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:389531-390171 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12576 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:410614-411114 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:411115-411615 Neighboring gene TBC1 domain family member 20 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:442560-442708 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12577 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12578 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:456844-457048 Neighboring gene casein kinase 2 alpha 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17440 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:522754-523447 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12579 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:524141-524834

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    Go to the top of the pageHelp

    Related articles in PubMed

    1. RBCK1-related disease: A rare multisystem disorder with polyglucosan storage, auto-inflammation, recurrent infections, skeletal, and cardiac myopathy-Four additional patients and a review of the current literature. Phadke R, et al. J Inherit Metab Dis, 2020 Sep. PMID 32187699
    2. RBCK1 contributes to chemoresistance and stemness in colorectal cancer (CRC). Liu ML, et al. Biomed Pharmacother, 2019 Oct. PMID 31545242
    3. Mutations outside the N-terminal part of RBCK1 may cause polyglucosan body myopathy with immunological dysfunction: expanding the genotype-phenotype spectrum. Krenn M, et al. J Neurol, 2018 Feb. PMID 29260357, Free PMC Article
    4. Polyglucosan body myopathy caused by defective ubiquitin ligase RBCK1. Nilsson J, et al. Ann Neurol, 2013 Dec. PMID 23798481
    5. Cytoplasmic tethering of a RING protein RBCK1 by its splice variant lacking the RING domain. Yoshimoto N, et al. Biochem Biophys Res Commun, 2005 Sep 23. PMID 16083853

    See all (147) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. HOIL-1L deficiency induces cell cycle alteration which causes immaturity of skeletal muscle and cardiomyocytes.
      Title: HOIL-1L deficiency induces cell cycle alteration which causes immaturity of skeletal muscle and cardiomyocytes.
    2. RBCK1 overexpression is associated with immune cell infiltration and poor prognosis in hepatocellular carcinoma.
      Title: RBCK1 overexpression is associated with immune cell infiltration and poor prognosis in hepatocellular carcinoma.
    3. Mechanistic insights into the homo-dimerization of HOIL-1L and SHARPIN.
      Title: Mechanistic insights into the homo-dimerization of HOIL-1L and SHARPIN.
    4. RBCK1 Overexpression Attenuates Inflammation and Mobility of Derp1-Induced Nasal Mucosal Cells by Downregulating NLRP3.
      Title: RBCK1 Overexpression Attenuates Inflammation and Mobility of Derp1-Induced Nasal Mucosal Cells by Downregulating NLRP3.
    5. RBCK1 regulates the progression of ER-positive breast cancer through the HIF1alpha signaling.
      Title: RBCK1 regulates the progression of ER-positive breast cancer through the HIF1α signaling.
    6. RBCK1 is an endogenous inhibitor for triple negative breast cancer via hippo/YAP axis.
      Title: RBCK1 is an endogenous inhibitor for triple negative breast cancer via hippo/YAP axis.
    7. HOIL-1 ubiquitin ligase activity targets unbranched glucosaccharides and is required to prevent polyglucosan accumulation.
      Title: HOIL-1 ubiquitin ligase activity targets unbranched glucosaccharides and is required to prevent polyglucosan accumulation.
    8. Regulation of PTEN and ovarian cancer progression by an E3 ubiquitin ligase RBCK1.
      Title: Regulation of PTEN and ovarian cancer progression by an E3 ubiquitin ligase RBCK1.
    9. RBCK1-related disease: A rare multisystem disorder with polyglucosan storage, auto-inflammation, recurrent infections, skeletal, and cardiac myopathy-Four additional patients and a review of the current literature.
      Title: RBCK1-related disease: A rare multisystem disorder with polyglucosan storage, auto-inflammation, recurrent infections, skeletal, and cardiac myopathy-Four additional patients and a review of the current literature.
    10. Linear Ubiquitin Code: Its Writer, Erasers, Decoders, Inhibitors, and Implications in Disorders.
      Title: Linear Ubiquitin Code: Its Writer, Erasers, Decoders, Inhibitors, and Implications in Disorders.
    Submit: New GeneRIF Correction See all GeneRIFs (39)

    Phenotypes

    Go to the top of the page Help

    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
    Polyglucosan body myopathy type 1
    MedGen: C4014605 OMIM: 615895 GeneReviews: Not available
    		Compare labs

    Variation

    Go to the top of the page Help

    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

    Go to the top of the page

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables ubiquitin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ubiquitin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables ubiquitin ligase activator activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ubiquitin-protein transferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ubiquitin-protein transferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in T cell receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in defense response to bacterium IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of NF-kappaB transcription factor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of necroptotic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of NF-kappaB transcription factor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of canonical NF-kappaB signal transduction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of canonical NF-kappaB signal transduction IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of extrinsic apoptotic signaling pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of non-canonical NF-kappaB signal transduction IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in proteasome-mediated ubiquitin-dependent protein catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in proteasome-mediated ubiquitin-dependent protein catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein linear polyubiquitination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein linear polyubiquitination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein polyubiquitination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of LUBAC complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of LUBAC complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of LUBAC complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    ranBP-type and C3HC4-type zinc finger-containing protein 1
    Names
    HBV-associated factor 4
    RBCC protein interacting with PKC1
    RING finger protein 54
    RING-type E3 ubiquitin transferase HOIL-1
    heme-oxidized IRP2 ubiquitin ligase 1
    hepatitis B virus X-associated protein 4
    ubiquitin conjugating enzyme 7 interacting protein 3
    NP_001310885.1
    NP_001310887.1
    NP_001310889.1
    NP_001397699.1
    NP_006453.1
    NP_112506.2
    XP_011527439.1
    XP_011527440.1
    XP_011527441.1
    XP_011527442.1
    XP_047295789.1
    XP_047295790.1
    XP_047295791.1
    XP_054178819.1
    XP_054178820.1
    XP_054178821.1
    XP_054178822.1
    XP_054178823.1
    XP_054178824.1
    XP_054178825.1

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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_033233.1 RefSeqGene

      Range
      5235..29075
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_728

    mRNA and Protein(s)

    1. NM_001323956.2 → NP_001310885.1  ranBP-type and C3HC4-type zinc finger-containing protein 1 isoform 3

      Status: REVIEWED

      Source sequence(s)
      AL121747, AW293635
      Conserved Domains (2) summary
      pfam01485
      Location:200 → 234
      IBR; IBR domain, a half RING-finger domain
      cl17238
      Location:136 → 162
      RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain

    2. NM_001323958.2 → NP_001310887.1  ranBP-type and C3HC4-type zinc finger-containing protein 1 isoform 3

      Status: REVIEWED

      Source sequence(s)
      AL121747, AW293635, BC000983, BC014116
      Conserved Domains (2) summary
      pfam01485
      Location:200 → 234
      IBR; IBR domain, a half RING-finger domain
      cl17238
      Location:136 → 162
      RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain

    3. NM_001323960.2 → NP_001310889.1  ranBP-type and C3HC4-type zinc finger-containing protein 1 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AK309414, BC014116, BC016301
      Consensus CDS
      CCDS82587.1
      UniProtKB/TrEMBL
      A0A8V8TLQ1, A6PVJ6
      Related
      ENSP00000417173.1, ENST00000475269.5

    4. NM_001410770.1 → NP_001397699.1  ranBP-type and C3HC4-type zinc finger-containing protein 1 isoform 5

      Status: REVIEWED

      Source sequence(s)
      AL121747
      Consensus CDS
      CCDS92997.1
      UniProtKB/TrEMBL
      A0A8V8TMZ2
      Related
      ENSP00000513446.1, ENST00000697805.1

    5. NM_006462.6 → NP_006453.1  ranBP-type and C3HC4-type zinc finger-containing protein 1 isoform 1

      See identical proteins and their annotated locations for NP_006453.1

      Status: REVIEWED

      Source sequence(s)
      AB107766, AL121747, AW293635, BC014116
      Consensus CDS
      CCDS12998.1
      UniProtKB/Swiss-Prot
      Q9BYM8
      Related
      ENSP00000254960.5, ENST00000353660.7
      Conserved Domains (5) summary
      cd01799
      Location:15 → 89
      Hoil1_N; Ubiquitin-like domain of HOIL1
      smart00547
      Location:155 → 175
      ZnF_RBZ; Zinc finger domain
      sd00029
      Location:155 → 174
      zf-RanBP2; RanBP2-type Zn finger [structural motif]
      pfam01485
      Location:328 → 362
      IBR; IBR domain, a half RING-finger domain
      cd16633
      Location:236 → 290
      mRING-HC-C3HC3D_RBR_HOIL1; Modified RING finger, HC subclass (C3HC3D-type), found in heme-oxidized IRP2 ubiquitin ligase 1 (HOIL-1) and similar proteins

    6. NM_031229.4 → NP_112506.2  ranBP-type and C3HC4-type zinc finger-containing protein 1 isoform 2

      See identical proteins and their annotated locations for NP_112506.2

      Status: REVIEWED

      Source sequence(s)
      AL121747, AW293635, BC014116, BC015219
      Consensus CDS
      CCDS13000.2
      UniProtKB/Swiss-Prot
      O95623, Q86SL2, Q96BS3, Q9BYM8, Q9BYM9
      Related
      ENSP00000348632.6, ENST00000356286.10
      Conserved Domains (5) summary
      smart00547
      Location:197 → 217
      ZnF_RBZ; Zinc finger domain
      sd00029
      Location:197 → 216
      zf-RanBP2; RanBP2-type Zn finger [structural motif]
      cd16633
      Location:278 → 332
      mRING-HC-C3HC3D_RBR_HOIL1; Modified RING finger, HC subclass (C3HC3D-type), found in heme-oxidized IRP2 ubiquitin ligase 1 (HOIL-1) and similar proteins
      cd01799
      Location:53 → 133
      Ubl_HOIL1; ubiquitin-like (Ubl) domain found in heme-oxidized IRP2 ubiquitin ligase 1 (HOIL-1) and similar proteins
      pfam01485
      Location:370 → 404
      IBR; IBR domain, a half RING-finger domain

    RNA

    1. NR_136659.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL121747, AW293635, BC014116

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      408299..432139
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011529137.3 → XP_011527439.1  ranBP-type and C3HC4-type zinc finger-containing protein 1 isoform X1

      Conserved Domains (5) summary
      cd01799
      Location:115 → 189
      Hoil1_N; Ubiquitin-like domain of HOIL1
      smart00547
      Location:255 → 275
      ZnF_RBZ; Zinc finger domain
      sd00029
      Location:255 → 274
      zf-RanBP2; RanBP2-type Zn finger [structural motif]
      pfam01485
      Location:428 → 462
      IBR; IBR domain, a half RING-finger domain
      pfam13445
      Location:340 → 382
      zf-RING_UBOX; RING-type zinc-finger

    2. XM_011529138.2 → XP_011527440.1  ranBP-type and C3HC4-type zinc finger-containing protein 1 isoform X2

      Conserved Domains (5) summary
      cd01799
      Location:98 → 172
      Hoil1_N; Ubiquitin-like domain of HOIL1
      smart00547
      Location:238 → 258
      ZnF_RBZ; Zinc finger domain
      sd00029
      Location:238 → 257
      zf-RanBP2; RanBP2-type Zn finger [structural motif]
      pfam01485
      Location:411 → 445
      IBR; IBR domain, a half RING-finger domain
      pfam13445
      Location:323 → 365
      zf-RING_UBOX; RING-type zinc-finger

    3. XM_011529139.4 → XP_011527441.1  ranBP-type and C3HC4-type zinc finger-containing protein 1 isoform X3

      UniProtKB/TrEMBL
      A0A8V8TMQ4
      Conserved Domains (5) summary
      cd01799
      Location:115 → 189
      Hoil1_N; Ubiquitin-like domain of HOIL1
      smart00547
      Location:255 → 275
      ZnF_RBZ; Zinc finger domain
      sd00029
      Location:255 → 274
      zf-RanBP2; RanBP2-type Zn finger [structural motif]
      pfam01485
      Location:406 → 462
      IBR; IBR domain, a half RING-finger domain
      pfam13445
      Location:340 → 382
      zf-RING_UBOX; RING-type zinc-finger

    4. XM_047439833.1 → XP_047295789.1  ranBP-type and C3HC4-type zinc finger-containing protein 1 isoform X5

    5. XM_047439835.1 → XP_047295791.1  ranBP-type and C3HC4-type zinc finger-containing protein 1 isoform X7

      Related
      ENSP00000405288.1, ENST00000415942.5

    6. XM_011529140.3 → XP_011527442.1  ranBP-type and C3HC4-type zinc finger-containing protein 1 isoform X4

      Conserved Domains (3) summary
      cd01799
      Location:115 → 189
      Hoil1_N; Ubiquitin-like domain of HOIL1
      smart00547
      Location:255 → 275
      ZnF_RBZ; Zinc finger domain
      sd00029
      Location:255 → 274
      zf-RanBP2; RanBP2-type Zn finger [structural motif]

    7. XM_047439834.1 → XP_047295790.1  ranBP-type and C3HC4-type zinc finger-containing protein 1 isoform X6

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      451838..475908
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054322844.1 → XP_054178819.1  ranBP-type and C3HC4-type zinc finger-containing protein 1 isoform X1

    2. XM_054322845.1 → XP_054178820.1  ranBP-type and C3HC4-type zinc finger-containing protein 1 isoform X2

    3. XM_054322846.1 → XP_054178821.1  ranBP-type and C3HC4-type zinc finger-containing protein 1 isoform X3

    4. XM_054322848.1 → XP_054178823.1  ranBP-type and C3HC4-type zinc finger-containing protein 1 isoform X5

    5. XM_054322850.1 → XP_054178825.1  ranBP-type and C3HC4-type zinc finger-containing protein 1 isoform X7

    6. XM_054322847.1 → XP_054178822.1  ranBP-type and C3HC4-type zinc finger-containing protein 1 isoform X4

    7. XM_054322849.1 → XP_054178824.1  ranBP-type and C3HC4-type zinc finger-containing protein 1 isoform X6

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_031227.1: Suppressed sequence

      Description
      NM_031227.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.

    2. NM_031228.1: Suppressed sequence

      Description
      NM_031228.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BYM8.2 GenPept UniProtKB/Swiss-Prot:Q9BYM8

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous