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

Gene ID: 10616, updated on 11-Apr-2024

Summary

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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
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Genomic context

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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

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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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. 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.
  2. Mechanistic insights into the homo-dimerization of HOIL-1L and SHARPIN.
    Title: Mechanistic insights into the homo-dimerization of HOIL-1L and SHARPIN.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. HOIL-1, an atypical E3 ligase that controls MyD88 signalling by forming ester bonds between ubiquitin and components of the Myddosome.
    Title: HOIL-1, an atypical E3 ligase that controls MyD88 signalling by forming ester bonds between ubiquitin and components of the Myddosome.
Submit: New GeneRIF Correction See all GeneRIFs (38)

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

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

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

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

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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)

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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_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

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