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

Summary

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 protein sequestering activity; transcription coactivator activity; and ubiquitin binding activity. Involved in several processes, including positive regulation of canonical NF-kappaB signal transduction; protein linear polyubiquitination; and regulation of DNA-binding transcription factor activity. Part of LUBAC complex. Implicated in glycogen storage disease. [provided by Alliance of Genome Resources, Oct 2024]
Expression: Ubiquitous expression in spleen (RPKM 15.0), prostate (RPKM 9.4) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 20p13

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	20	NC_000020.11 (408299..432139)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	20	NC_060944.1 (451838..475908)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	20	NC_000020.10 (388943..412783)

Chromosome 20 - NC_000020.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

E3 ubiquitin ligase RBCK1 confers ferroptosis resistance in pancreatic cancer by facilitating MFN2 degradation.
Title: E3 ubiquitin ligase RBCK1 confers ferroptosis resistance in pancreatic cancer by facilitating MFN2 degradation.
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.
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.
Mechanistic insights into the homo-dimerization of HOIL-1L and SHARPIN.
Title: Mechanistic insights into the homo-dimerization of HOIL-1L and SHARPIN.
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.
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.
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.
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.
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.
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.

Submit: New GeneRIF Correction See all GeneRIFs (40)

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	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH94121 (e-PCR)
- UniSTS:92033

RH48717 (e-PCR)
- UniSTS:69528

RH17493 (e-PCR)
- UniSTS:82349

SHGC-34689 (e-PCR)
- UniSTS:2530

STS-T99066 (e-PCR)
- UniSTS:70629

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 protein sequestering activity	IDA Inferred from Direct Assay more info	PubMed
enables transcription coactivator activity	IDA Inferred from Direct Assay 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 cytoplasmic sequestering of protein	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 DNA-templated transcription	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 non-canonical NF-kappaB signal transduction	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of ubiquitin protein ligase activity	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

EC 2.3.2.31

NP_001310887.1

EC 2.3.2.31

NP_001310889.1

EC 2.3.2.31

NP_001397699.1

EC 2.3.2.31

NP_006453.1

EC 2.3.2.31

NP_112506.2

EC 2.3.2.31

XP_011527439.1

EC 2.3.2.31

XP_011527440.1

EC 2.3.2.31

XP_011527441.1

EC 2.3.2.31

XP_011527442.1

EC 2.3.2.31

XP_047295789.1

EC 2.3.2.31

XP_047295790.1

EC 2.3.2.31

XP_047295791.1

EC 2.3.2.31

XP_054178819.1

EC 2.3.2.31

XP_054178820.1

EC 2.3.2.31

XP_054178821.1

EC 2.3.2.31

XP_054178822.1

EC 2.3.2.31

XP_054178823.1

EC 2.3.2.31

XP_054178824.1

EC 2.3.2.31

XP_054178825.1

EC 2.3.2.31

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

NG_033233.1 RefSeqGene

Range

5235..29075

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_728

mRNA and Protein(s)

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
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
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
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
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
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

NR_136659.2 RNA Sequence

Status: REVIEWED

Source sequence(s)

AL121747, AW293635, BC014116

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

NC_000020.11 Reference GRCh38.p14 Primary Assembly

Range

408299..432139

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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
XM_047439833.1 → XP_047295789.1 ranBP-type and C3HC4-type zinc finger-containing protein 1 isoform X5
XM_047439835.1 → XP_047295791.1 ranBP-type and C3HC4-type zinc finger-containing protein 1 isoform X7

Related

ENSP00000405288.1, ENST00000415942.5
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]
XM_047439834.1 → XP_047295790.1 ranBP-type and C3HC4-type zinc finger-containing protein 1 isoform X6

Alternate T2T-CHM13v2.0

Genomic

NC_060944.1 Alternate T2T-CHM13v2.0

Range

451838..475908

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054322844.1 → XP_054178819.1 ranBP-type and C3HC4-type zinc finger-containing protein 1 isoform X1
XM_054322845.1 → XP_054178820.1 ranBP-type and C3HC4-type zinc finger-containing protein 1 isoform X2
XM_054322846.1 → XP_054178821.1 ranBP-type and C3HC4-type zinc finger-containing protein 1 isoform X3
XM_054322848.1 → XP_054178823.1 ranBP-type and C3HC4-type zinc finger-containing protein 1 isoform X5
XM_054322850.1 → XP_054178825.1 ranBP-type and C3HC4-type zinc finger-containing protein 1 isoform X7
XM_054322847.1 → XP_054178822.1 ranBP-type and C3HC4-type zinc finger-containing protein 1 isoform X4
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

NM_031227.1: Suppressed sequence

Description

NM_031227.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
NM_031228.1: Suppressed sequence

Description

NM_031228.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.