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OTUD6B OTU deubiquitinase 6B [ Homo sapiens (human) ]

Gene ID: 51633, updated on 23-Nov-2023

Summary

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Official Symbol
OTUD6Bprovided by HGNC
Official Full Name
OTU deubiquitinase 6Bprovided by HGNC
Primary source
HGNC:HGNC:24281
See related
Ensembl:ENSG00000155100 MIM:612021; AllianceGenome:HGNC:24281
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
DUBA5; CGI-77; DUBA-5; IDDFSDA
Summary
This gene encodes a member of the ovarian tumor domain (OTU)-containing subfamily of deubiquitinating enzymes. Deubiquitinating enzymes are primarily involved in removing ubiquitin from proteins targeted for degradation. This protein may function as a negative regulator of the cell cycle in B cells. [provided by RefSeq, Nov 2013]
Expression
Ubiquitous expression in brain (RPKM 6.6), testis (RPKM 5.6) and 25 other tissues See more
Orthologs
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Genomic context

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See OTUD6B in Genome Data Viewer
Location:
8q21.3
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (91070344..91087093)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (92195269..92212018)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (92082572..92099321)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene phosphatidylinositol-4,5-bisphosphate 4-phosphatase 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19355 Neighboring gene OTUD6B antisense RNA 1 (head to head) Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27614 Neighboring gene MPRA-validated peak7106 silencer Neighboring gene leucine rich repeat containing 69 Neighboring gene ceruloplasmin pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:92209377-92209886 Neighboring gene microRNA 4661

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. Novel biallelic variants affecting the OTU domain of the gene OTUD6B associate with severe intellectual disability syndrome and molecular dynamics simulations. Cingöz S, et al. Eur J Med Genet, 2022 Jun. PMID 35430327, Free PMC Article
  2. OTUD6B-associated intellectual disability: novel variants and genetic exclusion of retinal degeneration as part of a refined phenotype. Abdel-Salam GMH, et al. J Hum Genet, 2022 Jan. PMID 34354232
  3. Deubiquitylase OTUD6B stabilizes the mutated pVHL and suppresses cell migration in clear cell renal cell carcinoma. Guo K, et al. Cell Death Dis, 2022 Feb 2. PMID 35110537, Free PMC Article
  4. Compound Heterozygote of Point Mutation and Chromosomal Microdeletion Involving OTUD6B Coinciding with ZMIZ1 Variant in Syndromic Intellectual Disability. Phetthong T, et al. Genes (Basel), 2021 Oct 7. PMID 34680978, Free PMC Article
  5. Studying OTUD6B-OTUB1 Protein-Protein Interaction by Low-Throughput GFP-Trap Assays and High-Throughput AlphaScreen Assays. Weber E, et al. Methods Mol Biol, 2021. PMID 33421002

See all (40) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. MCTS1 enhances the proliferation of laryngeal squamous cell carcinoma via promoting OTUD6B-1 mediated LIN28B deubiquitination.
    Title: MCTS1 enhances the proliferation of laryngeal squamous cell carcinoma via promoting OTUD6B-1 mediated LIN28B deubiquitination.
  2. The OTUD6B-LIN28B-MYC axis determines the proliferative state in multiple myeloma.
    Title: The OTUD6B-LIN28B-MYC axis determines the proliferative state in multiple myeloma.
  3. Novel biallelic variants affecting the OTU domain of the gene OTUD6B associate with severe intellectual disability syndrome and molecular dynamics simulations.
    Title: Novel biallelic variants affecting the OTU domain of the gene OTUD6B associate with severe intellectual disability syndrome and molecular dynamics simulations.
  4. OTUD6B-associated intellectual disability: novel variants and genetic exclusion of retinal degeneration as part of a refined phenotype.
    Title: OTUD6B-associated intellectual disability: novel variants and genetic exclusion of retinal degeneration as part of a refined phenotype.
  5. Deubiquitylase OTUD6B stabilizes the mutated pVHL and suppresses cell migration in clear cell renal cell carcinoma.
    Title: Deubiquitylase OTUD6B stabilizes the mutated pVHL and suppresses cell migration in clear cell renal cell carcinoma.
  6. Compound Heterozygote of Point Mutation and Chromosomal Microdeletion Involving OTUD6B Coinciding with ZMIZ1 Variant in Syndromic Intellectual Disability.
    Title: Compound Heterozygote of Point Mutation and Chromosomal Microdeletion Involving OTUD6B Coinciding with ZMIZ1 Variant in Syndromic Intellectual Disability.
  7. DUB-independent regulation of pVHL by OTUD6B suppresses hepatocellular carcinoma.
    Title: DUB-independent regulation of pVHL by OTUD6B suppresses hepatocellular carcinoma.
  8. OTUD6B-AS1 Might Be a Novel Regulator of Apoptosis in Systemic Sclerosis.
    Title: OTUD6B-AS1 Might Be a Novel Regulator of Apoptosis in Systemic Sclerosis.
  9. The global OTUD6B expression level does not change significantly between nonneoplastic and malignant tissues, suggesting that modifications of splicing factors during the process of transformation are responsible for this isoform switch.
    Title: Deubiquitinase OTUD6B Isoforms Are Important Regulators of Growth and Proliferation.
  10. OTUD6B encodes a deubiquitinating enzyme; study reports biallelic pathogenic variants in OTUD6B in 12 individuals from 6 families with intellectual disability syndrome associated with seizures & dysmorphic features; other features include developmental delay, microcephaly, absent speech, hypotonia, growth retardation, feeding difficulties, structural brain abnormalities, malformations of heart & musculoskeleton.
    Title: Biallelic Variants in OTUD6B Cause an Intellectual Disability Syndrome Associated with Seizures and Dysmorphic Features.
Submit: New GeneRIF Correction See all GeneRIFs (11)

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, seizures, and distal limb anomalies
MedGen: C4479520 OMIM: 617452 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

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
retropepsin gag-pol Positional proteomics analysis identifies the cleavage of human OTU domain containing 6B (OTUD6B) at amino acid residues 5-6 by the HIV-1 protease PubMed

Go to the HIV-1, Human Interaction Database

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 cysteine-type deubiquitinase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables cysteine-type deubiquitinase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in cell population proliferation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in proteasome assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein deubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein deubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein deubiquitination IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
part_of eukaryotic translation initiation factor 4F complex IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
deubiquitinase OTUD6B
Names
OTU domain containing 6B
OTU domain-containing protein 6B
NP_001273674.1
NP_001402951.1
NP_057107.4
XP_011515431.2
XP_047277820.1
XP_054216621.1
XP_054216622.1

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.

mRNA and Protein(s)

  1. NM_001286745.3 → NP_001273674.1  deubiquitinase OTUD6B isoform 2

    See identical proteins and their annotated locations for NP_001273674.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) contains an alternate exon in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is shorter than isoform 1.
    Source sequence(s)
    AC087439, AK293843, BQ000463
    Consensus CDS
    CCDS69513.1
    UniProtKB/Swiss-Prot
    Q8N6M0
    Related
    ENSP00000481196.1, ENST00000615618.1
    Conserved Domains (1) summary
    pfam02338
    Location:52 → 177
    OTU; OTU-like cysteine protease

  2. NM_001416022.1 → NP_001402951.1  deubiquitinase OTUD6B isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC087439
    UniProtKB/TrEMBL
    A0A087X0W9

  3. NM_016023.5 → NP_057107.4  deubiquitinase OTUD6B isoform 1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AA748163, BC029760, BI712470, DA034027
    Consensus CDS
    CCDS6253.3
    UniProtKB/Swiss-Prot
    A8K6I1, B4DEY0, Q8N6M0, Q9NTA4, Q9Y387
    UniProtKB/TrEMBL
    A0A087X0W9
    Related
    ENSP00000384190.4, ENST00000404789.8
    Conserved Domains (2) summary
    COG5539
    Location:18 → 280
    COG5539; Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
    pfam02338
    Location:153 → 278
    OTU; OTU-like cysteine protease

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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    91070344..91087093
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047421864.1 → XP_047277820.1  deubiquitinase OTUD6B isoform X2

  2. XM_011517129.3 → XP_011515431.2  deubiquitinase OTUD6B isoform X1

    UniProtKB/Swiss-Prot
    Q8N6M0
    Conserved Domains (1) summary
    pfam02338
    Location:52 → 177
    OTU; OTU-like cysteine protease

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    92195269..92212018
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054360647.1 → XP_054216622.1  deubiquitinase OTUD6B isoform X2

  2. XM_054360646.1 → XP_054216621.1  deubiquitinase OTUD6B isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8N6M0.1 GenPept UniProtKB/Swiss-Prot:Q8N6M0

Gene LinkOut

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