OTUD7B

OTU deubiquitinase 7B, the group of OTU domain containing

Basic information

Region (hg38): 1:149937812-150010726

Previous symbols: [ "ZA20D1" ]

Links

ENSG00000264522 ∙ NCBI:56957 ∙ OMIM:611748 ∙ HGNC:16683 ∙ Uniprot:Q6GQQ9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the OTUD7B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OTUD7B gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					3	3
missense			38	1		39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	38	1	3

Variants in OTUD7B

This is a list of pathogenic ClinVar variants found in the OTUD7B region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-149943965-G-T		not specified	Uncertain significance (Mar 31, 2024)
1-149944009-C-T		not specified	Uncertain significance (Mar 16, 2022)
1-149944011-C-T		not specified	Uncertain significance (Nov 21, 2022)
1-149944012-G-A		not specified	Uncertain significance (Dec 07, 2023)
1-149944056-C-A		not specified	Uncertain significance (Dec 08, 2023)
1-149944087-G-C		not specified	Uncertain significance (Mar 31, 2024)
1-149944089-G-C		not specified	Uncertain significance (Apr 01, 2024)
1-149944090-G-T		not specified	Uncertain significance (Dec 19, 2023)
1-149944228-C-A		not specified	Uncertain significance (Sep 17, 2021)
1-149944278-C-T		not specified	Uncertain significance (Dec 22, 2023)
1-149944286-C-A			Benign (Jul 23, 2018)
1-149944291-G-C		not specified	Uncertain significance (Mar 25, 2024)
1-149944297-T-C		not specified	Uncertain significance (Apr 20, 2023)
1-149944323-G-C		not specified	Uncertain significance (Feb 11, 2022)
1-149944359-G-A		not specified	Uncertain significance (Dec 16, 2022)
1-149944501-G-A		not specified	Uncertain significance (Aug 13, 2021)
1-149944515-T-C		not specified	Uncertain significance (Oct 29, 2021)
1-149944531-G-A		not specified	Uncertain significance (Jul 12, 2023)
1-149944698-T-C		not specified	Uncertain significance (May 23, 2024)
1-149944794-G-C		not specified	Uncertain significance (Nov 09, 2023)
1-149944824-C-T		not specified	Uncertain significance (Jan 24, 2024)
1-149944826-C-G		not specified	Uncertain significance (Dec 01, 2022)
1-149944875-T-G		not specified	Uncertain significance (Oct 22, 2021)
1-149944904-G-T		not specified	Likely benign (Apr 25, 2023)
1-149944914-C-T		not specified	Uncertain significance (Jan 26, 2022)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Negative regulator of the non-canonical NF-kappa-B pathway that acts by mediating deubiquitination of TRAF3, an inhibitor of the NF-kappa-B pathway, thereby acting as a negative regulator of B-cell responses. In response to non-canonical NF- kappa-B stimuli, deubiquitinates 'Lys-48'-linked polyubiquitin chains of TRAF3, preventing TRAF3 proteolysis and over-activation of non-canonical NF-kappa-B. Negatively regulates mucosal immunity against infections (By similarity). Deubiquitinates ZAP70, and thereby regulates T cell receptor (TCR) signaling that leads to the activation of NF-kappa-B (PubMed:26903241). Plays a role in T cell homeostasis and is required for normal T cell responses, including production of IFNG and IL2 (By similarity). Mediates deubiquitination of EGFR (PubMed:22179831). Has deubiquitinating activity toward 'Lys-11', 'Lys-48' and 'Lys-63'-linked polyubiquitin chains (PubMed:27732584). Has a much higher catalytic rate with 'Lys-11'-linked polyubiquitin chains (in vitro); however the physiological significance of these data are unsure (PubMed:27732584). Hydrolyzes both linear and branched forms of polyubiquitin. {ECO:0000250|UniProtKB:B2RUR8, ECO:0000269|PubMed:11463333, ECO:0000269|PubMed:12682062, ECO:0000269|PubMed:18178551, ECO:0000269|PubMed:20622874, ECO:0000269|PubMed:22179831, ECO:0000269|PubMed:23827681, ECO:0000269|PubMed:27732584}.
• Pathway: TNF alpha Signaling Pathway;Signal Transduction;Post-translational protein modification;Metabolism of proteins;TNFR1-induced NFkappaB signaling pathway;TNFR1-induced proapoptotic signaling;TNF signaling;Ovarian tumor domain proteases;Deubiquitination;Death Receptor Signalling (Consensus)

Recessive Scores

• pRec: 0.0997

Intolerance Scores

• loftool: 0.433
• rvis_EVS: -1.09
• rvis_percentile_EVS: 7.11

Haploinsufficiency Scores

• pHI: 0.143
• hipred: N
• hipred_score: 0.492
• ghis: 0.454

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.993

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Otud7b
• Phenotype: immune system phenotype; skeleton phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; cellular phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype

Zebrafish Information Network

• Gene name: otud7b
• Affected structure: neuron
• Phenotype tag: abnormal
• Phenotype quality: hyperplastic

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;adaptive immune response;mucosal immune response;protein deubiquitination;negative regulation of interleukin-8 production;protein K11-linked deubiquitination;negative regulation of I-kappaB kinase/NF-kappaB signaling;protein K63-linked deubiquitination;protein K48-linked deubiquitination;protein deubiquitination involved in ubiquitin-dependent protein catabolic process;negative regulation of protein localization to nucleus
• Cellular component: nucleus;cytoplasm;cytosol
• Molecular function: DNA binding;thiol-dependent ubiquitin-specific protease activity;protein binding;cysteine-type peptidase activity;zinc ion binding;thiol-dependent ubiquitinyl hydrolase activity;K63-linked polyubiquitin modification-dependent protein binding;Lys48-specific deubiquitinase activity