GeneBe

OTUD3

OTU deubiquitinase 3, the group of OTU domain containing

Basic information

Region (hg38): 1:19882395-19912945

Links

ENSG00000169914 ∙ NCBI:23252 ∙ OMIM:611758 ∙ HGNC:29038 ∙ Uniprot:Q5T2D3 ∙ 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 OTUD3 gene.

  • not_specified (41 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OTUD3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000015207.2. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
0
missense
39
clinvar
2
clinvar
 41
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 39 2 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
OTUD3protein_codingprotein_codingENST00000375120 830433
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.00003560.9521247300761248060.000305
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.7661691990.8470.00001102627
Missense in Polyphen3956.3020.6927750
Synonymous1.106173.00.8360.00000418723
Loss of Function1.811018.40.5440.00000103226

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001190.00119
Ashkenazi Jewish0.000.00
East Asian0.0002310.000222
Finnish0.000.00
European (Non-Finnish)0.0001340.000132
Middle Eastern0.0002310.000222
South Asian0.0004580.000458
Other0.0003300.000330

dbNSFP

Source: dbNSFP

Function
FUNCTION: Deubiquitinating enzyme that hydrolyzes 'Lys-6'- and 'Lys-11'-linked polyubiquitin. Also hydrolyzes heterotypic (mixed and branched) and homotypic chains. {ECO:0000269|PubMed:23827681}.;
Pathway
Signal Transduction;Regulation of PTEN stability and activity;Post-translational protein modification;Metabolism of proteins;PTEN Regulation;PIP3 activates AKT signaling;Ovarian tumor domain proteases;Deubiquitination;Intracellular signaling by second messengers (Consensus)

Recessive Scores

pRec
0.103

Intolerance Scores

loftool
0.789
rvis_EVS
0.35
rvis_percentile_EVS
74.18

Haploinsufficiency Scores

pHI
0.126
hipred
N
hipred_score
0.282
ghis
0.505

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.543

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Otud3
Phenotype

Zebrafish Information Network

Gene name
otud3
Affected structure
post-vent region
Phenotype tag
abnormal
Phenotype quality
curled

Gene ontology

Biological process
protein deubiquitination;protein K11-linked deubiquitination;protein K6-linked deubiquitination;protein stabilization;negative regulation of protein kinase B signaling;protein K48-linked deubiquitination;protein K27-linked deubiquitination
Cellular component
cytoplasm;cytosol
Molecular function
thiol-dependent ubiquitin-specific protease activity;protein binding;thiol-dependent ubiquitinyl hydrolase activity