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.

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.

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						0
missense			20	1		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	1	0

Variants in OTUD3

This is a list of pathogenic ClinVar variants found in the OTUD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-19882547-G-A		not specified	Uncertain significance (Feb 14, 2023)
1-19882570-G-T		not specified	Uncertain significance (Jan 29, 2024)
1-19882583-C-T		not specified	Uncertain significance (Apr 04, 2023)
1-19882602-G-A		not specified	Uncertain significance (Jan 16, 2024)
1-19882602-G-T		not specified	Uncertain significance (Jun 12, 2023)
1-19882610-C-G		not specified	Uncertain significance (Dec 08, 2023)
1-19882644-G-A		not specified	Uncertain significance (Oct 26, 2022)
1-19890472-G-C		not specified	Uncertain significance (Dec 06, 2021)
1-19897544-G-A		not specified	Uncertain significance (Apr 01, 2024)
1-19897579-A-G		not specified	Uncertain significance (Jul 14, 2022)
1-19897592-A-G		not specified	Uncertain significance (Dec 12, 2023)
1-19897625-A-C		not specified	Uncertain significance (May 15, 2024)
1-19897625-A-G		not specified	Uncertain significance (Jul 15, 2021)
1-19904891-G-A		not specified	Uncertain significance (Dec 20, 2023)
1-19904903-A-G		not specified	Uncertain significance (Feb 13, 2024)
1-19904957-G-A		not specified	Likely benign (Sep 01, 2021)
1-19904960-C-T		not specified	Uncertain significance (Apr 22, 2022)
1-19904963-C-G		not specified	Uncertain significance (Mar 13, 2023)
1-19906483-C-G		not specified	Uncertain significance (Dec 22, 2023)
1-19907605-G-T		not specified	Uncertain significance (Dec 18, 2023)
1-19907670-G-C		not specified	Uncertain significance (Apr 21, 2022)
1-19907706-A-C		not specified	Uncertain significance (Sep 27, 2021)
1-19907741-A-T		not specified	Uncertain significance (Dec 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OTUD3	protein_coding	protein_coding	ENST00000375120	8	30433

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000356	0.952	124730	0	76	124806	0.000305

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.766	169	199	0.847	0.0000110	2627
Missense in Polyphen		39	56.302	0.6927		750
Synonymous	1.10	61	73.0	0.836	0.00000418	723
Loss of Function	1.81	10	18.4	0.544	0.00000103	226

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00119	0.00119
Ashkenazi Jewish	0.00	0.00
East Asian	0.000231	0.000222
Finnish	0.00	0.00
European (Non-Finnish)	0.000134	0.000132
Middle Eastern	0.000231	0.000222
South Asian	0.000458	0.000458
Other	0.000330	0.000330

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

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

Mouse Genome Informatics

• Gene name: Otud3

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