OTUB2

OTU deubiquitinase, ubiquitin aldehyde binding 2, the group of OTU domain containing

Basic information

Region (hg38): 14:94026340-94048930

Previous symbols: [ "C14orf137" ]

Links

ENSG00000089723 ∙ NCBI:78990 ∙ OMIM:608338 ∙ HGNC:20351 ∙ Uniprot:Q96DC9 ∙ 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 OTUB2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OTUB2 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			16	2		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	2	0

Variants in OTUB2

This is a list of pathogenic ClinVar variants found in the OTUB2 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-94037461-C-T		not specified	Uncertain significance (Aug 31, 2022)
14-94037462-G-A		not specified	Likely benign (Aug 09, 2021)
14-94037465-G-A		not specified	Uncertain significance (May 18, 2022)
14-94038966-C-G		not specified	Uncertain significance (Mar 07, 2023)
14-94038974-A-C		not specified	Uncertain significance (Jun 29, 2023)
14-94038984-G-A		not specified	Uncertain significance (Aug 23, 2021)
14-94038990-C-T		not specified	Uncertain significance (Jun 28, 2022)
14-94039005-G-C		not specified	Uncertain significance (Mar 25, 2022)
14-94043981-C-T		not specified	Uncertain significance (Nov 08, 2022)
14-94043982-G-A		not specified	Uncertain significance (May 26, 2024)
14-94043993-A-G		not specified	Uncertain significance (May 10, 2024)
14-94044607-G-A		not specified	Uncertain significance (Oct 20, 2023)
14-94044698-C-T		not specified	Uncertain significance (Jun 07, 2023)
14-94044718-C-G		not specified	Uncertain significance (Nov 03, 2023)
14-94044733-C-T		not specified	Uncertain significance (Mar 25, 2024)
14-94044742-A-G		not specified	Uncertain significance (Dec 01, 2022)
14-94044770-T-A		not specified	Uncertain significance (Mar 07, 2023)
14-94045730-G-A		not specified	Uncertain significance (Mar 28, 2024)
14-94045735-C-T		not specified	Likely benign (Mar 07, 2023)
14-94045809-G-A		not specified	Uncertain significance (Feb 09, 2023)
14-94045836-G-A		not specified	Uncertain significance (Jul 14, 2021)
14-94045858-C-A		not specified	Uncertain significance (Jul 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OTUB2	protein_coding	protein_coding	ENST00000203664	6	22602

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.54e-11	0.0153	125703	0	45	125748	0.000179

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.452	126	141	0.893	0.00000865	1559
Missense in Polyphen		43	46.235	0.93004		509
Synonymous	-0.530	67	61.7	1.09	0.00000433	445
Loss of Function	-0.908	14	10.8	1.30	6.33e-7	126

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000236	0.000236
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.0000930	0.0000924
European (Non-Finnish)	0.000133	0.000132
Middle Eastern	0.000163	0.000163
South Asian	0.000525	0.000523
Other	0.000331	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Hydrolase that can remove conjugated ubiquitin from proteins in vitro and may therefore play an important regulatory role at the level of protein turnover by preventing degradation. Mediates deubiquitination of 'Lys-11'-,'Lys-48'- and 'Lys-63'- linked polyubiquitin chains, with a preference for 'Lys-63'-linked polyubiquitin chains. {ECO:0000269|PubMed:12704427, ECO:0000269|PubMed:18954305, ECO:0000269|PubMed:23827681}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Ovarian tumor domain proteases;Deubiquitination (Consensus)

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.638
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.66

Haploinsufficiency Scores

• pHI: 0.733
• hipred: N
• hipred_score: 0.282
• ghis: 0.567

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.745

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Otub2

Gene ontology

• Biological process: protein deubiquitination;protein K11-linked deubiquitination;protein K63-linked deubiquitination;protein K48-linked deubiquitination
• Cellular component: nucleus
• Molecular function: thiol-dependent ubiquitin-specific protease activity;protein binding;NEDD8-specific protease activity;ubiquitin binding