UBE2O

ubiquitin conjugating enzyme E2 O

Basic information

Region (hg38): 17:76389456-76453152

Links

ENSG00000175931 ∙ NCBI:63893 ∙ OMIM:617649 ∙ HGNC:29554 ∙ Uniprot:Q9C0C9 ∙ 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 UBE2O gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBE2O 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					1	1
missense			50			50
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	50	0	1

Variants in UBE2O

This is a list of pathogenic ClinVar variants found in the UBE2O region.

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

Position	Type	Phenotype	Significance	ClinVar
17-76391001-G-A		not specified	Uncertain significance (May 10, 2022)
17-76391013-C-T		not specified	Uncertain significance (Dec 26, 2023)
17-76391142-G-A		not specified	Uncertain significance (May 03, 2024)
17-76391151-G-A		not specified	Uncertain significance (Dec 19, 2022)
17-76391202-C-T		not specified	Uncertain significance (Dec 13, 2022)
17-76391280-C-A		not specified	Uncertain significance (Dec 04, 2024)
17-76391284-A-G		not specified	Uncertain significance (Jul 17, 2024)
17-76391292-A-G		not specified	Uncertain significance (Jun 07, 2023)
17-76391314-C-T		not specified	Uncertain significance (Oct 29, 2024)
17-76391319-G-A		not specified	Uncertain significance (May 26, 2023)
17-76391328-G-A		not specified	Uncertain significance (Jun 29, 2023)
17-76391343-T-C		not specified	Uncertain significance (Nov 21, 2024)
17-76391401-G-A		not specified	Uncertain significance (Sep 14, 2023)
17-76391404-T-C		not specified	Uncertain significance (Nov 21, 2022)
17-76391413-G-A		not specified	Uncertain significance (Nov 10, 2022)
17-76391461-C-T		not specified	Uncertain significance (Sep 30, 2022)
17-76396260-C-T		not specified	Uncertain significance (Oct 08, 2024)
17-76396284-C-T		not specified	Uncertain significance (Jul 12, 2022)
17-76396287-C-T		not specified	Uncertain significance (Dec 21, 2023)
17-76396413-C-T		not specified	Uncertain significance (May 01, 2024)
17-76396449-C-T		not specified	Uncertain significance (Aug 14, 2024)
17-76396481-T-C		not specified	Uncertain significance (May 24, 2023)
17-76396532-G-C		not specified	Uncertain significance (Oct 25, 2024)
17-76396548-C-T		not specified	Uncertain significance (May 21, 2024)
17-76396553-A-G		not specified	Uncertain significance (Sep 29, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UBE2O	protein_coding	protein_coding	ENST00000319380	18	63757

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	2.65e-7	125742	0	6	125748	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.44	482	747	0.645	0.0000466	8439
Missense in Polyphen		149	302.77	0.49212		3296
Synonymous	0.597	304	318	0.957	0.0000223	2576
Loss of Function	6.51	3	55.3	0.0543	0.00000301	627

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E2/E3 hybrid ubiquitin-protein ligase that displays both E2 and E3 ligase activities and mediates monoubiquitination of target proteins (PubMed:23455153, PubMed:24703950). Negatively regulates TRAF6-mediated NF-kappa-B activation independently of its E2 activity (PubMed:23381138). Acts as a positive regulator of BMP7 signaling by mediating monoubiquitination of SMAD6, thereby regulating adipogenesis (PubMed:23455153). Mediates monoubiquitination at different sites of the nuclear localization signal (NLS) of BAP1, leading to cytoplasmic retention of BAP1. Also able to monoubiquitinate the NLS of other chromatin- associated proteins, such as INO80 and CXXC1, affecting their subcellular location (PubMed:24703950). Acts as a regulator of retrograde transport by assisting the TRIM27:MAGEL2 E3 ubiquitin ligase complex to mediate 'Lys-63'-linked ubiquitination of WASHC1, leading to promote endosomal F-actin assembly (PubMed:23452853). {ECO:0000269|PubMed:23381138, ECO:0000269|PubMed:23452853, ECO:0000269|PubMed:23455153, ECO:0000269|PubMed:24703950}.
• Pathway: Ubiquitin mediated proteolysis - Homo sapiens (human);protein ubiquitylation;Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation (Consensus)

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.163
• rvis_EVS: -0.81
• rvis_percentile_EVS: 12.05

Haploinsufficiency Scores

• pHI: 0.536
• hipred: Y
• hipred_score: 0.825
• ghis: 0.553

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.871

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ube2o
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); cellular phenotype; homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); neoplasm

Gene ontology

• Biological process: protein monoubiquitination;positive regulation of BMP signaling pathway;retrograde transport, endosome to Golgi;protein K63-linked ubiquitination
• Cellular component: nucleus;cytoplasm;cytosol;nuclear body
• Molecular function: RNA binding;ubiquitin-protein transferase activity;protein binding;ATP binding;ubiquitin protein ligase activity;ubiquitin conjugating enzyme activity