UBE2U

ubiquitin conjugating enzyme E2 U, the group of Ubiquitin conjugating enzymes E2

Basic information

Region (hg38): 1:64203623-64267368

Links

ENSG00000177414 ∙ NCBI:148581 ∙ ∙ HGNC:28559 ∙ Uniprot:Q5VVX9 ∙ 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 UBE2U gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBE2U 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			12	1		13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	1	0

Variants in UBE2U

This is a list of pathogenic ClinVar variants found in the UBE2U region.

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

Position	Type	Phenotype	Significance	ClinVar
1-64205639-G-A		not specified	Uncertain significance (Mar 25, 2024)
1-64205657-G-A		not specified	Uncertain significance (Nov 01, 2021)
1-64206789-T-A		not specified	Uncertain significance (Jan 22, 2025)
1-64210750-C-T		not specified	Uncertain significance (Mar 31, 2024)
1-64214837-T-A		not specified	Uncertain significance (Sep 25, 2023)
1-64214854-T-G		not specified	Uncertain significance (Feb 24, 2025)
1-64214883-T-G		not specified	Uncertain significance (Jun 02, 2023)
1-64214921-G-A		not specified	Uncertain significance (Jul 21, 2021)
1-64220891-C-T		not specified	Uncertain significance (Aug 08, 2022)
1-64220901-G-A		not specified	Uncertain significance (Jun 16, 2023)
1-64232581-T-A		not specified	Uncertain significance (Jun 04, 2024)
1-64232626-C-G		not specified	Uncertain significance (May 26, 2024)
1-64232641-G-A		not specified	Uncertain significance (Feb 24, 2025)
1-64241672-A-G		not specified	Uncertain significance (Oct 19, 2024)
1-64241704-T-A		not specified	Likely benign (Dec 06, 2023)
1-64241720-G-A		not specified	Uncertain significance (Dec 10, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UBE2U	protein_coding	protein_coding	ENST00000371076	9	63742

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.35e-7	0.379	125621	0	87	125708	0.000346

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.315	101	110	0.916	0.00000499	1489
Missense in Polyphen		21	31.915	0.658		443
Synonymous	-0.107	38	37.2	1.02	0.00000178	380
Loss of Function	0.665	12	14.8	0.813	6.22e-7	190

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000434	0.000431
Ashkenazi Jewish	0.00	0.00
East Asian	0.00160	0.00158
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000373	0.000369
Middle Eastern	0.00160	0.00158
South Asian	0.000138	0.000131
Other	0.000496	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the covalent attachment of ubiquitin to other proteins. {ECO:0000269|PubMed:22496338}.
• 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: 0.0714

Intolerance Scores

• loftool: 0.788
• rvis_EVS: 0.39
• rvis_percentile_EVS: 76.05

Haploinsufficiency Scores

• pHI: 0.0619
• hipred: N
• hipred_score: 0.144

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.273

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ube2u
• Phenotype: normal phenotype; 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)

Gene ontology

• Biological process: protein polyubiquitination;DNA repair;proteasome-mediated ubiquitin-dependent protein catabolic process
• Cellular component: nuclear chromatin;HULC complex
• Molecular function: protein binding;ATP binding;ubiquitin conjugating enzyme activity