UBE2E3

ubiquitin conjugating enzyme E2 E3, the group of Ubiquitin conjugating enzymes E2

Basic information

Region (hg38): 2:180967248-181076585

Links

ENSG00000170035

∙ NCBI:10477 ∙ OMIM:604151 ∙ HGNC:12479 ∙ Uniprot:Q969T4 ∙ 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 UBE2E3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBE2E3 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			2 clinvar			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	0	0

Variants in UBE2E3

This is a list of pathogenic ClinVar variants found in the UBE2E3 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-180982173-A-G		not specified	Uncertain significance (Dec 28, 2022)	2339918
2-181060702-A-G		not specified	Uncertain significance (Nov 20, 2024)	3465066

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UBE2E3	protein_coding	protein_coding	ENST00000410062	5	109338

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.426	0.567	125665	0	2	125667	0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.75	29	110	0.263	0.00000529	1353
Missense in Polyphen		3	36.268	0.082718		443
Synonymous	-0.158	42	40.7	1.03	0.00000222	395
Loss of Function	2.27	2	9.61	0.208	4.46e-7	124

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000885	0.00000880
Middle Eastern	0.00	0.00
South Asian	0.0000329	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro catalyzes 'Lys- 11'- and 'Lys-48'-, as well as 'Lys-63'-linked polyubiquitination. Participates in the regulation of transepithelial sodium transport in renal cells. May be involved in cell growth arrest. {ECO:0000269|PubMed:10343118, ECO:0000269|PubMed:20061386}.;
Pathway: Ubiquitin mediated proteolysis - Homo sapiens (human);Post-translational protein modification;protein ubiquitylation;Metabolism of proteins;Synthesis of active ubiquitin: roles of E1 and E2 enzymes;Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation;Protein ubiquitination (Consensus)

Intolerance Scores

loftool: 0.412
rvis_EVS: 0.06
rvis_percentile_EVS: 58

Haploinsufficiency Scores

pHI: 0.137
hipred: Y
hipred_score: 0.514
ghis: 0.525

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: H
gene_indispensability_pred: E
gene_indispensability_score: 0.800

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Ube2e3
Phenotype

Gene ontology

Biological process: protein ubiquitination;regulation of growth;protein K63-linked ubiquitination;protein K48-linked ubiquitination;protein K11-linked ubiquitination
Cellular component: nucleoplasm;cytosol
Molecular function: ubiquitin-protein transferase activity;protein binding;ATP binding;ubiquitin conjugating enzyme activity