UBE2E1

ubiquitin conjugating enzyme E2 E1, the group of Ubiquitin conjugating enzymes E2

Basic information

Region (hg38): 3:23805955-23891640

Links

ENSG00000170142

∙ NCBI:7324 ∙ OMIM:602916 ∙ HGNC:12477 ∙ Uniprot:P51965 ∙ 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 UBE2E1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBE2E1 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 clinvar	1 clinvar	2
missense			4 clinvar			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	1	1

Variants in UBE2E1

This is a list of pathogenic ClinVar variants found in the UBE2E1 region.

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

Position	Phenotype	Significance	ClinVar
3-23807365-G-C	not specified	Uncertain significance (Jul 28, 2021)	2239789
3-23807390-A-C	not specified	Uncertain significance (Jan 31, 2024)	3185515
3-23887582-C-T		Benign/Likely benign (Apr 01, 2022)	781706
3-23889189-T-C		Benign (May 04, 2018)	779087
3-23890535-A-G	not specified	Uncertain significance (Sep 09, 2024)	3465063
3-23890542-A-G	not specified	Uncertain significance (Oct 13, 2021)	2255225

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UBE2E1	protein_coding	protein_coding	ENST00000306627	5	85414

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.705	0.291	125705	0	2	125707	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.99	49	107	0.458	0.00000514	1269
Missense in Polyphen		8	33.952	0.23563		422
Synonymous	0.522	35	39.2	0.894	0.00000205	360
Loss of Function	2.35	1	8.32	0.120	3.48e-7	114

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000893	0.00000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. Catalyzes the covalent attachment of ISG15 to other proteins. Mediates the selective degradation of short-lived and abnormal proteins. In vitro also catalyzes 'Lys-48'-linked polyubiquitination. {ECO:0000269|PubMed:16428300, ECO:0000269|PubMed:20061386}.;
Pathway: Ubiquitin mediated proteolysis - Homo sapiens (human);Photodynamic therapy-induced unfolded protein response;Cytokine Signaling in Immune system;Senescence-Associated Secretory Phenotype (SASP);Cellular Senescence;Cellular responses to stress;Post-translational protein modification;protein ubiquitylation;Metabolism of proteins;Inactivation of APC/C via direct inhibition of the APC/C complex;Inhibition of the proteolytic activity of APC/C required for the onset of anaphase by mitotic spindle checkpoint components;Mitotic Spindle Checkpoint;Cell Cycle Checkpoints;Synthesis of active ubiquitin: roles of E1 and E2 enzymes;Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;DNA Replication;Switching of origins to a post-replicative state;Class I MHC mediated antigen processing & presentation;Synthesis of DNA;S Phase;Cellular responses to external stimuli;Separation of Sister Chromatids;Mitotic Anaphase;Mitotic Metaphase and Anaphase;M Phase;Protein ubiquitination;Regulation of APC/C activators between G1/S and early anaphase;Phosphorylation of the APC/C;CDK-mediated phosphorylation and removal of Cdc6;Cdc20:Phospho-APC/C mediated degradation of Cyclin A;APC-Cdc20 mediated degradation of Nek2A;APC:Cdc20 mediated degradation of cell cycle proteins prior to satisfation of the cell cycle checkpoint;APC/C:Cdc20 mediated degradation of Cyclin B;APC/C:Cdc20 mediated degradation of Securin;APC/C:Cdc20 mediated degradation of mitotic proteins;Activation of APC/C and APC/C:Cdc20 mediated degradation of mitotic proteins;Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase;APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1;Autodegradation of Cdh1 by Cdh1:APC/C;APC/C-mediated degradation of cell cycle proteins;Regulation of mitotic cell cycle;Cell Cycle;Cell Cycle, Mitotic;ISG15 antiviral mechanism;Antiviral mechanism by IFN-stimulated genes;Interferon Signaling;E3 ubiquitin ligases ubiquitinate target proteins (Consensus)

Recessive Scores

pRec: 0.113

Intolerance Scores

loftool: 0.166
rvis_EVS: 0.28
rvis_percentile_EVS: 70.87

Haploinsufficiency Scores

pHI: 0.629
hipred: Y
hipred_score: 0.771
ghis

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: K
gene_indispensability_pred: E
gene_indispensability_score: 0.683

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Ube2e1
Phenotype

Gene ontology

Biological process: protein polyubiquitination;ubiquitin-dependent protein catabolic process;histone monoubiquitination;protein ubiquitination;anaphase-promoting complex-dependent catabolic process;ISG15-protein conjugation;histone H2B ubiquitination;protein K48-linked ubiquitination;regulation of mitotic cell cycle phase transition
Cellular component: ubiquitin ligase complex;nucleus;nucleoplasm;cytosol
Molecular function: ubiquitin-protein transferase activity;protein binding;ATP binding;ISG15 transferase activity;ubiquitin conjugating enzyme activity