UBE2L3

ubiquitin conjugating enzyme E2 L3, the group of Ubiquitin conjugating enzymes E2

Basic information

Region (hg38): 22:21549446-21624034

Links

ENSG00000185651 ∙ NCBI:7332 ∙ OMIM:603721 ∙ HGNC:12488 ∙ Uniprot:P68036 ∙ 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 UBE2L3 gene.

• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBE2L3 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	0	1

Variants in UBE2L3

This is a list of pathogenic ClinVar variants found in the UBE2L3 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-21550753-C-T		not specified	Likely benign (Oct 22, 2021)
22-21566528-G-C			Benign (Feb 26, 2021)
22-21610864-C-G		not specified	Uncertain significance (Nov 22, 2023)
22-21611009-C-G			Benign (Jul 15, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UBE2L3	protein_coding	protein_coding	ENST00000458578	4	74588

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.838	0.159	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.88	9	82.6	0.109	0.00000471	1382
Missense in Polyphen		1	29.266	0.03417		423
Synonymous	1.35	21	30.5	0.688	0.00000184	429
Loss of Function	2.27	0	6.00	0.00	2.52e-7	103

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Ubiquitin-conjugating enzyme E2 that specifically acts with HECT-type and RBR family E3 ubiquitin-protein ligases. Does not function with most RING-containing E3 ubiquitin-protein ligases because it lacks intrinsic E3-independent reactivity with lysine: in contrast, it has activity with the RBR family E3 enzymes, such as PRKN and ARIH1, that function like function like RING-HECT hybrids. Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro catalyzes 'Lys-11'-linked polyubiquitination. Involved in the selective degradation of short-lived and abnormal proteins. Down- regulated during the S-phase it is involved in progression through the cell cycle. Regulates nuclear hormone receptors transcriptional activity. May play a role in myelopoiesis. {ECO:0000269|PubMed:10888878, ECO:0000269|PubMed:15367689, ECO:0000269|PubMed:17003263, ECO:0000269|PubMed:18946090, ECO:0000269|PubMed:19340006, ECO:0000269|PubMed:20061386, ECO:0000269|PubMed:21532592}.
• Pathway: Ubiquitin mediated proteolysis - Homo sapiens (human);Parkinson,s disease - Homo sapiens (human);Parkin-Ubiquitin Proteasomal System pathway;Parkinsons Disease Pathway;role of parkin in ubiquitin-proteasomal pathway;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;BARD1 signaling events;E3 ubiquitin ligases ubiquitinate target proteins;Alpha-synuclein signaling (Consensus)

Recessive Scores

• pRec: 0.268

Intolerance Scores

• rvis_EVS: 0.15
• rvis_percentile_EVS: 63.81

Haploinsufficiency Scores

• pHI: 0.810
• hipred: Y
• hipred_score: 0.687
• ghis: 0.574

Essentials

• essential_gene_CRISPR: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 1.00

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ube2l3
• Phenotype: growth/size/body region phenotype; 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); 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); embryo phenotype

Gene ontology

• Biological process: protein polyubiquitination;regulation of transcription, DNA-templated;cellular protein modification process;ubiquitin-dependent protein catabolic process;cell population proliferation;protein ubiquitination;positive regulation of protein ubiquitination;cell cycle phase transition;positive regulation of ubiquitin-protein transferase activity;protein K11-linked ubiquitination;cellular response to steroid hormone stimulus;cellular response to glucocorticoid stimulus;positive regulation of nucleic acid-templated transcription;positive regulation of protein targeting to mitochondrion
• Cellular component: ubiquitin ligase complex;nucleus;nucleoplasm;cytoplasm;cytosol
• Molecular function: transcription coactivator activity;RNA binding;ubiquitin-protein transferase activity;protein binding;ATP binding;enzyme binding;ubiquitin protein ligase binding;ubiquitin conjugating enzyme activity;ubiquitin-protein transferase activator activity