UBE3D

ubiquitin protein ligase E3D

Basic information

Region (hg38): 6:82892389-83065841

Previous symbols: [ "C6orf157", "UBE2CBP" ]

Links

ENSG00000118420 ∙ NCBI:90025 ∙ OMIM:612495 ∙ HGNC:21381 ∙ Uniprot:Q7Z6J8 ∙ 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 UBE3D gene.

• Inborn genetic diseases (24 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBE3D 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			21	3		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	3	0

Variants in UBE3D

This is a list of pathogenic ClinVar variants found in the UBE3D region.

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

Position	Type	Phenotype	Significance	ClinVar
6-82893029-T-G		not specified	Uncertain significance (Mar 06, 2023)
6-82957329-G-A		not specified	Likely benign (Jan 31, 2022)
6-82957331-C-T		not specified	Uncertain significance (Apr 12, 2022)
6-82957404-G-C		not specified	Uncertain significance (Oct 06, 2021)
6-83019033-C-A		not specified	Uncertain significance (Dec 01, 2022)
6-83019040-C-T		not specified	Uncertain significance (Jan 20, 2023)
6-83019052-T-C		not specified	Uncertain significance (May 04, 2022)
6-83019069-A-T		not specified	Uncertain significance (Jun 16, 2023)
6-83022454-A-C		not specified	Uncertain significance (Feb 10, 2022)
6-83022557-A-C		not specified	Uncertain significance (Aug 08, 2022)
6-83022560-A-G		not specified	Uncertain significance (Sep 07, 2022)
6-83038452-G-A		not specified	Uncertain significance (Aug 04, 2023)
6-83044438-T-C		not specified	Uncertain significance (Aug 09, 2021)
6-83044442-T-G		not specified	Uncertain significance (Aug 15, 2023)
6-83044459-C-T		not specified	Uncertain significance (Mar 31, 2023)
6-83044578-A-C		not specified	Uncertain significance (Apr 05, 2023)
6-83044643-G-A		not specified	Uncertain significance (Jan 22, 2024)
6-83054151-T-G		not specified	Uncertain significance (Sep 23, 2023)
6-83054152-C-T		not specified	Uncertain significance (Nov 22, 2021)
6-83054161-T-G		not specified	Uncertain significance (Jul 19, 2022)
6-83057876-A-G		not specified	Likely benign (Mar 20, 2023)
6-83057894-C-T		not specified	Uncertain significance (Aug 12, 2021)
6-83057928-G-A		not specified	Uncertain significance (Jun 07, 2023)
6-83057931-G-A		not specified	Uncertain significance (Oct 03, 2023)
6-83057946-A-C		not specified	Uncertain significance (Aug 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UBE3D	protein_coding	protein_coding	ENST00000369747	10	173444

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.98e-7	0.884	125718	0	30	125748	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.284	196	208	0.944	0.0000105	2532
Missense in Polyphen		48	55.415	0.86619		686
Synonymous	-0.455	86	80.8	1.06	0.00000454	734
Loss of Function	1.60	13	20.9	0.622	9.27e-7	262

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000210	0.000210
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.00	0.00
South Asian	0.000402	0.000327
Other	0.000329	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 ubiquitin-protein ligase which accepts ubiquitin from specific E2 ubiquitin-conjugating enzymes, and transfers it to substrates, generally promoting their degradation by the proteasome. {ECO:0000269|PubMed:15749827}.
• Pathway: Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation (Consensus)

Recessive Scores

• pRec: 0.0736

Intolerance Scores

• rvis_EVS: 0.6
• rvis_percentile_EVS: 82.66

Haploinsufficiency Scores

• pHI: 0.0396
• hipred: N
• hipred_score: 0.438
• ghis: 0.439

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ube2cbp
• Phenotype: pigmentation 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); vision/eye phenotype

Gene ontology

• Biological process: protein polyubiquitination;protein monoubiquitination;protein autoubiquitination
• Cellular component: ubiquitin ligase complex;cytoplasm
• Molecular function: cyclin binding;ubiquitin-like protein conjugating enzyme binding;ubiquitin protein ligase activity