UBE3D

ubiquitin protein ligase E3D

Basic information

Region (hg38): 6:82892390-83065841

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

Links

ENSG00000118420NCBI:90025OMIM:612495HGNC:21381Uniprot:Q7Z6J8AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the UBE3D gene.

  • not_specified (62 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. These statistics are base on transcript: NM_000198920.3. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
0
missense
55
clinvar
7
clinvar
62
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 55 7 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
UBE3Dprotein_codingprotein_codingENST00000369747 10173444
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
5.98e-70.8841257180301257480.000119
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.2841962080.9440.00001052532
Missense in Polyphen4855.4150.86619686
Synonymous-0.4558680.81.060.00000454734
Loss of Function1.601320.90.6229.27e-7262

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002100.000210
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.00004620.0000462
European (Non-Finnish)0.0001060.000105
Middle Eastern0.000.00
South Asian0.0004020.000327
Other0.0003290.000326

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

loftool
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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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