UBE3B

ubiquitin protein ligase E3B, the group of HECT domain containing

Basic information

Region (hg38): 12:109477402-109536705

Links

ENSG00000151148NCBI:89910OMIM:608047HGNC:13478Uniprot:Q7Z3V4AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • oculocerebrofacial syndrome, Kaufman type (Definitive), mode of inheritance: AR
  • oculocerebrofacial syndrome, Kaufman type (Supportive), mode of inheritance: AR
  • oculocerebrofacial syndrome, Kaufman type (Strong), mode of inheritance: AR
  • oculocerebrofacial syndrome, Kaufman type (Definitive), mode of inheritance: AR
  • oculocerebrofacial syndrome, Kaufman type (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Kaufman oculocerebrofacial syndrome (Blepharophimosis-ptosis-intellectual disability syndrome)ARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingCraniofacial; Neurologic; Ophthalmologic23200864

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the UBE3B gene.

  • not_provided (361 variants)
  • Inborn_genetic_diseases (134 variants)
  • Oculocerebrofacial_syndrome,_Kaufman_type (50 variants)
  • UBE3B-related_disorder (8 variants)
  • not_specified (2 variants)
  • Intellectual_disability (2 variants)
  • Blepharophimosis_-_intellectual_disability_syndrome (1 variants)
  • Optic_nerve_hypoplasia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBE3B gene is commonly pathogenic or not. These statistics are base on transcript: NM_000130466.4. 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
1
clinvar
112
clinvar
14
clinvar
127
missense
3
clinvar
4
clinvar
195
clinvar
10
clinvar
1
clinvar
213
nonsense
12
clinvar
5
clinvar
17
start loss
1
1
frameshift
16
clinvar
6
clinvar
1
clinvar
23
splice donor/acceptor (+/-2bp)
11
clinvar
8
clinvar
19
Total 42 24 197 122 15

Highest pathogenic variant AF is 0.0000560951

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
UBE3Bprotein_codingprotein_codingENST00000342494 2659301
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
4.19e-81.001256730751257480.000298
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.365396350.8480.00003926997
Missense in Polyphen130186.440.697262048
Synonymous0.8612322490.9310.00001532101
Loss of Function4.472462.00.3870.00000352661

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0009010.000901
Ashkenazi Jewish0.00009930.0000992
East Asian0.0003280.000326
Finnish0.0001390.000139
European (Non-Finnish)0.0003290.000325
Middle Eastern0.0003280.000326
South Asian0.0001640.000163
Other0.0001640.000163

dbNSFP

Source: dbNSFP

Function
FUNCTION: E3 ubiquitin-protein ligase which accepts ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. {ECO:0000250}.;
Pathway
Ubiquitin mediated proteolysis - Homo sapiens (human);Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation (Consensus)

Recessive Scores

pRec
0.0934

Intolerance Scores

loftool
0.874
rvis_EVS
-2.23
rvis_percentile_EVS
1.32

Haploinsufficiency Scores

pHI
0.194
hipred
Y
hipred_score
0.528
ghis
0.648

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.531

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Ube3b
Phenotype
growth/size/body region phenotype; homeostasis/metabolism phenotype; vision/eye 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); reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hearing/vestibular/ear phenotype;

Gene ontology

Biological process
protein polyubiquitination;ubiquitin-dependent protein catabolic process
Cellular component
Molecular function
ubiquitin conjugating enzyme activity