UBE3B
Basic information
Region (hg38): 12:109477402-109536705
Links
Phenotypes
GenCC
Source:
- 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:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Kaufman oculocerebrofacial syndrome (Blepharophimosis-ptosis-intellectual disability syndrome) | AR | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Craniofacial; Neurologic; Ophthalmologic | 23200864 |
ClinVar
This is a list of variants' phenotypes submitted to
- 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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 112 | 14 | 127 | |||
missense | 195 | 10 | 213 | |||
nonsense | 12 | 17 | ||||
start loss | 1 | 1 | ||||
frameshift | 16 | 23 | ||||
splice donor/acceptor (+/-2bp) | 11 | 19 | ||||
Total | 42 | 24 | 197 | 122 | 15 |
Highest pathogenic variant AF is 0.0000560951
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
UBE3B | protein_coding | protein_coding | ENST00000342494 | 26 | 59301 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
4.19e-8 | 1.00 | 125673 | 0 | 75 | 125748 | 0.000298 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.36 | 539 | 635 | 0.848 | 0.0000392 | 6997 |
Missense in Polyphen | 130 | 186.44 | 0.69726 | 2048 | ||
Synonymous | 0.861 | 232 | 249 | 0.931 | 0.0000153 | 2101 |
Loss of Function | 4.47 | 24 | 62.0 | 0.387 | 0.00000352 | 661 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000901 | 0.000901 |
Ashkenazi Jewish | 0.0000993 | 0.0000992 |
East Asian | 0.000328 | 0.000326 |
Finnish | 0.000139 | 0.000139 |
European (Non-Finnish) | 0.000329 | 0.000325 |
Middle Eastern | 0.000328 | 0.000326 |
South Asian | 0.000164 | 0.000163 |
Other | 0.000164 | 0.000163 |
dbNSFP
Source:
- 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
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
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