UBE3B

ubiquitin protein ligase E3B, the group of HECT domain containing

Basic information

Region (hg38): 12:109477402-109536705

Links

ENSG00000151148

∙ NCBI:89910 ∙ OMIM:608047 ∙ HGNC:13478 ∙ Uniprot:Q7Z3V4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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

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 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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
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

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: 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

	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