UBE3C
Basic information
Region (hg38): 7:157138926-157269370
Links
Phenotypes
GenCC
Source:
- neurodevelopmental disorder with absent speech and movement and behavioral abnormalities (Limited), mode of inheritance: AR
- neurodevelopmental disorder with absent speech and movement and behavioral abnormalities (Strong), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Neurodevelopmental disorder with absent speech and movement and behavioral abnormalities | 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 | 36401616 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (97 variants)
- UBE3C-related_disorder (7 variants)
- not_provided (3 variants)
- Neurodevelopmental_disorder_with_absent_speech_and_movement_and_behavioral_abnormalities (2 variants)
- See_cases (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBE3C gene is commonly pathogenic or not. These statistics are base on transcript: NM_000014671.3. 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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 6 | |||||
missense | 97 | 99 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 1 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 1 | 97 | 8 | 0 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
UBE3C | protein_coding | protein_coding | ENST00000348165 | 23 | 130460 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.00 | 0.00000326 | 125708 | 1 | 38 | 125747 | 0.000155 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 2.54 | 421 | 596 | 0.707 | 0.0000326 | 7097 |
Missense in Polyphen | 67 | 148.43 | 0.45138 | 1779 | ||
Synonymous | 0.797 | 216 | 231 | 0.933 | 0.0000135 | 2075 |
Loss of Function | 6.41 | 5 | 57.4 | 0.0871 | 0.00000316 | 673 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000310 | 0.000309 |
Ashkenazi Jewish | 0.000199 | 0.000198 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000973 | 0.0000967 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.000827 | 0.000653 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: E3 ubiquitin-protein ligase that accepts ubiquitin from the E2 ubiquitin-conjugating enzyme UBE2D1 in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. Can assemble unanchored poly-ubiquitin chains in either 'Lys-29'- or 'Lys-48'-linked polyubiquitin chains. Has preference for 'Lys-48' linkages. It can target itself for ubiquitination in vitro and may promote its own degradation in vivo. {ECO:0000269|PubMed:11278995, ECO:0000269|PubMed:12692129, ECO:0000269|PubMed:16341092, ECO:0000269|PubMed:16601690}.;
- 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
- 0.229
Intolerance Scores
- loftool
- 0.473
- rvis_EVS
- -1.06
- rvis_percentile_EVS
- 7.54
Haploinsufficiency Scores
- pHI
- 0.0768
- hipred
- Y
- hipred_score
- 0.816
- ghis
- 0.600
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.877
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ube3c
- Phenotype
- growth/size/body region phenotype; homeostasis/metabolism phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; skeleton phenotype; hearing/vestibular/ear phenotype; limbs/digits/tail phenotype;
Gene ontology
- Biological process
- protein polyubiquitination;ubiquitin-dependent protein catabolic process
- Cellular component
- proteasome complex;nucleus
- Molecular function
- ubiquitin-protein transferase activity;protein binding;ubiquitin conjugating enzyme activity