UBR2
Basic information
Region (hg38): 6:42564029-42693505
Previous symbols: [ "C6orf133" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (163 variants)
- not_provided (13 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBR2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001363705.2. 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 | 151 | 157 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 151 | 11 | 1 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
UBR2 | protein_coding | protein_coding | ENST00000372899 | 47 | 129443 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.00 | 2.23e-7 | 125714 | 0 | 34 | 125748 | 0.000135 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 3.15 | 651 | 919 | 0.708 | 0.0000468 | 11595 |
Missense in Polyphen | 115 | 215.97 | 0.53247 | 2585 | ||
Synonymous | 0.252 | 306 | 312 | 0.982 | 0.0000160 | 3123 |
Loss of Function | 8.33 | 15 | 109 | 0.138 | 0.00000558 | 1347 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000180 | 0.000179 |
Ashkenazi Jewish | 0.000201 | 0.000198 |
East Asian | 0.000110 | 0.000109 |
Finnish | 0.0000463 | 0.0000462 |
European (Non-Finnish) | 0.000223 | 0.000211 |
Middle Eastern | 0.000110 | 0.000109 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: E3 ubiquitin-protein ligase which is a component of the N-end rule pathway. Recognizes and binds to proteins bearing specific N-terminal residues that are destabilizing according to the N-end rule, leading to their ubiquitination and subsequent degradation. Plays a critical role in chromatin inactivation and chromosome-wide transcriptional silencing during meiosis via ubiquitination of histone H2A. Binds leucine and is a negative regulator of the leucine-mTOR signaling pathway, thereby controlling cell growth. Required for spermatogenesis, promotes, with Tex19.1, SPO11-dependent recombination foci to accumulate and drive robust homologous chromosome synapsis (By similarity). Polyubiquitinates LINE-1 retrotransposon encoded, LIRE1, which induces degradation, inhibiting LINE-1 retranstoposon mobilization (By similarity). {ECO:0000250|UniProtKB:Q6WKZ8, ECO:0000269|PubMed:15548684, ECO:0000269|PubMed:20298436, ECO:0000269|PubMed:20835242}.;
- Pathway
- Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation
(Consensus)
Recessive Scores
- pRec
- 0.259
Intolerance Scores
- loftool
- 0.470
- rvis_EVS
- -1.37
- rvis_percentile_EVS
- 4.52
Haploinsufficiency Scores
- pHI
- 0.728
- hipred
- Y
- hipred_score
- 0.696
- ghis
- 0.577
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.821
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | High |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ubr2
- Phenotype
- embryo 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); 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; 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); growth/size/body region phenotype; endocrine/exocrine gland phenotype; muscle phenotype; homeostasis/metabolism phenotype; cellular phenotype;
Gene ontology
- Biological process
- protein polyubiquitination;chromatin silencing;reciprocal meiotic recombination;male meiotic nuclear division;male meiosis I;spermatogenesis;negative regulation of transposition;protein ubiquitination;negative regulation of TOR signaling;histone H2A ubiquitination;cellular response to leucine;ubiquitin-dependent protein catabolic process via the N-end rule pathway
- Cellular component
- ubiquitin ligase complex;chromatin;nucleus;cytoplasm;cytosol
- Molecular function
- ubiquitin-protein transferase activity;protein binding;zinc ion binding;ubiquitin protein ligase activity;leucine binding