UBA52
ubiquitin A-52 residue ribosomal protein fusion product 1, the group of L ribosomal proteins
Basic information
Region (hg38): 19:18571730-18577550
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBA52 gene is commonly pathogenic or not.
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.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 2 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 2 | 0 | 0 |
Variants in UBA52
This is a list of pathogenic ClinVar variants found in the UBA52 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 19-18573368-T-C | not specified | Uncertain significance (Dec 20, 2022) | ||
| 19-18573706-C-G | not specified | Uncertain significance (Aug 08, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| UBA52 | protein_coding | protein_coding | ENST00000442744 | 4 | 5821 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.598 | 0.393 | 125603 | 0 | 1 | 125604 | 0.00000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.88 | 35 | 83.5 | 0.419 | 0.00000539 | 838 |
| Missense in Polyphen | 4 | 13.092 | 0.30554 | 187 | ||
| Synonymous | 0.961 | 21 | 27.4 | 0.766 | 0.00000142 | 245 |
| Loss of Function | 2.12 | 1 | 7.08 | 0.141 | 3.84e-7 | 78 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000880 | 0.00000880 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Ubiquitin: Exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.;
- Pathway
- Ribosome - Homo sapiens (human);DNA Replication;Cytoplasmic Ribosomal Proteins;Developmental Biology;Signaling by PTK6;Negative regulation of FGFR2 signaling;Signaling by FGFR2;HDR through Homologous Recombination (HR) or Single Strand Annealing (SSA);Degradation of beta-catenin by the destruction complex;Disorders of transmembrane transporters;Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha;Regulation of Hypoxia-inducible Factor (HIF) by oxygen;Cellular response to hypoxia;Transcriptional regulation by RUNX2;Toll Like Receptor 7/8 (TLR7/8) Cascade;Regulation of RUNX3 expression and activity;Fanconi Anemia Pathway;DNA Repair;Interleukin-17 signaling;Disease;Negative regulation of FGFR3 signaling;Signaling by FGFR3;Signaling by WNT;Signal Transduction;Gene expression (Transcription);DNA Double-Strand Break Repair;Signaling by Interleukins;Negative regulation of FGFR4 signaling;Signaling by FGFR4;Signaling by FGFR;p75NTR signals via NF-kB;Transcriptional regulation by RUNX3;Defective CFTR causes cystic fibrosis;Spry regulation of FGF signaling;Vesicle-mediated transport;GLI3 is processed to GLI3R by the proteasome;Regulation of PTEN localization;SRP-dependent cotranslational protein targeting to membrane;Membrane Trafficking;Generic Transcription Pathway;Regulation of PTEN stability and activity;Stimuli-sensing channels;Ion channel transport;Oncogene Induced Senescence;Cytokine Signaling in Immune system;ER Quality Control Compartment (ERQC);Calnexin/calreticulin cycle;Assembly Of The HIV Virion;Toll Like Receptor 9 (TLR9) Cascade;Oxidative Stress Induced Senescence;Budding and maturation of HIV virion;Late Phase of HIV Life Cycle;HIV Life Cycle;Host Interactions of HIV factors;HIV Infection;Eukaryotic Translation Initiation;MyD88 cascade initiated on plasma membrane;Toll Like Receptor 10 (TLR10) Cascade;TICAM1, RIP1-mediated IKK complex recruitment ;Toll Like Receptor 3 (TLR3) Cascade;MAPK6/MAPK4 signaling;Toll Like Receptor 5 (TLR5) Cascade;Toll-Like Receptors Cascades;Senescence-Associated Secretory Phenotype (SASP);Cellular Senescence;Homology Directed Repair;Eukaryotic Translation Termination;Translation;Cellular responses to stress;Josephin domain DUBs;Post-translational protein modification;Endosomal Sorting Complex Required For Transport (ESCRT);Selenocysteine synthesis;Metabolism of proteins;Regulation of innate immune responses to cytosolic DNA;Metabolism of amino acids and derivatives;Interleukin-1 signaling;RNA Polymerase II Transcription;Autodegradation of the E3 ubiquitin ligase COP1;Stabilization of p53;p53-Dependent G1 DNA Damage Response;p53-Dependent G1/S DNA damage checkpoint;Ubiquitin Mediated Degradation of Phosphorylated Cdc25A;p53-Independent DNA Damage Response;p53-Independent G1/S DNA damage checkpoint;G1/S DNA Damage Checkpoints;Metabolism of RNA;Receptor-ligand binding initiates the second proteolytic cleavage of Notch receptor;Formation of a pool of free 40S subunits;Cell Cycle Checkpoints;Infectious disease;Synthesis of active ubiquitin: roles of E1 and E2 enzymes;Innate Immune System;Immune System;Metabolism;Regulation of RAS by GAPs;Cyclin D associated events in G1;G1 Phase;Adaptive Immune System;SCF(Skp2)-mediated degradation of p27/p21;Cyclin E associated events during G1/S transition ;SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription;Peroxisomal protein import;Nonsense-Mediated Decay (NMD);Downregulation of SMAD2/3:SMAD4 transcriptional activity;Signaling by NOTCH1;PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1;Antigen processing: Ubiquitination & Proteasome degradation;Mitotic G1-G1/S phases;Signaling by NOTCH2;Transport of small molecules;Selenoamino acid metabolism;Pink/Parkin Mediated Mitophagy;Cyclin A:Cdk2-associated events at S phase entry;Amyloid fiber formation;Mitophagy;Membrane binding and targetting of GAG proteins;Synthesis And Processing Of GAG, GAGPOL Polyproteins;Orc1 removal from chromatin;Downregulation of ERBB4 signaling;DNA Replication;NOTCH3 Activation and Transmission of Signal to the Nucleus;Switching of origins to a post-replicative state;Class I MHC mediated antigen processing & presentation;Signaling by NOTCH3;Signaling by NOTCH;Regulation of FZD by ubiquitination;Hedgehog ligand biogenesis;Synthesis of DNA;Ubiquitin-dependent degradation of Cyclin D1;Ubiquitin-dependent degradation of Cyclin D;Metalloprotease DUBs;S Phase;EGFR downregulation;Signaling by EGFR;Degradation of GLI2 by the proteasome;Deactivation of the beta-catenin transactivating complex;Degradation of GLI1 by the proteasome;Hedgehog ,off, state;Downregulation of ERBB2:ERBB3 signaling;Downregulation of ERBB2 signaling;Cellular responses to external stimuli;Hedgehog ,on, state;Signaling by Hedgehog;Clathrin-mediated endocytosis;UCH proteinases;Asymmetric localization of PCP proteins;Regulation of PLK1 Activity at G2/M Transition;Transcriptional activity of SMAD2/SMAD3:SMAD4 heterotrimer;PCP/CE pathway;MAP3K8 (TPL2)-dependent MAPK1/3 activation;Asparagine N-linked glycosylation;MAP kinase activation;TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation;Beta-catenin independent WNT signaling;NRIF signals cell death from the nucleus;ABC-family proteins mediated transport;Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC);Neddylation;MyD88 dependent cascade initiated on endosome;Ub-specific processing proteases;Negative regulation of MAPK pathway;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades;Regulation of TP53 Degradation;Regulation of TP53 Expression and Degradation;FBXL7 down-regulates AURKA during mitotic entry and in early mitosis;Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC);G2/M Transition;Mitotic G2-G2/M phases;PTEN Regulation;PIP3 activates AKT signaling;Ovarian tumor domain proteases;NOTCH2 Activation and Transmission of Signal to the Nucleus;Signaling by Non-Receptor Tyrosine Kinases;Deubiquitination;G1/S Transition;Regulation of TP53 Activity through Phosphorylation;NF-kB is activated and signals survival;Death Receptor Signalling;Regulation of TP53 Activity through Methylation;p75 NTR receptor-mediated signalling;Regulation of expression of SLITs and ROBOs;Cargo recognition for clathrin-mediated endocytosis;Signaling by ROBO receptors;Regulation of TP53 Activity;Transcriptional Regulation by TP53;Recognition of DNA damage by PCNA-containing replication complex;Translesion synthesis by REV1;Separation of Sister Chromatids;Mitotic Anaphase;Mitotic Metaphase and Anaphase;Axon guidance;Translesion Synthesis by POLH;M Phase;Degradation of DVL;Translesion synthesis by POLK;Protein ubiquitination;L13a-mediated translational silencing of Ceruloplasmin expression;Vif-mediated degradation of APOBEC3G;CDT1 association with the CDC6:ORC:origin complex;Assembly of the pre-replicative complex;DNA Replication Pre-Initiation;M/G1 Transition;Translesion synthesis by POLI;SCF-beta-TrCP mediated degradation of Emi1;Regulation of APC/C activators between G1/S and early anaphase;Signaling by ERBB2;CDK-mediated phosphorylation and removal of Cdc6;Cdc20:Phospho-APC/C mediated degradation of Cyclin A;APC-Cdc20 mediated degradation of Nek2A;APC:Cdc20 mediated degradation of cell cycle proteins prior to satisfation of the cell cycle checkpoint;Termination of translesion DNA synthesis;Translesion synthesis by Y family DNA polymerases bypasses lesions on DNA template;DNA Damage Bypass;APC/C:Cdc20 mediated degradation of Cyclin B;APC/C:Cdc20 mediated degradation of Securin;APC/C:Cdc20 mediated degradation of mitotic proteins;Activation of APC/C and APC/C:Cdc20 mediated degradation of mitotic proteins;Constitutive Signaling by NOTCH1 HD Domain Mutants;Signaling by NOTCH1 HD Domain Mutants in Cancer;RUNX1 regulates transcription of genes involved in differentiation of HSCs;Signaling by ERBB4;APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1;Autodegradation of Cdh1 by Cdh1:APC/C;APC/C-mediated degradation of cell cycle proteins;Regulation of mitotic cell cycle;Cell Cycle;Constitutive Signaling by NOTCH1 PEST Domain Mutants;Signaling by NOTCH1 PEST Domain Mutants in Cancer;Iron uptake and transport;Peptide chain elongation;Eukaryotic Translation Elongation;N-glycan trimming in the ER and Calnexin/Calreticulin cycle;Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants;Signaling by NOTCH1 HD+PEST Domain Mutants in Cancer;Signaling by NOTCH1 in Cancer;Cytosolic sensors of pathogen-associated DNA ;DNA Damage Recognition in GG-NER;IKK complex recruitment mediated by RIP1;TRIF(TICAM1)-mediated TLR4 signaling ;MyD88-independent TLR4 cascade ;Toll Like Receptor 4 (TLR4) Cascade;Vpu mediated degradation of CD4;Hh mutants that don,t undergo autocatalytic processing are degraded by ERAD;Hh mutants abrogate ligand secretion;Negative regulation of MET activity;Signaling by MET;Signaling by Receptor Tyrosine Kinases;Signaling by TGF-beta Receptor Complex;Formation of Incision Complex in GG-NER;GTP hydrolysis and joining of the 60S ribosomal subunit;Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks;DNA Double Strand Break Response;ABC transporter disorders;Dual Incision in GG-NER;Gap-filling DNA repair synthesis and ligation in GG-NER;Global Genome Nucleotide Excision Repair (GG-NER);Signaling by TGF-beta family members;Cell Cycle, Mitotic;Downregulation of TGF-beta receptor signaling;Cap-dependent Translation Initiation;TGF-beta receptor signaling activates SMADs;Intracellular signaling by second messengers;Formation of TC-NER Pre-Incision Complex;MyD88:Mal cascade initiated on plasma membrane;Toll Like Receptor TLR1:TLR2 Cascade;Toll Like Receptor TLR6:TLR2 Cascade;Toll Like Receptor 2 (TLR2) Cascade;Transcriptional regulation by RUNX1;Diseases of signal transduction;E3 ubiquitin ligases ubiquitinate target proteins;Processing of DNA double-strand break ends;TCF dependent signaling in response to WNT;Cell death signalling via NRAGE, NRIF and NADE;NOTCH1 Intracellular Domain Regulates Transcription;TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition);Interleukin-1 family signaling;Degradation of AXIN;Dual incision in TC-NER;Activated NOTCH1 Transmits Signal to the Nucleus;Gap-filling DNA repair synthesis and ligation in TC-NER;Transcription-Coupled Nucleotide Excision Repair (TC-NER);Nucleotide Excision Repair;Regulation of RUNX2 expression and activity;InlA-mediated entry of Listeria monocytogenes into host cells;Negative regulation of FGFR1 signaling;Signaling by FGFR1;HDR through Homologous Recombination (HRR);InlB-mediated entry of Listeria monocytogenes into host cell;Listeria monocytogenes entry into host cells
(Consensus)
Recessive Scores
- pRec
- 0.186
Intolerance Scores
- loftool
- 0.615
- rvis_EVS
- -0.03
- rvis_percentile_EVS
- 51.04
Haploinsufficiency Scores
- pHI
- hipred
- Y
- hipred_score
- 0.743
- ghis
- 0.548
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.860
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Uba52
- Phenotype
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;activation of MAPK activity;protein polyubiquitination;nucleotide-excision repair, DNA damage recognition;MyD88-dependent toll-like receptor signaling pathway;transcription-coupled nucleotide-excision repair;nucleotide-excision repair, preincision complex assembly;nucleotide-excision repair, DNA incision, 5'-to lesion;nucleotide-excision repair, DNA gap filling;translational initiation;cellular protein modification process;SRP-dependent cotranslational protein targeting to membrane;protein targeting to peroxisome;transforming growth factor beta receptor signaling pathway;I-kappaB kinase/NF-kappaB signaling;JNK cascade;Wnt signaling pathway;endosomal transport;protein ubiquitination;protein deubiquitination;response to insecticide;viral life cycle;virion assembly;cytokine-mediated signaling pathway;modification-dependent protein catabolic process;translesion synthesis;negative regulation of transforming growth factor beta receptor signaling pathway;anaphase-promoting complex-dependent catabolic process;nucleotide-excision repair, DNA incision;TRIF-dependent toll-like receptor signaling pathway;interstrand cross-link repair;error-prone translesion synthesis;DNA damage response, detection of DNA damage;positive regulation of apoptotic process;negative regulation of apoptotic process;regulation of mRNA stability;cellular protein metabolic process;positive regulation of transcription by RNA polymerase II;positive regulation of NF-kappaB transcription factor activity;stress-activated MAPK cascade;transmembrane transport;membrane organization;regulation of transcription from RNA polymerase II promoter in response to hypoxia;nucleotide-binding oligomerization domain containing signaling pathway;interleukin-1-mediated signaling pathway;global genome nucleotide-excision repair;error-free translesion synthesis;intracellular transport of virus
- Cellular component
- extracellular space;nucleus;nucleoplasm;cytoplasm;mitochondrial outer membrane;lysosomal membrane;endoplasmic reticulum;endoplasmic reticulum membrane;cytosol;plasma membrane;endosome membrane;cytosolic large ribosomal subunit;cytosolic small ribosomal subunit;endocytic vesicle membrane;vesicle;host cell;extracellular exosome
- Molecular function
- structural constituent of ribosome;protein binding;protein tag;ubiquitin protein ligase binding