UBA52

protein-coding

ubiquitin A-52 residue ribosomal protein fusion product 1, the group of L ribosomal proteins

Gene summary

Ubiquitin is a highly conserved nuclear and cytoplasmic protein that has a major role in targeting cellular proteins for degradation by the 26S proteosome. It is also involved in the maintenance of chromatin structure, the regulation of gene expression, and the stress response. Ubiquitin is synthesized as a precursor protein consisting of either polyubiquitin chains or a single ubiquitin moiety fused to an unrelated protein. This gene encodes a fusion protein consisting of ubiquitin at the N terminus and ribosomal protein L40 at the C terminus, a C-terminal extension protein (CEP). Multiple processed pseudogenes derived from this gene are present in the genome. [provided by RefSeq, Jul 2008]

MANE transcript

NM_001033930.3

Inheritance

—

ClinVar variants

U:12

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.14

Max pathogenic AF

—

Genomic locus

chr19:18,571,730-18,577,550

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~5.8 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to UBA52 variants in ClinVar

1 Conditions Cataloged
not specifiedTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001033930.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
1
clinvar
1
missense
7
clinvar
7
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
4
clinvar
4
Total00120012
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 107 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_001033930.3RefSeqNP_001029102.14MANE Select
ENST00000442744.7EnsemblENSP00000388107.14MANE Select
NM_001321017.2RefSeqNP_001307946.14Standard
NM_001321018.2RefSeqNP_001307947.14Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Ribosome - Homo sapiens (human)
  • DNA Replication
  • Cytoplasmic Ribosomal Proteins
  • Developmental Biology
  • Signaling by PTK6

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

Molecular Function

  • structural constituent of ribosome
  • protein binding
  • protein tag
  • ubiquitin protein ligase binding

Cellular Component

  • extracellular space
  • nucleus
  • nucleoplasm
  • cytoplasm
  • mitochondrial outer membrane

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000442744
Coding exons
4
Length
5821
Individuals with no LoFs
125603
Homozygous LoFs
0
Heterozygous LoFs
1
Defined
125604
p
0.00000398
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense1.883583.50.4190.00000539838
Missense (PolyPhen)413.0920.30554187
Synonymous0.9612127.40.7660.00000142245
Loss of Function2.1217.080.1413.84e-778

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)0.00000880.0000088rare
South Asian00.0absent
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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.;

Recessive Scores

pRec
0.186

Intolerance Scores

LoFtool
0.615
RVIS EVS
-0.03
RVIS percentile EVS
51.04

Essentials

Essential (CRISPR)
E
Essential (gene trap)
E
Indispensability pred.
E
Indispensability score
0.860

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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