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PUS3 pseudouridine synthase 3 [ Homo sapiens (human) ]

Gene ID: 83480, updated on 3-Nov-2024

Summary

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Official Symbol
PUS3provided by HGNC
Official Full Name
pseudouridine synthase 3provided by HGNC
Primary source
HGNC:HGNC:25461
See related
Ensembl:ENSG00000110060 MIM:616283; AllianceGenome:HGNC:25461
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
DEG1; MRT55; FKSG32; NEDMIGS; 2610020J05Rik
Summary
The protein encoded by this gene catalyzes the formation of tRNA pseudouridine from tRNA uridine at position 39 in the anticodon stem and loop of transfer RNAs. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2012]
Expression
Ubiquitous expression in liver (RPKM 5.1), appendix (RPKM 3.5) and 25 other tissues See more
Orthologs
mouse all
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Genomic context

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See PUS3 in Genome Data Viewer
Location:
11q24.2
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (125893485..125903206, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (125922358..125932075, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (125763380..125773101, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene prostate and testis expressed 4 Neighboring gene long intergenic non-protein coding RNA 3136 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5702 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4042 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4043 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4044 Neighboring gene HYLS1 centriolar and ciliogenesis associated Neighboring gene DEAD-box helicase 25 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:125802853-125803806 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:125805158-125805722 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4045 Neighboring gene V-set and immunoglobulin domain containing 10 like 2

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. The molecular basis of tRNA selectivity by human pseudouridine synthase 3. Lin TY, et al. Mol Cell, 2024 Jul 11. PMID 38996458, Free PMC Article
  2. Destabilization of mutated human PUS3 protein causes intellectual disability. Lin TY, et al. Hum Mutat, 2022 Dec. PMID 36125428, Free PMC Article
  3. Clinical and molecular delineation of PUS3-associated neurodevelopmental disorders. Nøstvik M, et al. Clin Genet, 2021 Nov. PMID 34415064
  4. A homozygous truncating mutation in PUS3 expands the role of tRNA modification in normal cognition. Shaheen R, et al. Hum Genet, 2016 Jul. PMID 27055666, Free PMC Article
  5. Pseudouridine synthase 3 from mouse modifies the anticodon loop of tRNA. Chen J, et al. Biochemistry, 2000 Oct 17. PMID 11027153

See all (16) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The molecular basis of tRNA selectivity by human pseudouridine synthase 3.
    Title: The molecular basis of tRNA selectivity by human pseudouridine synthase 3.
  2. Destabilization of mutated human PUS3 protein causes intellectual disability.
    Title: Destabilization of mutated human PUS3 protein causes intellectual disability.
  3. Clinical and molecular delineation of PUS3-associated neurodevelopmental disorders.
    Title: Clinical and molecular delineation of PUS3-associated neurodevelopmental disorders.
  4. Consistent with the known role of Pus3 in isomerizing uracil to pseudouridine at positions 38 and 39 in tRNA, we found a significant reduction in this post-transcriptional modification of tRNA in patient cells
    Title: A homozygous truncating mutation in PUS3 expands the role of tRNA modification in normal cognition.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Severe growth deficiency-strabismus-extensive dermal melanocytosis-intellectual disability syndrome
MedGen: C4310745 OMIM: 617051 GeneReviews: Not available
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Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ23638

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding IEA
Inferred from Electronic Annotation
more info
  
enables pseudouridine synthase activity EXP
Inferred from Experiment
more info
 PubMed 
enables pseudouridine synthase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables tRNA pseudouridine(38/39) synthase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Process Evidence Code Pubs
involved_in mRNA pseudouridine synthesis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in tRNA modification TAS
Traceable Author Statement
more info
  
involved_in tRNA pseudouridine synthesis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in tRNA pseudouridine synthesis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
tRNA pseudouridine(38/39) synthase
Names
pseudouridylate synthase 3
tRNA pseudouridine synthase 3
tRNA pseudouridylate synthase 3
tRNA-uridine isomerase 3
NP_001258914.1
NP_112597.4
XP_005271745.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_033067.2 RefSeqGene

    Range
    5000..14721
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001271985.2 → NP_001258914.1  tRNA pseudouridine(38/39) synthase isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate coding exon and uses a downstream start codon compared to variant 1. It encodes isoform 2, which has a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    AF325689, AP000842, BC004822, BM786445
    Consensus CDS
    CCDS73411.1
    UniProtKB/TrEMBL
    A0A087WY59
    Related
    ENSP00000481536.1, ENST00000613398.4
    Conserved Domains (1) summary
    cl00130
    Location:1 → 121
    PseudoU_synth; Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi)

  2. NM_031307.4 → NP_112597.4  tRNA pseudouridine(38/39) synthase isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AP000842
    Consensus CDS
    CCDS8466.1
    UniProtKB/Swiss-Prot
    B2RAM0, Q96D17, Q96J23, Q96NB4, Q9BZE2
    Related
    ENSP00000227474.3, ENST00000227474.8
    Conserved Domains (1) summary
    cd02569
    Location:67 → 329
    PseudoU_synth_ScPus3; Pseudouridine synthase, Saccharomyces cerevisiae Pus3 like

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    125893485..125903206 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005271688.5 → XP_005271745.1  tRNA pseudouridine(38/39) synthase isoform X1

    UniProtKB/TrEMBL
    E9PRI9
    Conserved Domains (2) summary
    pfam11853
    Location:10 → 50
    DUF3373; Protein of unknown function (DUF3373)
    cl00130
    Location:67 → 166
    PseudoU_synth; Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    125922358..125932075 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9BZE2.3 GenPept UniProtKB/Swiss-Prot:Q9BZE2

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