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PUS1 pseudouridine synthase 1 [ Homo sapiens (human) ]

Gene ID: 80324, updated on 5-Mar-2024

Summary

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Official Symbol
PUS1provided by HGNC
Official Full Name
pseudouridine synthase 1provided by HGNC
Primary source
HGNC:HGNC:15508
See related
Ensembl:ENSG00000177192 MIM:608109; AllianceGenome:HGNC:15508
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
MLASA1
Summary
This gene encodes a pseudouridine synthase that converts uridine to pseudouridine once it has been incorporated into an RNA molecule. The encoded enzyme may play an essential role in tRNA function and in stabilizing the secondary and tertiary structure of many RNAs. A mutation in this gene has been linked to mitochondrial myopathy and sideroblastic anemia. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Sep 2009]
Expression
Ubiquitous expression in appendix (RPKM 5.5), lymph node (RPKM 5.4) and 25 other tissues See more
Orthologs
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Genomic context

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See PUS1 in Genome Data Viewer
Location:
12q24.33
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (131929276..131945896)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (131977320..131993946)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (132413821..132430441)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5102 Neighboring gene Sharpr-MPRA regulatory region 8404 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5105 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:132381351-132382148 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:132384711-132385228 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:132385229-132385746 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:132385901-132386674 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:132386675-132387447 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_25936 Neighboring gene unc-51 like autophagy activating kinase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7371 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7372 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7373 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:132409300-132410176 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5106 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5107 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_25941 Neighboring gene PUS1 antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 9670 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5109 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5108 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:132434951-132435658 Neighboring gene Sharpr-MPRA regulatory region 13568 Neighboring gene E1A binding protein p400 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:132470576-132471195 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:132471868-132472518 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:132473169-132473818 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:132490339-132491538 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:132498351-132499144 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:132499145-132499938 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:132499948-132500448 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:132508440-132509639 Neighboring gene Sharpr-MPRA regulatory region 9648 Neighboring gene small nucleolar RNA, H/ACA box 49 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:132534021-132534992 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:132567429-132567930 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5110 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5111 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:132569347-132570207 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:132570983-132571159 Neighboring gene EP400 pseudogene 1 Neighboring gene uncharacterized LOC107987169

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
  • 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. Partial activity is seen with many substitutions of highly conserved active site residues in human Pseudouridine synthase 1. Sibert BS, et al. RNA, 2008 Sep. PMID 18648068, Free PMC Article
  2. Nonsense mutation in pseudouridylate synthase 1 (PUS1) in two brothers affected by myopathy, lactic acidosis and sideroblastic anaemia (MLASA). Fernandez-Vizarra E, et al. J Med Genet, 2007 Mar. PMID 17056637, Free PMC Article
  3. Missense mutation in pseudouridine synthase 1 (PUS1) causes mitochondrial myopathy and sideroblastic anemia (MLASA). Bykhovskaya Y, et al. Am J Hum Genet, 2004 Jun. PMID 15108122, Free PMC Article
  4. Steroid receptor RNA activator (SRA) modification by the human pseudouridine synthase 1 (hPus1p): RNA binding, activity, and atomic model. Huet T, et al. PLoS One, 2014. PMID 24722331, Free PMC Article
  5. In human pseudouridine synthase 1 (hPus1), a C-terminal helical insert blocks tRNA from binding in the same orientation as in the Pus1 bacterial homologue TruA, consistent with their different target selectivities. Czudnochowski N, et al. J Mol Biol, 2013 Oct 23. PMID 23707380, Free PMC Article

See all (62) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Pseudouridine synthases modify human pre-mRNA co-transcriptionally and affect pre-mRNA processing.
    Title: Pseudouridine synthases modify human pre-mRNA co-transcriptionally and affect pre-mRNA processing.
  2. These results demonstrate a structure-dependent mode of mRNA target recognition by a conserved pseudouridine synthase and implicate modulation of RNA structure as the probable mechanism to regulate mRNA pseudouridylation.
    Title: mRNA structure determines modification by pseudouridine synthase 1.
  3. results show that the NTD of ERalpha and AR contains a novel RBM that directly binds SRA, and that STR5 can serve as a novel class of RNA inhibitor of ERalpha and AR signaling by interfering with Pus1p-mediated SRA pseudouridylation
    Title: A small RNA derived from RNA coactivator SRA blocks steroid receptor signaling via inhibition of Pus1p-mediated pseudouridylation of SRA: evidence of a novel RNA binding domain in the N-terminus of steroid receptors.
  4. Investigation of the sequence and structural requirements for hPus1p activity on human tRNASer.
    Title: Pseudouridine synthase 1: a site-specific synthase without strict sequence recognition requirements.
  5. We identified one novel homozygous null mutation in a familial case. It predicts a nonsense mutation at glutamine 154 (Q154X) that would lead to a protein lacking the 266 C-terminal amino acids
    Title: Systematic molecular genetic analysis of congenital sideroblastic anemia: evidence for genetic heterogeneity and identification of novel mutations.
  6. Three residues (R116, Y173, R267) that correspond to amino acids known to compose the active site of TruA, a bacterial Psi synthase that is homologous to Pus1p, were mutated in human Pus1p.
    Title: Partial activity is seen with many substitutions of highly conserved active site residues in human Pseudouridine synthase 1.
  7. Missense mutation in pseudouridine synthase 1 causes mitochondrial myopathy and sideroblastic anemia
    Title: Missense mutation in pseudouridine synthase 1 (PUS1) causes mitochondrial myopathy and sideroblastic anemia (MLASA).
  8. MLASA is associated with absent or greatly reduced tRNA pseudouridylation at specific sites, implicating this pathway in its molecular pathogenesis.
    Title: Mitochondrial myopathy and sideroblastic anemia (MLASA): missense mutation in the pseudouridine synthase 1 (PUS1) gene is associated with the loss of tRNA pseudouridylation.
  9. A new homozygous stop mutation (E220X)predicts a protein missing 208/427 amino acid residues on the C terminus. The nuclear isoform has an N-terminal extension absent in the mature mitochondrial isoform.
    Title: Nonsense mutation in pseudouridylate synthase 1 (PUS1) in two brothers affected by myopathy, lactic acidosis and sideroblastic anaemia (MLASA).
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
Myopathy, lactic acidosis, and sideroblastic anemia 1
MedGen: C4551958 OMIM: 600462 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)

Genotypes

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

  • MGC11268

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 
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 pseudouridine synthase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables pseudouridine synthase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables steroid receptor RNA activator RNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables tRNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables tRNA pseudouridine synthase activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in RNA splicing IEA
Inferred from Electronic Annotation
more info
  
involved_in mRNA processing IEA
Inferred from Electronic Annotation
more info
  
involved_in mRNA pseudouridine synthesis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in mRNA pseudouridine synthesis IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in mitochondrial tRNA pseudouridine synthesis 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
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in mitochondrial matrix TAS
Traceable Author Statement
more info
  
located_in mitochondrion IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
pseudouridylate synthase 1 homolog
Names
mitochondrial tRNA pseudouridine synthase A
pseudouridylate synthase 1
tRNA pseudouridine synthase 1
tRNA pseudouridine synthase A, mitochondrial
tRNA pseudouridine(38-40) synthase
tRNA pseudouridylate synthase I
tRNA uridine isomerase I
NP_001002019.1
NP_001002020.1
NP_079491.2

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_013039.2 RefSeqGene

    Range
    5002..21622
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001002019.3 → NP_001002019.1  pseudouridylate synthase 1 homolog isoform 2

    See identical proteins and their annotated locations for NP_001002019.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus, compared to isoform 1. Variants 2 and 3 encode the same isoform (2).
    Source sequence(s)
    AC131009, AF116238, AI566545, BM923133, BX340929
    Consensus CDS
    CCDS31928.1
    UniProtKB/TrEMBL
    E5KMT6, G8JLB3
    Conserved Domains (2) summary
    cd02568
    Location:60 → 312
    PseudoU_synth_PUS1_PUS2; Pseudouridine synthase, PUS1/ PUS2 like
    COG0101
    Location:56 → 335
    TruA; tRNA U38,U39,U40 pseudouridine synthase TruA [Translation, ribosomal structure and biogenesis]

  2. NM_001002020.3 → NP_001002020.1  pseudouridylate synthase 1 homolog isoform 2

    See identical proteins and their annotated locations for NP_001002020.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus, compared to isoform 1. Variants 2 and 3 encode the same isoform (2).
    Source sequence(s)
    AC131009, AI566545, BC002901, CB118952
    Consensus CDS
    CCDS31928.1
    UniProtKB/TrEMBL
    E5KMT6, G8JLB3
    Related
    ENSP00000392451.2, ENST00000443358.6
    Conserved Domains (2) summary
    cd02568
    Location:60 → 312
    PseudoU_synth_PUS1_PUS2; Pseudouridine synthase, PUS1/ PUS2 like
    COG0101
    Location:56 → 335
    TruA; tRNA U38,U39,U40 pseudouridine synthase TruA [Translation, ribosomal structure and biogenesis]

  3. NM_025215.6 → NP_079491.2  pseudouridylate synthase 1 homolog isoform 1

    See identical proteins and their annotated locations for NP_079491.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC131009, AI566545, AK074659
    Consensus CDS
    CCDS9275.2
    UniProtKB/Swiss-Prot
    A8K877, B3KQC1, Q8WYT2, Q9BU44, Q9Y606
    UniProtKB/TrEMBL
    E5KMT5, G8JLB3
    Related
    ENSP00000365837.3, ENST00000376649.8
    Conserved Domains (2) summary
    cd02568
    Location:88 → 340
    PseudoU_synth_PUS1_PUS2; Pseudouridine synthase, PUS1/ PUS2 like
    COG0101
    Location:84 → 363
    TruA; tRNA U38,U39,U40 pseudouridine synthase TruA [Translation, ribosomal structure and biogenesis]

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    131929276..131945896
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    131977320..131993946
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9Y606.3 GenPept UniProtKB/Swiss-Prot:Q9Y606

Gene LinkOut

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