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    PRUNE1 prune exopolyphosphatase 1 [ Homo sapiens (human) ]

    Gene ID: 58497, updated on 3-Apr-2024

    Summary

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    Official Symbol
    PRUNE1provided by HGNC
    Official Full Name
    prune exopolyphosphatase 1provided by HGNC
    Primary source
    HGNC:HGNC:13420
    See related
    Ensembl:ENSG00000143363 MIM:617413; AllianceGenome:HGNC:13420
    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
    PRUNE; DRES17; HTCD37; NMIHBA; DRES-17; H-PRUNE
    Summary
    This gene encodes a member of the DHH protein superfamily of phosphoesterases. This protein has been found to function as both a nucleotide phosphodiesterase and an exopolyphosphatase. This protein is believed to stimulate cancer progression and metastases through the induction of cell motility. A pseuodgene has been identified on chromosome 13. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]
    Expression
    Ubiquitous expression in thyroid (RPKM 21.1), heart (RPKM 13.3) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    1q21.3
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (151008449..151035713)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (150132139..150159408)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (150980925..151008189)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105371438 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:150955292-150956153 Neighboring gene annexin A9 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1700 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:150970021-150970520 Neighboring gene MINDY lysine 48 deubiquitinase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1701 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1702 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:150980776-150981318 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:150981319-150981859 Neighboring gene RNA, U6 small nuclear 884, pseudogene Neighboring gene BCL2 interacting protein like Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1704 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1705 Neighboring gene chromosome 1 open reading frame 56 Neighboring gene CDC42 small effector 1

    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. Neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies in a consanguineous Iranian family is associated with a homozygous start loss variant in the PRUNE1 gene. Gholizadeh MA, et al. BMC Med Genomics, 2022 Apr 4. PMID 35379233, Free PMC Article
    2. An identical-by-descent novel splice-donor variant in PRUNE1 causes a neurodevelopmental syndrome with prominent dystonia in two consanguineous Sudanese families. Koko M, et al. Ann Hum Genet, 2021 Sep. PMID 34111303
    3. Bi-allelic mutations in PRUNE lead to neurodegeneration with spinal motor neuron involvement and hyperCKaemia. Okur D, et al. Turk J Pediatr, 2019. PMID 32134588
    4. A homozygous canonical splice acceptor site mutation in PRUNE1 is responsible for a rare childhood neurodegenerative disease in Manitoba Cree families. Hartley JN, et al. Am J Med Genet A, 2019 Feb. PMID 30556349
    5. PRUNE1 Deficiency: Expanding the Clinical and Genetic Spectrum. Alhaddad B, et al. Neuropediatrics, 2018 Oct. PMID 29940663

    See all (54) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. PRUNE1 (located on chromosome 1q21.3) promotes multiple myeloma with 1q21 Gain by enhancing the links between purine and mitochondrion.
      Title: PRUNE1 (located on chromosome 1q21.3) promotes multiple myeloma with 1q21 Gain by enhancing the links between purine and mitochondrion.
    2. Neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies in a consanguineous Iranian family is associated with a homozygous start loss variant in the PRUNE1 gene.
      Title: Neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies in a consanguineous Iranian family is associated with a homozygous start loss variant in the PRUNE1 gene.
    3. An identical-by-descent novel splice-donor variant in PRUNE1 causes a neurodevelopmental syndrome with prominent dystonia in two consanguineous Sudanese families.
      Title: An identical-by-descent novel splice-donor variant in PRUNE1 causes a neurodevelopmental syndrome with prominent dystonia in two consanguineous Sudanese families.
    4. NMIHBA results from hypomorphic PRUNE1 variants that lack short-chain exopolyphosphatase activity.
      Title: NMIHBA results from hypomorphic PRUNE1 variants that lack short-chain exopolyphosphatase activity.
    5. The PRUNE gene should be considered in all the individuals with non-5q spinal muscular atrophy. High creatine kinase values may be a part of PRUNE disease spectrum.
      Title: Bi-allelic mutations in PRUNE lead to neurodegeneration with spinal motor neuron involvement and hyperCKaemia.
    6. Exome sequencing and homozygosity mapping identified a homozygous PRUNE1 mutation in a canonical splice site, which produces two abnormal PRUNE1 mRNA products. Based on our studies and the histopathology and phenotypic data, we provide further evidence that this disorder leads to a neurodegenerative disease affecting both the peripheral and central nervous systems and suggest that the pathogenic c.521-2A>G mutation could
      Title: A homozygous canonical splice acceptor site mutation in PRUNE1 is responsible for a rare childhood neurodegenerative disease in Manitoba Cree families.
    7. show that mutant PRUNE1 mRNA can be subject to nonsense-mediated mRNA decay
      Title: PRUNE1-related disorder: Expanding the clinical spectrum.
    8. PRUNE1 deficiency causes severe early-onset disease affecting the central and peripheral nervous systems.
      Title: PRUNE1 Deficiency: Expanding the Clinical and Genetic Spectrum.
    9. This study demonstrated that the role for PRUNE1 in metastatic MBGroup3.
      Title: Metastatic group 3 medulloblastoma is driven by PRUNE1 targeting NME1-TGF-β-OTX2-SNAIL via PTEN inhibition.
    10. PRUNE is crucial for normal brain development and mutated in microcephaly with neurodevelopmental impairment.
      Title: PRUNE is crucial for normal brain development and mutated in microcephaly with neurodevelopmental impairment.
    Submit: New GeneRIF Correction See all GeneRIFs (21)

    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
    Neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies
    MedGen: C4479566 OMIM: 617481 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Genome-wide association study identifies genetic risk underlying primary rhegmatogenous retinal detachment.
    EBI GWAS Catalog
    New loci associated with kidney function and chronic kidney disease.
    EBI GWAS Catalog

    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables exopolyphosphatase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables inorganic diphosphate phosphatase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables phosphatase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables tubulin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in regulation of microtubule polymerization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of neurogenesis 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 IDA
    Inferred from Direct Assay
    more info
    		  
    located_in focal adhesion IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    exopolyphosphatase PRUNE1
    Names
    Drosophila-related expressed sequence 17
    protein prune homolog 1
    NP_001290158.1
    NP_001290171.1
    NP_001290172.1
    NP_067045.1
    XP_005245450.1
    XP_011508134.1
    XP_016857444.1
    XP_047282563.1
    XP_047282566.1
    XP_054193969.1
    XP_054193970.1
    XP_054193971.1
    XP_054193972.1
    XP_054193973.1

    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_052875.1 RefSeqGene

      Range
      5059..32323
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001303229.2 → NP_001290158.1  exopolyphosphatase PRUNE1 isoform 2

      See identical proteins and their annotated locations for NP_001290158.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks one alternate internal exon resulting in a distinct 5' UTR and the use of an in-frame downstream start codon compared to variant 1. The resulting protein (isoform 2) has a shorter N-terminus than isoform 1.
      Source sequence(s)
      AK027875, BC014886, BC025304, DA719664
      Consensus CDS
      CCDS76211.1
      UniProtKB/Swiss-Prot
      Q86TP1
      Related
      ENSP00000357932.1, ENST00000368936.5
      Conserved Domains (1) summary
      pfam02833
      Location:36 → 175
      DHHA2; DHHA2 domain

    2. NM_001303242.2 → NP_001290171.1  exopolyphosphatase PRUNE1 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 3' coding region compared to variant 1. The resulting protein (isoform 3) is shorter than isoform 1.
      Source sequence(s)
      AF123538, AK027875, BC025304, BM554427, DA719664
      UniProtKB/TrEMBL
      A0A3B3ITN0
      Conserved Domains (3) summary
      COG1227
      Location:21 → 265
      PPX1; Inorganic pyrophosphatase/exopolyphosphatase [Energy production and conversion, Inorganic ion transport and metabolism]
      pfam01368
      Location:100 → 172
      DHH; DHH family
      pfam02833
      Location:218 → 304
      DHHA2; DHHA2 domain

    3. NM_001303243.2 → NP_001290172.1  exopolyphosphatase PRUNE1 isoform 4

      See identical proteins and their annotated locations for NP_001290172.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks two alternate exons in the 5' coding region resulting in a distinct 5' UTR and the use of an alternate downstream start codon, compared to variant 1. The resulting protein (isoform 4) has a distinct N-terminus and is shorter compared to isoform 1.
      Source sequence(s)
      AK027875, BC025304, DA719664
      UniProtKB/Swiss-Prot
      Q86TP1
      Conserved Domains (1) summary
      pfam02833
      Location:27 → 157
      DHHA2; DHHA2 domain

    4. NM_021222.3 → NP_067045.1  exopolyphosphatase PRUNE1 isoform 1

      See identical proteins and their annotated locations for NP_067045.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AK027875, BC025304, DA719664
      Consensus CDS
      CCDS977.1
      UniProtKB/Swiss-Prot
      B2RCH8, B4DFL7, Q5SZF9, Q659E5, Q6P4E0, Q86TP1, Q8N654, Q96JU5, Q9C071, Q9C072, Q9UIV0
      UniProtKB/TrEMBL
      A0A3B3ITN0
      Related
      ENSP00000271620.3, ENST00000271620.8
      Conserved Domains (3) summary
      COG1227
      Location:21 → 361
      PPX1; Inorganic pyrophosphatase/exopolyphosphatase [Energy production and conversion, Inorganic ion transport and metabolism]
      pfam01368
      Location:100 → 172
      DHH; DHH family
      pfam02833
      Location:218 → 357
      DHHA2; DHHA2 domain

    RNA

    1. NR_130130.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks several alternate internal exons, compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
      Source sequence(s)
      AF123538, AK027875, BC025304, DA719664

    2. NR_130131.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) lacks several alternate internal exons, compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
      Source sequence(s)
      AK027875, AK294154, BC025304, DA719664

    3. NR_130132.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) lacks several alternate internal exons, compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
      Source sequence(s)
      AK027875, BC025304, BC063481, DA719664
      Related
      ENST00000368935.1

    4. NR_130135.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (8) lacks several alternate internal exons, compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
      Source sequence(s)
      AK027875, BC014886, BC025304, DA719664, DA942287

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      151008449..151035713
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005245393.6 → XP_005245450.1  exopolyphosphatase PRUNE1 isoform X1

      UniProtKB/TrEMBL
      A0A3B3ITN0
      Related
      ENSP00000497847.1, ENST00000650332.1
      Conserved Domains (1) summary
      COG1227
      Location:21 → 331
      PPX1; Inorganic pyrophosphatase/exopolyphosphatase [Energy production and conversion, Inorganic ion transport and metabolism]

    2. XM_017001955.3 → XP_016857444.1  exopolyphosphatase PRUNE1 isoform X2

      UniProtKB/TrEMBL
      A0A3B3ITN0

    3. XM_011509832.3 → XP_011508134.1  exopolyphosphatase PRUNE1 isoform X3

      See identical proteins and their annotated locations for XP_011508134.1

      UniProtKB/Swiss-Prot
      Q86TP1
      Related
      ENSP00000357930.1, ENST00000368934.1
      Conserved Domains (1) summary
      pfam02833
      Location:36 → 175
      DHHA2; DHHA2 domain

    4. XM_047426610.1 → XP_047282566.1  exopolyphosphatase PRUNE1 isoform X4

    5. XM_047426607.1 → XP_047282563.1  exopolyphosphatase PRUNE1 isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      150132139..150159408
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054337994.1 → XP_054193969.1  exopolyphosphatase PRUNE1 isoform X1

    2. XM_054337995.1 → XP_054193970.1  exopolyphosphatase PRUNE1 isoform X2

    3. XM_054337996.1 → XP_054193971.1  exopolyphosphatase PRUNE1 isoform X3

    4. XM_054337998.1 → XP_054193973.1  exopolyphosphatase PRUNE1 isoform X4

    5. XM_054337997.1 → XP_054193972.1  exopolyphosphatase PRUNE1 isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q86TP1.2 GenPept UniProtKB/Swiss-Prot:Q86TP1

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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