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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
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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
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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

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