PRUNE1 prune exopolyphosphatase 1 [Homo sapiens (human)] - Gene

Summary

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

Location:: 1q21.3

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (151008449..151035713)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (150132139..150159408)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (150980925..151008189)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
show that mutant PRUNE1 mRNA can be subject to nonsense-mediated mRNA decay
Title: PRUNE1-related disorder: Expanding the clinical spectrum.
PRUNE1 deficiency causes severe early-onset disease affecting the central and peripheral nervous systems.
Title: PRUNE1 Deficiency: Expanding the Clinical and Genetic Spectrum.
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.
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 EBI GWAS CatalogPubMed
New loci associated with kidney function and chronic kidney disease. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

A004A12 (e-PCR)
- UniSTS:60256

D1S2426 (e-PCR)
- UniSTS:71081

D1S1855E (e-PCR)
- UniSTS:150967

RH104459 (e-PCR)
- UniSTS:98783

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

EC 3.6.1.1

NP_001290171.1

EC 3.6.1.1

NP_001290172.1

EC 3.6.1.1

NP_067045.1

EC 3.6.1.1

XP_005245450.1

EC 3.6.1.1

XP_011508134.1

EC 3.6.1.1

XP_016857444.1

EC 3.6.1.1

XP_047282563.1

EC 3.6.1.1

XP_047282566.1

EC 3.6.1.1

XP_054193969.1

EC 3.6.1.1

XP_054193970.1

EC 3.6.1.1

XP_054193971.1

EC 3.6.1.1

XP_054193972.1

EC 3.6.1.1

XP_054193973.1

EC 3.6.1.1

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

NG_052875.1 RefSeqGene

Range

5059..32323

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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
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

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
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
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
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_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

151008449..151035713

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

A0A3B3ITN0
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
XM_047426610.1 → XP_047282566.1 exopolyphosphatase PRUNE1 isoform X4
XM_047426607.1 → XP_047282563.1 exopolyphosphatase PRUNE1 isoform X3