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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 15 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
PRUNE1
prune exopolyphosphatase 1
Chromosome 1 Β· 1q21.3
NCBI Gene: 58497Ensembl: ENSG00000143363.18HGNC: HGNC:13420UniProt: Q86TP1
62PubMed Papers
21Diseases
0Drugs
27Pathogenic Variants
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
regulation of microtubule polymerizationcytosolprotein bindingtubulin bindingneurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomaliesgenetic disorderAbnormal brain morphologychronic rhinosinusitis with nasal polyps
✦AI Summary

PRUNE1 encodes a phosphodiesterase enzyme that preferentially hydrolyzes cAMP over cGMP and functions as a critical regulator of cellular processes including proliferation, migration, and neurogenesis 1. The protein contains a DHH (aspartic acid-histidine-histidine) phosphodiesterase domain essential for its enzymatic activity and acts as a negative regulator of NME1/NME2 tumor metastasis suppressors through direct protein interactions 1. PRUNE1 plays important roles in microtubule polymerization regulation and neurogenesis 2. Loss-of-function mutations in PRUNE1 cause neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies (NMIHBA), characterized by developmental delay, intellectual disability, and structural brain abnormalities including corpus callosum thinning and cerebellar atrophy 324. The clinical spectrum is variable, with some patients lacking typical microcephaly 24. In cancer contexts, PRUNE1 promotes multiple myeloma progression by enhancing purine metabolism and mitochondrial function 5, and is epigenetically regulated by PAD2-mediated histone citrullination in pancreatic cancer, where it modulates the tumor microenvironment 6. These findings establish PRUNE1 as both a neurodevelopmental disease gene and oncogenic factor.

Sources cited
1
PRUNE1 is a phosphodiesterase with higher activity toward cAMP than cGMP and acts as negative regulator of NME1/NME2
PMID: 38180572
2
Loss-of-function PRUNE1 mutations cause neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies
PMID: 35379233
3
PRUNE1 regulates cell migration and proliferation during brain development and contains DHH phosphodiesterase domain
PMID: 35194938
4
PRUNE1 mutations show variable phenotypes including cases without progressive microcephaly
PMID: 29797509
5
PRUNE1 promotes multiple myeloma proliferation by stimulating purine metabolism and mitochondrial functions
PMID: 37666675
6
PAD2-mediated histone citrullination epigenetically regulates PRUNE1 expression in pancreatic cancer
PMID: 40506250
Disease Associationsβ“˜21
neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomaliesOpen Targets
0.81Strong
genetic disorderOpen Targets
0.46Moderate
Abnormal brain morphologyOpen Targets
0.38Weak
chronic rhinosinusitis with nasal polypsOpen Targets
0.16Weak
obesityOpen Targets
0.14Weak
triple-negative breast cancerOpen Targets
0.08Suggestive
lung cancerOpen Targets
0.08Suggestive
Mobius syndromeOpen Targets
0.07Suggestive
hepatocellular carcinomaOpen Targets
0.07Suggestive
breast cancerOpen Targets
0.07Suggestive
skin neoplasmOpen Targets
0.06Suggestive
neoplasmOpen Targets
0.06Suggestive
atopic eczemaOpen Targets
0.06Suggestive
non-small cell lung carcinomaOpen Targets
0.04Suggestive
gastric cancerOpen Targets
0.03Suggestive
cancerOpen Targets
0.03Suggestive
hypothyroidismOpen Targets
0.03Suggestive
medulloblastomaOpen Targets
0.02Suggestive
esophageal squamous cell carcinomaOpen Targets
0.02Suggestive
microcephalyOpen Targets
0.02Suggestive
Neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomaliesUniProt
Pathogenic Variants27
NM_021222.3(PRUNE1):c.88G>A (p.Asp30Asn)Pathogenic
not provided|Abnormal brain morphology|Neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies
β˜…β˜…β˜†β˜†2025β†’ Residue 30
NM_021222.3(PRUNE1):c.196C>T (p.Arg66Ter)Pathogenic
not provided|Neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies
β˜…β˜…β˜†β˜†2025β†’ Residue 66
NM_021222.3(PRUNE1):c.316G>A (p.Asp106Asn)Pathogenic
Abnormal brain morphology|Neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 106
NM_021222.3(PRUNE1):c.383G>A (p.Arg128Gln)Pathogenic
not provided|Abnormal brain morphology|Neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies
β˜…β˜…β˜†β˜†2024β†’ Residue 128
NM_021222.3(PRUNE1):c.132+2T>CPathogenic
Neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies|not provided
β˜…β˜…β˜†β˜†2023
NM_021222.3(PRUNE1):c.1036del (p.Val346fs)Likely pathogenic
Neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies
β˜…β˜†β˜†β˜†2025β†’ Residue 346
NM_021222.3(PRUNE1):c.385_392dup (p.Glu131fs)Pathogenic
Neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies
β˜…β˜†β˜†β˜†2025β†’ Residue 131
NM_021222.3(PRUNE1):c.762T>A (p.Tyr254Ter)Pathogenic
Neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies
β˜…β˜†β˜†β˜†2024β†’ Residue 254
NM_021222.3(PRUNE1):c.712C>T (p.Gln238Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 238
NM_021222.3(PRUNE1):c.889C>T (p.Arg297Trp)Pathogenic
Neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies|not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 297
GRCh38/hg38 1q21.3(chr1:151017715-151018767)x0Pathogenic
Neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies
β˜…β˜†β˜†β˜†2023
NM_021222.3(PRUNE1):c.285C>G (p.Tyr95Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2023β†’ Residue 95
NM_021222.3(PRUNE1):c.723_726del (p.Tyr242fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2023β†’ Residue 242
NM_021222.3(PRUNE1):c.39+1G>TLikely pathogenic
not provided
β˜…β˜†β˜†β˜†2023
NM_021222.3(PRUNE1):c.380A>G (p.His127Arg)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2020β†’ Residue 127
NM_021222.3(PRUNE1):c.809T>C (p.Leu270Pro)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2017β†’ Residue 270
NM_021222.3(PRUNE1):c.661del (p.Ala221fs)Pathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2017β†’ Residue 221
NM_021222.3(PRUNE1):c.3_7dup (p.Asp3fs)Pathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2017β†’ Residue 3
NM_021222.3(PRUNE1):c.521-2A>GLikely pathogenic
not provided|Neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies|PRUNE1-related disorder|Squamous cell lung carcinoma
β˜…β˜†β˜†β˜†2017
NM_021222.3(PRUNE1):c.520G>T (p.Gly174Ter)Likely pathogenic
Abnormal brain morphology|Neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies
β˜…β˜†β˜†β˜†β†’ Residue 174
View on ClinVar β†—
Related Genes
NME1Protein interaction94%HDDC3Protein interaction90%GSK3BProtein interaction88%APRTProtein interaction82%BNIP2Protein interaction74%HES3Shared pathway33%
Tissue Expression6 tissues
Heart
100%
Brain
53%
Ovary
33%
Liver
32%
Lung
26%
Bone Marrow
12%
Gene Interaction Network
Click a node to explore
PRUNE1NME1HDDC3GSK3BAPRTBNIP2HES3
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt Q86TP1
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
0.90LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.63 [0.44–0.90]
RankingsWhere PRUNE1 stands among ~20K protein-coding genes
  • #7,498of 20,598
    Most Researched62
  • #1,909of 5,498
    Most Pathogenic Variants27
  • #8,165of 17,882
    Most Constrained (LOEUF)0.90
Genes detectedPRUNE1
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
PRUNE1 and NME/NDPK family proteins influence energy metabolism and signaling in cancer metastases.
PMID: 38180572
Cancer Metastasis Rev Β· 2024
1.00
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.
PMID: 35379233
BMC Med Genomics Β· 2022
0.90
3
PRUNE1 c.933G>A synonymous variant induces exon 7 skipping, disrupts the DHHA2 domain, and leads to an atypical NMIHBA syndrome presentation: Case report and review of the literature.
PMID: 35194938
Am J Med Genet A Β· 2022
0.80
4
MRT-ModSeq - Rapid Detection of RNA Modifications with MarathonRT.
PMID: 37802215
J Mol Biol Β· 2023
0.70
5
PRUNE1-related disorder: Expanding the clinical spectrum.
PMID: 29797509
Clin Genet Β· 2018
0.60