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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 15 days ago
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NPRL2
NPR2 like, GATOR1 complex subunit
Chromosome 3 Β· 3p21.31
NCBI Gene: 10641Ensembl: ENSG00000114388.15HGNC: HGNC:24969UniProt: Q8WTW4
78PubMed Papers
21Diseases
0Drugs
25Pathogenic Variants
FUNCTIONAL ROLE
Tumor Suppressor
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
GTPase activator activityprotein bindingnegative regulation of kinase activitycellular response to amino acid starvationfamilial focal epilepsy with variable focigenetic disorderSeizureneurodegenerative disease
✦AI Summary

NPRL2 is a core component of the GATOR1 complex, a negative regulator of mTORC1 signaling that functions as a tumor suppressor 1. NPRL2 displays GTPase-activating protein (GAP) activity toward Rag GTPases, inactivating them under amino acid-deficient conditions to suppress mTORC1 pathway activation 1. In cancer cells with NPRL2 inactivation, mTORC1 becomes hyperactive and insensitive to amino acid starvation 1. Pathogenic NPRL2 variants cause familial focal epilepsy with variable foci, manifesting primarily as focal seizures (70% of cases), often sleep-related and drug-resistant 23. Loss-of-function variants predominate (approximately 67% of epilepsy-related GATOR1 variants), with focal cortical dysplasia present in ~20% of cases 43. Mean seizure onset occurs at 4.4 years, with sudden unexpected death in epilepsy (SUDEP) occurring in ~10% of families 4. Clinically, NPRL2 loss accelerates c-MYC-driven lymphoma development and renders tumors sensitive to mTOR inhibitors 5. NPRL2 restoration in non-small cell lung cancer activates CD8+ T cell-mediated antitumor immunity through downregulation of mTOR signaling and immunosuppressive molecules 6. These findings establish NPRL2 as a critical regulator linking metabolic sensing to both neuronal excitability and immune-mediated tumor control.

Sources cited
1
GATOR1 complex containing NPRL2 has GAP activity for Rag GTPases and acts as a tumor suppressor; loss of GATOR1 components causes mTORC1 hyperactivation resistant to amino acid deprivation
PMID: 23723238
2
NPRL2 variants cause focal epilepsies with mean onset at 4.4 years; 68% are loss-of-function pathogenic; SUDEP occurred in 10% of families; focal seizures predominate in 50%
PMID: 30093711
3
NPRL2 functions as an mTOR pathway repressor; germline mutations in NPRL2 cause focal epilepsies and cortical dysplasias through excessive mTOR activation
PMID: 37149062
4
NPRL2-related epilepsy presents as focal epilepsy (70%), infantile spasms (10%), and focal cortical dysplasia (30%); two-thirds of variants are loss-of-function
PMID: 37741786
5
Loss of NPRL2 accelerates MYC-driven lymphoma development with constitutive mTOR activation and sensitivity to mTOR inhibitors
PMID: 40841511
6
NPRL2 restoration induces CD8+ T cell-mediated antitumor immunity through downregulation of mTOR and immunosuppressive signaling in KRAS-mutant lung cancer
PMID: 39932765
Disease Associationsβ“˜21
familial focal epilepsy with variable fociOpen Targets
0.77Strong
genetic disorderOpen Targets
0.51Moderate
SeizureOpen Targets
0.48Moderate
neurodegenerative diseaseOpen Targets
0.42Moderate
partial epilepsyOpen Targets
0.38Weak
Malignant Pancreatic NeoplasmOpen Targets
0.31Weak
Neonatal respiratory distressOpen Targets
0.27Weak
neoplasmOpen Targets
0.11Weak
hepatocellular carcinomaOpen Targets
0.08Suggestive
colorectal carcinomaOpen Targets
0.08Suggestive
gastric adenocarcinomaOpen Targets
0.07Suggestive
non-small cell lung carcinomaOpen Targets
0.07Suggestive
gliomaOpen Targets
0.07Suggestive
cancerOpen Targets
0.05Suggestive
epilepsyOpen Targets
0.04Suggestive
Abnormality of the skeletal systemOpen Targets
0.04Suggestive
gastric cancerOpen Targets
0.03Suggestive
osteosarcomaOpen Targets
0.03Suggestive
schizophreniaOpen Targets
0.03Suggestive
Neoplasm of the lungOpen Targets
0.03Suggestive
Epilepsy, familial focal, with variable foci 2UniProt
Pathogenic Variants25
NM_006545.5(NPRL2):c.883C>T (p.Arg295Ter)Pathogenic
Epilepsy, familial focal, with variable foci 2|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 295
NM_006545.5(NPRL2):c.57_58delinsC (p.Gly20fs)Pathogenic
not provided|Epilepsy, familial focal, with variable foci 2|Inborn genetic diseases
β˜…β˜…β˜†β˜†2025β†’ Residue 20
NM_006545.5(NPRL2):c.847C>T (p.Gln283Ter)Pathogenic
Inborn genetic diseases|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 283
NM_006545.5(NPRL2):c.932+1G>APathogenic
Epilepsy, familial focal, with variable foci 2
β˜…β˜…β˜†β˜†2024
NM_006545.5(NPRL2):c.52_53del (p.Thr18fs)Likely pathogenic
Epilepsy, familial focal, with variable foci 2
β˜…β˜†β˜†β˜†2025β†’ Residue 18
NM_006545.5(NPRL2):c.941_948dup (p.Gly317fs)Pathogenic
Epilepsy, familial focal, with variable foci 2
β˜…β˜†β˜†β˜†2025β†’ Residue 317
NM_006545.5(NPRL2):c.367G>T (p.Glu123Ter)Pathogenic
Seizure
β˜…β˜†β˜†β˜†2025β†’ Residue 123
NM_006545.5(NPRL2):c.35dup (p.Ser13fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 13
NM_006545.5(NPRL2):c.754C>T (p.Gln252Ter)Pathogenic
Epilepsy, familial focal, with variable foci 2
β˜…β˜†β˜†β˜†2025β†’ Residue 252
NM_006545.5(NPRL2):c.814+2T>CLikely pathogenic
Epilepsy, familial focal, with variable foci 2
β˜…β˜†β˜†β˜†2024
NM_006545.5(NPRL2):c.279del (p.Lys94fs)Pathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2024β†’ Residue 94
NM_006545.5(NPRL2):c.170+1G>CPathogenic
Seizure
β˜…β˜†β˜†β˜†2024
NM_006545.5(NPRL2):c.233G>A (p.Arg78His)Likely pathogenic
Epilepsy, familial focal, with variable foci 2
β˜…β˜†β˜†β˜†2024β†’ Residue 78
NM_006545.5(NPRL2):c.170+5G>ALikely pathogenic
not provided
β˜…β˜†β˜†β˜†2023
NM_006545.5(NPRL2):c.865_871del (p.Ser289fs)Likely pathogenic
Epilepsy, familial focal, with variable foci 2
β˜…β˜†β˜†β˜†2021β†’ Residue 289
NM_006545.5(NPRL2):c.562C>T (p.Gln188Ter)Likely pathogenic
Epilepsy, familial focal, with variable foci 2
β˜…β˜†β˜†β˜†2021β†’ Residue 188
NM_006545.5(NPRL2):c.3G>T (p.Met1Ile)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2020β†’ Residue 1
NM_006545.5(NPRL2):c.491dup (p.Asp165fs)Likely pathogenic
Epilepsy, familial focal, with variable foci 2
β˜…β˜†β˜†β˜†2020β†’ Residue 165
NM_006545.5(NPRL2):c.445_448+3delLikely pathogenic
Epilepsy, familial focal, with variable foci 2
β˜…β˜†β˜†β˜†2018
NM_006545.5(NPRL2):c.943C>T (p.Gln315Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2017β†’ Residue 315
View on ClinVar β†—
Related Genes
LAMP1Protein interaction100%MTORProtein interaction99%RPTORProtein interaction97%LAMTOR3Protein interaction95%LAMTOR5Protein interaction95%RRAGAProtein interaction93%
Tissue Expression6 tissues
Ovary
100%
Bone Marrow
92%
Liver
90%
Lung
74%
Heart
64%
Brain
34%
Gene Interaction Network
Click a node to explore
NPRL2LAMP1MTORRPTORLAMTOR3LAMTOR5RRAGA
PROTEIN STRUCTURE
Preparing viewer…
PDB8FW5 Β· 3.08 Γ… Β· EM
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.56Moderately Constrained
pLIβ“˜
0.58Intermediate
Observed/Expected LoF0.39 [0.28–0.56]
RankingsWhere NPRL2 stands among ~20K protein-coding genes
  • #6,096of 20,598
    Most Researched78
  • #1,982of 5,498
    Most Pathogenic Variants25
  • #3,679of 17,882
    Most Constrained (LOEUF)0.56 Β· top quartile
Genes detectedNPRL2
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
The landscape of epilepsy-related GATOR1 variants.
PMID: 30093711
Genet Med Β· 2019
1.00
2
mTOR pathway: Insights into an established pathway for brain mosaicism in epilepsy.
PMID: 37149062
Neurobiol Dis Β· 2023
0.90
3
A Tumor suppressor complex with GAP activity for the Rag GTPases that signal amino acid sufficiency to mTORC1.
PMID: 23723238
Science Β· 2013
0.80
4
Clinical phenotype and genotype of NPRL2-related epilepsy: Four cases reports and literature review.
PMID: 37741786
Seizure Β· 2024
0.70
5
KLHL22 activates amino-acid-dependent mTORC1 signalling to promote tumorigenesis and ageing.
PMID: 29769719
Nature Β· 2018
0.60