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NPRL2 NPR2 like, GATOR1 complex subunit [ Homo sapiens (human) ]

Gene ID: 10641, updated on 5-Mar-2024

Summary

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Official Symbol
NPRL2provided by HGNC
Official Full Name
NPR2 like, GATOR1 complex subunitprovided by HGNC
Primary source
HGNC:HGNC:24969
See related
Ensembl:ENSG00000114388 MIM:607072; AllianceGenome:HGNC:24969
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
NPR2; NPR2L; TUSC4; FFEVF2
Summary
Enables protein kinase activity. Contributes to GTPase activator activity. Involved in cellular response to amino acid starvation; negative regulation of TOR signaling; and negative regulation of kinase activity. Located in lysosomal membrane. Part of GATOR1 complex. Implicated in focal epilepsy. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in lymph node (RPKM 7.6), ovary (RPKM 7.3) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
3p21.31
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (50347330..50350775, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (50377054..50380498, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (50384761..50388206, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50374977-50375548 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19903 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr3:50377372-50378195 and GRCh37_chr3:50378196-50379018 Neighboring gene RASSF1 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50380164-50380746 Neighboring gene Ras association domain family member 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50382474-50383024 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50383025-50383575 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19905 Neighboring gene CYB561D2-LOC101928965 Neighboring gene zinc finger MYND-type containing 10 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50396255-50397145 Neighboring gene cytochrome b561 family member D2 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr3:50401999-50402580 and GRCh37_chr3:50402581-50403164 Neighboring gene uncharacterized LOC101928965 Neighboring gene transmembrane protein 115 Neighboring gene calcium voltage-gated channel auxiliary subunit alpha2delta 2

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. Risk signature identification and NPRL2 affects sunitinib sensitivity in clear cell renal cell carcinoma. Du X, et al. Biochem Biophys Res Commun, 2023 Jun 30. PMID 37121122
  2. NPRL2 down-regulation facilitates the growth of hepatocellular carcinoma via the mTOR pathway and autophagy suppression. Wang YC, et al. Hepatol Commun, 2022 Dec. PMID 36321403, Free PMC Article
  3. Nitrogen Permease Regulator Like-2 (NPRL2 ) truncating mutation causes Ohtahara syndrome with incomplete penetrance: expanding the genotype-phenotype correlations. Zhou X, et al. Clin Dysmorphol, 2022 Oct 1. PMID 35731010
  4. A splicing variation in NPRL2 causing familial focal epilepsy with variable foci: additional cases and literature review. Zhang J, et al. J Hum Genet, 2022 Feb. PMID 34376795, Free PMC Article
  5. NPRL2 enhances autophagy and the resistance to Everolimus in castration-resistant prostate cancer. Chen Z, et al. Prostate, 2019 Jan. PMID 30178500

See all (59) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Seizure features and outcomes in 50 children with GATOR1 variants: A retrospective study, more favorable for epilepsy surgery.
    Title: Seizure features and outcomes in 50 children with GATOR1 variants: A retrospective study, more favorable for epilepsy surgery.
  2. Risk signature identification and NPRL2 affects sunitinib sensitivity in clear cell renal cell carcinoma.
    Title: Risk signature identification and NPRL2 affects sunitinib sensitivity in clear cell renal cell carcinoma.
  3. NPRL2 down-regulation facilitates the growth of hepatocellular carcinoma via the mTOR pathway and autophagy suppression.
    Title: NPRL2 down-regulation facilitates the growth of hepatocellular carcinoma via the mTOR pathway and autophagy suppression.
  4. Nitrogen Permease Regulator Like-2 (NPRL2 ) truncating mutation causes Ohtahara syndrome with incomplete penetrance: expanding the genotype-phenotype correlations.
    Title: Nitrogen Permease Regulator Like-2 (NPRL2 ) truncating mutation causes Ohtahara syndrome with incomplete penetrance: expanding the genotype-phenotype correlations.
  5. A splicing variation in NPRL2 causing familial focal epilepsy with variable foci: additional cases and literature review.
    Title: A splicing variation in NPRL2 causing familial focal epilepsy with variable foci: additional cases and literature review.
  6. FOXO1 inhibits prostate cancer cell proliferation via suppressing E2F1 activated NPRL2 expression.
    Title: FOXO1 inhibits prostate cancer cell proliferation via suppressing E2F1 activated NPRL2 expression.
  7. NPRL2 reduces the niraparib sensitivity of castration-resistant prostate cancer via interacting with UBE2M and enhancing neddylation.
    Title: NPRL2 reduces the niraparib sensitivity of castration-resistant prostate cancer via interacting with UBE2M and enhancing neddylation.
  8. NPRL2 promotes docetaxel chemoresistance in castration resistant prostate cancer cells by regulating autophagy through the mTOR pathway.
    Title: NPRL2 promotes docetaxel chemoresistance in castration resistant prostate cancer cells by regulating autophagy through the mTOR pathway.
  9. these results demonstrate a new role for the NPRL2, distinct from its function in mTORC1 regulation.
    Title: Tumor suppressor NPRL2 induces ROS production and DNA damage response.
  10. Arg-78 of Nprl2 catalyzes GATOR1-stimulated GTP hydrolysis by the Rag GTPases.
    Title: Arg-78 of Nprl2 catalyzes GATOR1-stimulated GTP hydrolysis by the Rag GTPases.
Submit: New GeneRIF Correction See all GeneRIFs (32)

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
Epilepsy, familial focal, with variable foci 2
MedGen: C4310709 OMIM: 617116 GeneReviews: Not available
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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

Pathways from PubChem

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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
contributes_to GTPase activator activity IBA
Inferred from Biological aspect of Ancestor
more info
  
contributes_to GTPase activator activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables GTPase activator activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in cellular response to amino acid starvation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cellular response to amino acid starvation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in cellular response to amino acid starvation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of TOR signaling IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of TORC1 signaling IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of TORC1 signaling IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of TORC1 signaling NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in negative regulation of kinase activity IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of autophagy IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
part_of GATOR1 complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of GATOR1 complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of GATOR1 complex IPI
Inferred from Physical Interaction
more info
 PubMed 
is_active_in lysosomal membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in lysosomal membrane NAS
Non-traceable Author Statement
more info
 PubMed 
located_in lysosomal membrane TAS
Traceable Author Statement
more info
  
is_active_in vacuolar membrane IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
GATOR1 complex protein NPRL2
Names
2810446G01Rik
G21 protein
GATOR complex protein NPRL2
NPR2-like protein
gene 21 protein
homologous to yeast nitrogen permease (candidate tumor suppressor)
mutant NPRL2
nitrogen permease regulator 2-like protein
tumor suppressor candidate 4

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.

mRNA and Protein(s)

  1. NM_006545.5 → NP_006536.3  GATOR1 complex protein NPRL2

    See identical proteins and their annotated locations for NP_006536.3

    Status: VALIDATED

    Source sequence(s)
    AC002481, BC008802, BC056861
    Consensus CDS
    CCDS2826.1
    UniProtKB/Swiss-Prot
    A8K831, Q6FGS2, Q8WTW4, Q9Y249, Q9Y497
    Related
    ENSP00000232501.3, ENST00000232501.8
    Conserved Domains (1) summary
    cl24021
    Location:7 → 370
    NPR3; Nitrogen Permease regulator of amino acid transport activity 3

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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    50347330..50350775 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047447310.1 → XP_047303266.1  GATOR1 complex protein NPRL2 isoform X1

  2. XM_011533288.4 → XP_011531590.1  GATOR1 complex protein NPRL2 isoform X2

    Related
    ENST00000479512.5
    Conserved Domains (1) summary
    cl24021
    Location:45 → 367
    NPR3; Nitrogen Permease regulator of amino acid transport activity 3

  3. XM_017005556.3 → XP_016861045.1  GATOR1 complex protein NPRL2 isoform X5

    Conserved Domains (1) summary
    cl24021
    Location:3 → 250
    NPR3; Nitrogen Permease regulator of amino acid transport activity 3

  4. XM_047447311.1 → XP_047303267.1  GATOR1 complex protein NPRL2 isoform X3

  5. XM_047447314.1 → XP_047303270.1  GATOR1 complex protein NPRL2 isoform X6

  6. XM_047447312.1 → XP_047303268.1  GATOR1 complex protein NPRL2 isoform X4

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    50377054..50380498 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054344961.1 → XP_054200936.1  GATOR1 complex protein NPRL2 isoform X1

  2. XM_054344962.1 → XP_054200937.1  GATOR1 complex protein NPRL2 isoform X2

  3. XM_054344963.1 → XP_054200938.1  GATOR1 complex protein NPRL2 isoform X3

  4. XM_054344965.1 → XP_054200940.1  GATOR1 complex protein NPRL2 isoform X6

  5. XM_054344964.1 → XP_054200939.1  GATOR1 complex protein NPRL2 isoform X4

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8WTW4.2 GenPept UniProtKB/Swiss-Prot:Q8WTW4

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