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NPRL3 NPR3 like, GATOR1 complex subunit [ Homo sapiens (human) ]

Gene ID: 8131, updated on 27-Nov-2024

Summary

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Official Symbol
NPRL3provided by HGNC
Official Full Name
NPR3 like, GATOR1 complex subunitprovided by HGNC
Primary source
HGNC:HGNC:14124
See related
Ensembl:ENSG00000103148 MIM:600928; AllianceGenome:HGNC:14124
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
MARE; NPR3; HS-40; RMD11; CGTHBA; FFEVF3; C16orf35
Summary
Predicted to enable GTPase activator activity. Involved in cellular response to amino acid starvation and negative regulation of TORC1 signaling. Part of GATOR1 complex. Is active in lysosomal membrane. Implicated in familial focal epilepsy with variable foci 3. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in testis (RPKM 11.3), ovary (RPKM 10.7) and 25 other tissues See more
Orthologs
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Genomic context

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See NPRL3 in Genome Data Viewer
Location:
16p13.3
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (85386..138673, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (78987..132241, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (135385..188672, complement)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6897 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6898 Neighboring gene small nuclear ribonucleoprotein U11/U12 subunit 25 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10199 Neighboring gene rhomboid 5 homolog 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:120389-121206 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:122199-122382 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6899 Neighboring gene uncharacterized LOC124903617 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:122843-123660 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:123661-124478 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:124479-125296 Neighboring gene Sharpr-MPRA regulatory region 13767 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:133607-134462 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6901 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10200 Neighboring gene N-methylpurine DNA glycosylase Neighboring gene alpha-globin locus control region Neighboring gene uncharacterized LOC107983982 Neighboring gene hemoglobin subunit zeta

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. Phenotypic and genotypic characterization of NPRL3-related epilepsy: Two case reports and literature review. Yang D, et al. Epilepsia Open, 2024 Feb. PMID 37902097, Free PMC Article
  2. Refining the electroclinical spectrum of NPRL3-related epilepsy: A novel multiplex family and literature review. Dainelli A, et al. Epilepsia Open, 2023 Dec. PMID 37491868, Free PMC Article
  3. A human minisatellite hosts an alternative transcription start site for NPRL3 driving its expression in a repeat number-dependent manner. Bertuzzi M, et al. Hum Mutat, 2020 Apr. PMID 31898848
  4. The clinical features of familial focal epilepsy with variable foci and NPRL3 gene variant. Wang Y, et al. PLoS One, 2023. PMID 37099548, Free PMC Article
  5. Clinical phenotypic and genotypic characterization of NPRL3-related epilepsy. Zhang H, et al. Front Neurol, 2023. PMID 36937533, Free PMC Article

See all (59) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Phenotypic and genotypic characterization of NPRL3-related epilepsy: Two case reports and literature review.
    Title: Phenotypic and genotypic characterization of NPRL3-related epilepsy: Two case reports and literature review.
  2. Refining the electroclinical spectrum of NPRL3-related epilepsy: A novel multiplex family and literature review.
    Title: Refining the electroclinical spectrum of NPRL3-related epilepsy: A novel multiplex family and literature review.
  3. 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.
  4. Functional characterization of novel NPRL3 mutations identified in three families with focal epilepsy.
    Title: Functional characterization of novel NPRL3 mutations identified in three families with focal epilepsy.
  5. The clinical features of familial focal epilepsy with variable foci and NPRL3 gene variant.
    Title: The clinical features of familial focal epilepsy with variable foci and NPRL3 gene variant.
  6. Hemimegalencephaly and intractable seizures associated with the NPRL3 gene variant in a newborn: A case report.
    Title: Hemimegalencephaly and intractable seizures associated with the NPRL3 gene variant in a newborn: A case report.
  7. A human minisatellite hosts an alternative transcription start site for NPRL3 driving its expression in a repeat number-dependent manner.
    Title: A human minisatellite hosts an alternative transcription start site for NPRL3 driving its expression in a repeat number-dependent manner.
  8. Diagnostic exome sequencing in non-acquired focal epilepsies highlights a major role of GATOR1 complex genes.
    Title: Diagnostic exome sequencing in non-acquired focal epilepsies highlights a major role of GATOR1 complex genes.
  9. GATOR1-related focal cortical dysplasia in epilepsy surgery patients and their families: A possible gradient in severity?
    Title: GATOR1-related focal cortical dysplasia in epilepsy surgery patients and their families: A possible gradient in severity?
  10. Our results implicate the association of NPRL3 with hemimegalencephaly, expanding the phenotypic spectrum of NPRL3 in FFEVF and underlining that partial deletions are part of the genotypic spectrum of NPRL3 variants
    Title: Inclusion of hemimegalencephaly into the phenotypic spectrum of NPRL3 pathogenic variants in familial focal epilepsy with variable foci.
Submit: New GeneRIF Correction See all GeneRIFs (17)

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 3
MedGen: C4310708 OMIM: 617118 GeneReviews: Not available
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Copy number response

Description
Copy number response
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated 2023-12-12)

ClinGen Genome Curation PagePubMed
Triplosensitivity

No evidence available (Last evaluated 2023-12-12)

ClinGen Genome Curation Page

EBI GWAS Catalog

Description
Genetic determinants of haemolysis in sickle cell anaemia.
EBI GWAS Catalog
Genome-wide association analysis of red blood cell traits in African Americans: the COGENT Network.
EBI GWAS Catalog
GWAS of blood cell traits identifies novel associated loci and epistatic interactions in Caucasian and African-American children.
EBI GWAS Catalog
Seventy-five genetic loci influencing the human red blood cell.
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)

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
enables GTPase activator activity IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in TORC1 signaling IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in aorta morphogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in cardiac muscle tissue development IEA
Inferred from Electronic Annotation
more info
  
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 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 positive regulation of autophagy IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in roof of mouth development IEA
Inferred from Electronic Annotation
more info
  
involved_in ventricular septum development IEA
Inferred from Electronic Annotation
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
  

General protein information

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Preferred Names
GATOR1 complex protein NPRL3
Names
-14 gene protein
GATOR complex protein NPRL3
alpha-globin regulatory element-containing gene protein
conserved gene telomeric to alpha globin cluster

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_029669.2 RefSeqGene

    Range
    4975..58287
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001039476.3 → NP_001034565.1  GATOR1 complex protein NPRL3 isoform 2

    See identical proteins and their annotated locations for NP_001034565.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (2) is shorter at the N-terminus compared to isoform 1.
    Source sequence(s)
    AK090717, Z69666, Z69720
    UniProtKB/TrEMBL
    Q9BTE2
    Conserved Domains (1) summary
    cl24021
    Location:15 → 237
    NPR3; Nitrogen Permease regulator of amino acid transport activity 3

  2. NM_001077350.3 → NP_001070818.1  GATOR1 complex protein NPRL3 isoform 1

    See identical proteins and their annotated locations for NP_001070818.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AK090717, DA258664, Z69666, Z69720
    Consensus CDS
    CCDS73795.1
    UniProtKB/Swiss-Prot
    D3DU40, Q12980, Q1W6H0, Q4TT56, Q92469
    UniProtKB/TrEMBL
    Q4TT55
    Related
    ENSP00000478273.1, ENST00000611875.5
    Conserved Domains (1) summary
    cl24021
    Location:64 → 416
    NPR3; Nitrogen Permease regulator of amino acid transport activity 3

  3. NM_001243247.2 → NP_001230176.1  GATOR1 complex protein NPRL3 isoform 3

    See identical proteins and their annotated locations for NP_001230176.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (3) is shorter at the N-terminus compared to isoform 1.
    Source sequence(s)
    AK294228, DA075508, DC384076, Z69720
    UniProtKB/TrEMBL
    B7Z220
    Conserved Domains (1) summary
    cl24021
    Location:1 → 338
    NPR3; Nitrogen Permease regulator of amino acid transport activity 3

  4. NM_001243248.2 → NP_001230177.1  GATOR1 complex protein NPRL3 isoform 4

    See identical proteins and their annotated locations for NP_001230177.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and lacks an alternate in-frame exon compared to variant 1. The resulting isoform (4) lacks an alternate internal segment compared to isoform 1. Variants 4 and 5 both encode the same isoform (4).
    Source sequence(s)
    AK300736, Z69666, Z69720
    Consensus CDS
    CCDS73794.1
    UniProtKB/TrEMBL
    B7Z6Q0, Q4TT55
    Conserved Domains (1) summary
    cl24021
    Location:64 → 391
    NPR3; Nitrogen Permease regulator of amino acid transport activity 3

  5. NM_001243249.2 → NP_001230178.1  GATOR1 complex protein NPRL3 isoform 4

    See identical proteins and their annotated locations for NP_001230178.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR and lacks an alternate in-frame exon compared to variant 1. The resulting isoform (4) lacks an alternate internal segment compared to isoform 1. Variants 4 and 5 both encode the same isoform (4).
    Source sequence(s)
    BC020392, Z69666, Z69720
    Consensus CDS
    CCDS73794.1
    UniProtKB/TrEMBL
    B7Z6Q0, Q4TT55
    Related
    ENSP00000382834.4, ENST00000399953.7
    Conserved Domains (1) summary
    cl24021
    Location:64 → 391
    NPR3; Nitrogen Permease regulator of amino acid transport activity 3

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

  1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    85386..138673 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    78987..132241 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_012075.1: Suppressed sequence

    Description
    NM_012075.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q12980.1 GenPept UniProtKB/Swiss-Prot:Q12980

Gene LinkOut

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