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    NEGR1 neuronal growth regulator 1 [ Homo sapiens (human) ]

    Gene ID: 257194, updated on 3-Apr-2024

    Summary

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    Official Symbol
    NEGR1provided by HGNC
    Official Full Name
    neuronal growth regulator 1provided by HGNC
    Primary source
    HGNC:HGNC:17302
    See related
    Ensembl:ENSG00000172260 MIM:613173; AllianceGenome:HGNC:17302
    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
    Ntra; KILON; IGLON4; DMML2433
    Summary
    Predicted to act upstream of or within several processes, including feeding behavior; locomotory behavior; and positive regulation of neuron projection development. Predicted to be located in extracellular region and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Broad expression in brain (RPKM 13.7), fat (RPKM 5.3) and 18 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    1p31.1
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (71395943..72282539, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (71273677..72161473, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (71861626..72748222, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 991 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1198 Neighboring gene uncharacterized LOC105378795 Neighboring gene ZRANB2 divergent transcript Neighboring gene zinc finger RANBP2-type containing 2 Neighboring gene microRNA 186 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:71927989-71928559 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:72203394-72203980 Neighboring gene NEGR1 intronic transcript 1 Neighboring gene NANOG hESC enhancer GRCh37_chr1:72328413-72328914 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:72466099-72467298 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 992 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 993 Neighboring gene uncharacterized LOC105378797 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:72750040-72751239 Neighboring gene ribosomal protein L31 pseudogene 12 Neighboring gene GDP dissociation inhibitor 2 pseudogene 2 Neighboring gene uncharacterized LOC105378796

    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. Depression in multiple sclerosis patients associated with risk variant near NEGR1. Brugger SW, et al. Mult Scler Relat Disord, 2020 Nov. PMID 33296963
    2. Association of the NEGR1 rs2815752 with obesity and related traits in Pakistani females. Rana S, et al. Ups J Med Sci, 2020 Aug. PMID 32419576, Free PMC Article
    3. 1p31.1 microdeletion including only NEGR1 gene in two patients. Tassano E, et al. Eur J Med Genet, 2020 Jun. PMID 32209393
    4. Integrating genome-wide association study and expression quantitative trait loci data identifies NEGR1 as a causal risk gene of major depression disorder. Wang X, et al. J Affect Disord, 2020 Mar 15. PMID 32090785
    5. Placental NEGR1 DNA methylation is associated with BMI and neurodevelopment in preschool-age children. Breton E, et al. Epigenetics, 2020 Mar. PMID 31510847, Free PMC Article

    See all (69) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Plasma Neuronal Growth Regulator 1 May Link Physical Activity to Reduced Risk of Type 2 Diabetes: A Proteome-Wide Study of ARIC Participants.
      Title: Plasma Neuronal Growth Regulator 1 May Link Physical Activity to Reduced Risk of Type 2 Diabetes: A Proteome-Wide Study of ARIC Participants.
    2. CircDLGAP4 overexpression relieves oxygen-glucose deprivation-induced neuronal injury by elevating NEGR1 through sponging miR-503-3p.
      Title: CircDLGAP4 overexpression relieves oxygen-glucose deprivation-induced neuronal injury by elevating NEGR1 through sponging miR-503-3p.
    3. Harnessing tissue-specific genetic variation to dissect putative causal pathways between body mass index and cardiometabolic phenotypes.
      Title: Harnessing tissue-specific genetic variation to dissect putative causal pathways between body mass index and cardiometabolic phenotypes.
    4. Na/K-ATPase beta1-subunit associates with neuronal growth regulator 1 (NEGR1) to participate in intercellular interactions.
      Title: Na/K-ATPase beta1-subunit associates with neuronal growth regulator 1 (NEGR1) to participate in intercellular interactions.
    5. Depression in multiple sclerosis patients associated with risk variant near NEGR1.
      Title: Depression in multiple sclerosis patients associated with risk variant near NEGR1.
    6. Association of the NEGR1 rs2815752 with obesity and related traits in Pakistani females.
      Title: Association of the NEGR1 rs2815752 with obesity and related traits in Pakistani females.
    7. Placental NEGR1 DNA methylation is associated with BMI and neurodevelopment in preschool-age children.
      Title: Placental NEGR1 DNA methylation is associated with BMI and neurodevelopment in preschool-age children.
    8. Highly Conserved Molecular Features in IgLONs Contrast Their Distinct Structural and Biological Outcomes.
      Title: Highly Conserved Molecular Features in IgLONs Contrast Their Distinct Structural and Biological Outcomes.
    9. Integrating genome-wide association study and expression quantitative trait loci data identifies NEGR1 as a causal risk gene of major depression disorder.
      Title: Integrating genome-wide association study and expression quantitative trait loci data identifies NEGR1 as a causal risk gene of major depression disorder.
    10. 1p31.1 microdeletion including only NEGR1 gene in two patients.
      Title: 1p31.1 microdeletion including only NEGR1 gene in two patients.
    Submit: New GeneRIF Correction See all GeneRIFs (35)

    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

    EBI GWAS Catalog

    Description
    Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index.
    EBI GWAS Catalog
    Association of systemic lupus erythematosus with C8orf13-BLK and ITGAM-ITGAX.
    EBI GWAS Catalog
    Common genetic variants associated with cognitive performance identified using the proxy-phenotype method.
    EBI GWAS Catalog
    Genome-wide analysis of BMI in adolescents and young adults reveals additional insight into the effects of genetic loci over the life course.
    EBI GWAS Catalog
    Genome-wide association and linkage analyses of hemostatic factors and hematological phenotypes in the Framingham Heart Study.
    EBI GWAS Catalog
    Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women.
    EBI GWAS Catalog
    Genome-wide association yields new sequence variants at seven loci that associate with measures of obesity.
    EBI GWAS Catalog
    Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.
    EBI GWAS Catalog
    Genome-wide SNP and CNV analysis identifies common and low-frequency variants associated with severe early-onset obesity.
    EBI GWAS Catalog
    Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
    EBI GWAS Catalog
    Six new loci associated with body mass index highlight a neuronal influence on body weight regulation.
    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)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC46680

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cell-cell adhesion IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in feeding behavior IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in locomotory behavior IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in neuron projection development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of neuron projection development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of synapse assembly IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in dendrite IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in extracellular region TAS
    Traceable Author Statement
    more info
    		  
    located_in neuronal cell body IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in side of membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    neuronal growth regulator 1
    Names
    IgLON family member 4
    a kindred of IgLON
    neurotractin

    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_173808.3 → NP_776169.2  neuronal growth regulator 1 precursor

      See identical proteins and their annotated locations for NP_776169.2

      Status: VALIDATED

      Source sequence(s)
      AL354949, AL356600, AL359821, AL627317, AL645724
      Consensus CDS
      CCDS661.1
      UniProtKB/Swiss-Prot
      Q5VT21, Q6UY06, Q7Z3B1, Q8N440, Q8NAQ3
      UniProtKB/TrEMBL
      B4DI94
      Related
      ENSP00000350364.4, ENST00000357731.10
      Conserved Domains (3) summary
      smart00408
      Location:152 → 210
      IGc2; Immunoglobulin C-2 Type
      smart00409
      Location:47 → 135
      IG; Immunoglobulin
      pfam13927
      Location:225 → 301
      Ig_3; Immunoglobulin domain

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      71395943..72282539 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011541200.4 → XP_011539502.1  neuronal growth regulator 1 isoform X1

      UniProtKB/TrEMBL
      B4DI94
      Conserved Domains (4) summary
      cd00096
      Location:243 → 309
      Ig; Immunoglobulin domain
      smart00408
      Location:152 → 210
      IGc2; Immunoglobulin C-2 Type
      smart00410
      Location:231 → 312
      IG_like; Immunoglobulin like
      cl11960
      Location:44 → 135
      Ig; Immunoglobulin domain

    2. XM_017000961.3 → XP_016856450.1  neuronal growth regulator 1 isoform X3

    3. XM_011541201.4 → XP_011539503.1  neuronal growth regulator 1 isoform X2

      See identical proteins and their annotated locations for XP_011539503.1

      Conserved Domains (3) summary
      smart00408
      Location:152 → 210
      IGc2; Immunoglobulin C-2 Type
      smart00410
      Location:145 → 221
      IG_like; Immunoglobulin like
      cl11960
      Location:44 → 135
      Ig; Immunoglobulin domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      71273677..72161473 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054335847.1 → XP_054191822.1  neuronal growth regulator 1 isoform X1

    2. XM_054335849.1 → XP_054191824.1  neuronal growth regulator 1 isoform X3

    3. XM_054335848.1 → XP_054191823.1  neuronal growth regulator 1 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q7Z3B1.3 GenPept UniProtKB/Swiss-Prot:Q7Z3B1

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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