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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
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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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