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

Summary

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 be involved in cell adhesion and regulation of synapse assembly. Predicted to act upstream of or within several processes, including cholesterol homeostasis; lipid droplet formation; and nervous system development. Predicted to be located in extracellular region and plasma membrane. Predicted to be active in postsynaptic density. [provided by Alliance of Genome Resources, Nov 2024]
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

Location:: 1p31.1

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (71395943..72282539, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (71273677..72161473, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (71861626..72748222, complement)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The Association between Obesity Susceptibility and Polymorphisms of MC4R, SH2B1, and NEGR1 in Tibetans.
Title: The Association between Obesity Susceptibility and Polymorphisms of MC4R, SH2B1, and NEGR1 in Tibetans.
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.
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.
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.
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.
Depression in multiple sclerosis patients associated with risk variant near NEGR1.
Title: Depression in multiple sclerosis patients associated with risk variant near NEGR1.
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.
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.
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.
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.

Submit: New GeneRIF Correction See all GeneRIFs (36)

Phenotypes

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH118958 (e-PCR)
- UniSTS:138243

SHGC-104652 (e-PCR)
- UniSTS:168963

RH67891 (e-PCR)
- UniSTS:9476

SHGC-84225 (e-PCR)
- UniSTS:104713

WI-4469 (e-PCR)
- UniSTS:19224

AL009401 (e-PCR)
- UniSTS:60696

D1S2490 (e-PCR)
- UniSTS:63512

RH119040 (e-PCR)
- UniSTS:138268

D1S224 (e-PCR), detects polymorphism
- UniSTS:27422

AL033860 (e-PCR)
- UniSTS:93736

SHGC-78108 (e-PCR)
- UniSTS:101680

RH123582 (e-PCR)
- UniSTS:136002

AL034194 (e-PCR)
- UniSTS:94020

RH80738 (e-PCR)
- UniSTS:88903

AFMb280xc1 (e-PCR)
- UniSTS:37191

SHGC-146367 (e-PCR)
- UniSTS:175175

RH118419 (e-PCR)
- UniSTS:137802

WI-18412 (e-PCR)
- UniSTS:53593

SHGC-82525 (e-PCR)
- UniSTS:100698

RH123142 (e-PCR)
- UniSTS:135523

AL034242 (e-PCR)
- UniSTS:94062

SHGC-106944 (e-PCR)
- UniSTS:181899

AL033950 (e-PCR)
- UniSTS:93854

WI-11980 (e-PCR)
- UniSTS:30879

SHGC-152670 (e-PCR)
- UniSTS:177574

AL034296 (e-PCR)
- UniSTS:94119

SHGC-829 (e-PCR)
- UniSTS:86957

RH79991 (e-PCR)
- UniSTS:88518

G29197 (e-PCR)
- UniSTS:76489

174 (e-PCR), detects polymorphism
- UniSTS:45533

RH119304 (e-PCR)
- UniSTS:133866

RH122381 (e-PCR)
- UniSTS:138478

AL010102 (e-PCR)
- UniSTS:4081

RH122276 (e-PCR)
- UniSTS:134902

SHGC-75028 (e-PCR)
- UniSTS:25078

AL010101 (e-PCR)
- UniSTS:47864

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 brain development	IEA Inferred from Electronic Annotation more info
involved_in cell-cell adhesion	IEA Inferred from Electronic Annotation more info
involved_in cholesterol homeostasis	IEA Inferred from Electronic Annotation more info
involved_in fat cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in feeding behavior	IEA Inferred from Electronic Annotation more info
involved_in lipid droplet formation	IEA Inferred from Electronic Annotation more info
involved_in locomotory behavior	IEA Inferred from Electronic Annotation more info
involved_in neuron projection morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of calcium-mediated signaling	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of neuron projection development	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of saliva secretion	IEA Inferred from Electronic Annotation more info
involved_in regulation of synapse assembly	IEA Inferred from Electronic Annotation more info
involved_in skeletal muscle organ development	IEA Inferred from Electronic Annotation more info
involved_in social behavior	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 postsynaptic density	IEA Inferred from Electronic Annotation 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)

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_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

71395943..72282539 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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