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NGEF neuronal guanine nucleotide exchange factor [ Homo sapiens (human) ]

Gene ID: 25791, updated on 26-Nov-2024

Summary

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Official Symbol
NGEFprovided by HGNC
Official Full Name
neuronal guanine nucleotide exchange factorprovided by HGNC
Primary source
HGNC:HGNC:7807
See related
Ensembl:ENSG00000066248 MIM:605991; AllianceGenome:HGNC:7807
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
EPHEXIN; ARHGEF27
Summary
Enables guanyl-nucleotide exchange factor activity. Predicted to be involved in ephrin receptor signaling pathway; negative regulation of dendritic spine morphogenesis; and regulation of synapse pruning. Predicted to be located in cytosol. Predicted to be active in glutamatergic synapse and postsynapse. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in brain (RPKM 32.1), duodenum (RPKM 14.9) and 8 other tissues See more
Orthologs
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Genomic context

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See NGEF in Genome Data Viewer
Location:
2q37.1
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (232878701..233013256, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (233365384..233500670, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (233743411..233877966, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene GRB10 interacting GYF protein 2 Neighboring gene RNA, U6 small nuclear 107, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:233736904-233737669 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12464 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:233755984-233756593 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:233756594-233757202 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:233765119-233765744 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:233766250-233767449 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:233769412-233770057 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:233770058-233770702 Neighboring gene secondary ossification center associated regulator of chondrocyte maturation Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17326 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17327 Neighboring gene uncharacterized LOC101928881 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12465 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17328 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12466 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17329 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:233926783-233927376 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:233927377-233927970 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17330 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12468 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:233937995-233938700 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17331 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17332 Neighboring gene Sharpr-MPRA regulatory region 10619 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17333 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:233953501-233954000 Neighboring gene neuraminidase 2 Neighboring gene inositol polyphosphate-5-phosphatase D Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:233972121-233972622 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:233972623-233973122 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17334 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:233982267-233982860 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:233987251-233987751 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:233988888-233989435 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:233989436-233989982 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:233993677-233994176 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:234072305-234072918 Neighboring gene RNA, 7SL, cytoplasmic 32, pseudogene

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. Akt-mediated Ephexin1-Ras interaction promotes oncogenic Ras signaling and colorectal and lung cancer cell proliferation. Kim J, et al. Cell Death Dis, 2021 Oct 28. PMID 34711817, Free PMC Article
  2. A Common Variant of NGEF Is Associated with Abdominal Visceral Fat in Korean Men. Kim HJ, et al. PLoS One, 2015. PMID 26340433, Free PMC Article
  3. Characterization of Ngef, a novel member of the Dbl family of genes expressed predominantly in the caudate nucleus. Rodrigues NR, et al. Genomics, 2000 Apr 1. PMID 10777665
  4. EphA receptors regulate growth cone dynamics through the novel guanine nucleotide exchange factor ephexin. Shamah SM, et al. Cell, 2001 Apr 20. PMID 11336673
  5. Eph-dependent tyrosine phosphorylation of ephexin1 modulates growth cone collapse. Sahin M, et al. Neuron, 2005 Apr 21. PMID 15848799

See all (39) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Akt-mediated Ephexin1-Ras interaction promotes oncogenic Ras signaling and colorectal and lung cancer cell proliferation.
    Title: Akt-mediated Ephexin1-Ras interaction promotes oncogenic Ras signaling and colorectal and lung cancer cell proliferation.
  2. A visceral-fat-associated SNP, rs11678490 of NGEF, was found in Korean men.
    Title: A Common Variant of NGEF Is Associated with Abdominal Visceral Fat in Korean Men.
  3. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  4. Observational study of gene-disease association. (HuGE Navigator)
    Title: Mutation of ARHGAP9 in patients with coronary spastic angina.
  5. FGFR-mediated phosphorylation of ephexin1 enhances the guanine nucleotide exchange activity toward RhoA without affecting the activity to Rac1 or Cdc42.
    Title: Regulation of ephexin1, a guanine nucleotide exchange factor of Rho family GTPases, by fibroblast growth factor receptor-mediated tyrosine phosphorylation.
Submit: New GeneRIF Correction

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
Biological insights from 108 schizophrenia-associated genetic loci.
EBI GWAS Catalog
Genome-wide association analysis identifies 13 new risk loci for schizophrenia.
EBI GWAS Catalog
Variants in the 1q21 risk region are associated with a visual endophenotype of autism and schizophrenia.
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)

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of neuronal guanine nucleotide exchange factor (NGEF) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells PubMed

Go to the HIV-1, Human Interaction Database

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 guanyl-nucleotide exchange factor activity EXP
Inferred from Experiment
more info
 PubMed 
enables guanyl-nucleotide exchange factor activity TAS
Traceable Author Statement
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in cell differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in ephrin receptor signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in ephrin receptor signaling pathway TAS
Traceable Author Statement
more info
  
involved_in negative regulation of dendritic spine morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in nervous system development IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of GTPase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of actin cytoskeleton organization IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of small GTPase mediated signal transduction TAS
Traceable Author Statement
more info
  
Component Evidence Code Pubs
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in growth cone IEA
Inferred from Electronic Annotation
more info
  
located_in membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
ephexin-1
Names
eph-interacting exchange protein
ephexin1

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_001114090.2 → NP_001107562.1  ephexin-1 isoform 2

    See identical proteins and their annotated locations for NP_001107562.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and coding region compared to variant 1. The resulting isoform (2) has a shorter and distinct N-terminus compared to isoform 1.
    Source sequence(s)
    AC016692, BC031573, BC073962, BX431262
    Consensus CDS
    CCDS46544.1
    UniProtKB/TrEMBL
    B4DV69
    Related
    ENSP00000362653.4, ENST00000373552.8
    Conserved Domains (3) summary
    cd11939
    Location:524 → 578
    SH3_ephexin1; Src homology 3 domain of the Rho guanine nucleotide exchange factor, ephexin-1 (also called NGEF or ARHGEF27)
    cd01221
    Location:385 → 511
    PH_ephexin; Ephexin Pleckstrin homology (PH) domain
    pfam00621
    Location:185 → 363
    RhoGEF; RhoGEF domain

  2. NM_019850.3 → NP_062824.2  ephexin-1 isoform 1

    See identical proteins and their annotated locations for NP_062824.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC016692, AC106876, BC031573, BC073962, BX431262, DB242442, DC388448
    Consensus CDS
    CCDS2500.1
    UniProtKB/Swiss-Prot
    B4DMB8, B9A045, E9PC42, Q53QQ4, Q53ST7, Q6GMQ5, Q8N5V2, Q9NQD6
    UniProtKB/TrEMBL
    A0A2X0SG27
    Related
    ENSP00000264051.3, ENST00000264051.8
    Conserved Domains (4) summary
    cd11939
    Location:616 → 670
    SH3_ephexin1; Src homology 3 domain of the Rho guanine nucleotide exchange factor, ephexin-1 (also called NGEF or ARHGEF27)
    cd01221
    Location:477 → 603
    PH_ephexin; Ephexin Pleckstrin homology (PH) domain
    pfam00169
    Location:490 → 596
    PH; PH domain
    pfam00621
    Location:277 → 456
    RhoGEF; RhoGEF 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

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    232878701..233013256 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011510923.4 → XP_011509225.1  ephexin-1 isoform X1

    See identical proteins and their annotated locations for XP_011509225.1

    UniProtKB/Swiss-Prot
    B4DMB8, B9A045, E9PC42, Q53QQ4, Q53ST7, Q6GMQ5, Q8N5V2, Q9NQD6
    UniProtKB/TrEMBL
    A0A2X0SG27
    Conserved Domains (4) summary
    cd11939
    Location:616 → 670
    SH3_ephexin1; Src homology 3 domain of the Rho guanine nucleotide exchange factor, ephexin-1 (also called NGEF or ARHGEF27)
    cd01221
    Location:477 → 603
    PH_ephexin; Ephexin Pleckstrin homology (PH) domain
    pfam00169
    Location:490 → 596
    PH; PH domain
    pfam00621
    Location:277 → 456
    RhoGEF; RhoGEF domain

  2. XM_047443880.1 → XP_047299836.1  ephexin-1 isoform X2

  3. XM_011510924.2 → XP_011509226.1  ephexin-1 isoform X3

    See identical proteins and their annotated locations for XP_011509226.1

    UniProtKB/TrEMBL
    B4DDI2
    Conserved Domains (4) summary
    cd11939
    Location:339 → 393
    SH3_ephexin1; Src homology 3 domain of the Rho guanine nucleotide exchange factor, ephexin-1 (also called NGEF or ARHGEF27)
    cd01221
    Location:200 → 326
    PH_ephexin; Ephexin Pleckstrin homology (PH) domain
    pfam00169
    Location:213 → 319
    PH; PH domain
    pfam00621
    Location:1 → 179
    RhoGEF; RhoGEF domain

  4. XM_011510925.2 → XP_011509227.1  ephexin-1 isoform X3

    See identical proteins and their annotated locations for XP_011509227.1

    UniProtKB/TrEMBL
    B4DDI2
    Conserved Domains (4) summary
    cd11939
    Location:339 → 393
    SH3_ephexin1; Src homology 3 domain of the Rho guanine nucleotide exchange factor, ephexin-1 (also called NGEF or ARHGEF27)
    cd01221
    Location:200 → 326
    PH_ephexin; Ephexin Pleckstrin homology (PH) domain
    pfam00169
    Location:213 → 319
    PH; PH domain
    pfam00621
    Location:1 → 179
    RhoGEF; RhoGEF domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    233365384..233500670 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054341301.1 → XP_054197276.1  ephexin-1 isoform X1

  2. XM_054341302.1 → XP_054197277.1  ephexin-1 isoform X2

  3. XM_054341303.1 → XP_054197278.1  ephexin-1 isoform X3

    UniProtKB/TrEMBL
    B4DDI2

  4. XM_054341304.1 → XP_054197279.1  ephexin-1 isoform X3

    UniProtKB/TrEMBL
    B4DDI2
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8N5V2.2 GenPept UniProtKB/Swiss-Prot:Q8N5V2

Gene LinkOut

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