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

    Gene ID: 25791, updated on 3-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
    mouse all
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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 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)

    Genotypes

    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

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

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