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FGD2 FYVE, RhoGEF and PH domain containing 2 [ Homo sapiens (human) ]

Gene ID: 221472, updated on 15-Jun-2019

Summary

Official Symbol
FGD2provided by HGNC
Official Full Name
FYVE, RhoGEF and PH domain containing 2provided by HGNC
Primary source
HGNC:HGNC:3664
See related
Ensembl:ENSG00000146192 MIM:605091
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
ZFYVE4
Summary
The protein encoded by this gene belongs to a family of guanine nucleotide exchange factors (GEFs) which control cytoskeleton-dependent membrane rearrangements by activating the cell division cycle 42 (CDC42) protein. This gene is expressed in B lymphocytes, macrophages, and dendritic cells. The encoded protein may play a role in leukocyte signaling and vesicle trafficking in antigen-presenting cells in the immune system. [provided by RefSeq, Oct 2016]
Expression
Biased expression in spleen (RPKM 19.9), lymph node (RPKM 9.1) and 13 other tissues See more
Orthologs

Genomic context

See FGD2 in Genome Data Viewer
Location:
6p21.2
Exon count:
20
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 6 NC_000006.12 (37005647..37029072)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (36973423..36996845)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene peptidase inhibitor 16 Neighboring gene mitochondrial carrier 1 Neighboring gene cytochrome c oxidase subunit 6A1 pseudogene 2 Neighboring gene ribosomal protein L12 pseudogene 2

Genomic regions, transcripts, and products

Expression

  • 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

Phenotypes

NHGRI GWAS Catalog

Description
Genome-wide association study identifies three novel susceptibility loci for severe Acne vulgaris.
NHGRI GWA Catalog

Pathways from BioSystems

  • Cell death signalling via NRAGE, NRIF and NADE, organism-specific biosystem (from REACTOME)
    Cell death signalling via NRAGE, NRIF and NADE, organism-specific biosystemp75NTR is a key regulator of neuronal apoptosis, both during development and after injury. Apoptosis is triggered by binding of either mature neurotrophin or proneurotrophin (proNGF, proBDNF). ProNG...
  • G alpha (12/13) signalling events, organism-specific biosystem (from REACTOME)
    G alpha (12/13) signalling events, organism-specific biosystemThe G12/13 family is probably the least well characterized subtype, partly because G12/13 coupling is difficult to determine when compared with the other subtypes which predominantly rely on assay te...
  • GPCR downstream signaling, organism-specific biosystem (from REACTOME)
    GPCR downstream signaling, organism-specific biosystemG protein-coupled receptors (GPCRs) are classically defined as the receptor, G-protein and downstream effectors, the alpha subunit of the G-protein being the primary signaling molecule. However, it h...
  • NRAGE signals death through JNK, organism-specific biosystem (from REACTOME)
    NRAGE signals death through JNK, organism-specific biosystemOnce bound by either NGF or proNGF, p75NTR interacts with NRAGE, thus leading to phosphorylation and activation of JUN Kinase (JNK). JNK controls apoptosis in two ways: it induces transcription of pr...
  • Rho GTPase cycle, organism-specific biosystem (from REACTOME)
    Rho GTPase cycle, organism-specific biosystemThe cycling of Rho GTPases is tightly controlled by three classes of protein. These are (1) guanine nucleotide dissociation inhibitors or GDIs, which maintain Rho proteins in an inactive state in the...
  • Signal Transduction, organism-specific biosystem (from REACTOME)
    Signal Transduction, organism-specific biosystemSignal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such a...
  • Signaling by GPCR, organism-specific biosystem (from REACTOME)
    Signaling by GPCR, organism-specific biosystemG protein-coupled receptors (GPCRs; 7TM receptors; seven transmembrane domain receptors; heptahelical receptors; G protein-linked receptors [GPLR]) are the largest family of transmembrane receptors i...
  • Signaling by Rho GTPases, organism-specific biosystem (from REACTOME)
    Signaling by Rho GTPases, organism-specific biosystemThe Rho family of small guanine nucleotide binding proteins is one of five generally recognized branches of the Ras superfamily. Like most Ras superfamily members, typical Rho proteins function as bi...
  • Signalling by NGF, organism-specific biosystem (from REACTOME)
    Signalling by NGF, organism-specific biosystemNeurotrophins (NGF, BDNF, NT-3, NT-4/5) play pivotal roles in survival, differentiation, and plasticity of neurons in the peripheral and central nervous system. They are produced, and secreted in mi...
  • p75 NTR receptor-mediated signalling, organism-specific biosystem (from REACTOME)
    p75 NTR receptor-mediated signalling, organism-specific biosystemBesides signalling through the tyrosine kinase receptors TRK A, B, and C, the mature neurotrophins NGF, BDNF, and NT3/4 signal through their common receptor p75NTR. NGF binding to p75NTR activates a ...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ00048, FLJ40929, MGC71330

Gene Ontology Provided by GOA

Function Evidence Code Pubs
Rho guanyl-nucleotide exchange factor activity IEA
Inferred from Electronic Annotation
more info
 
guanyl-nucleotide exchange factor activity ISS
Inferred from Sequence or Structural Similarity
more info
 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
phosphatidylinositol phosphate binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
small GTPase binding ISS
Inferred from Sequence or Structural Similarity
more info
 
Process Evidence Code Pubs
G protein-coupled receptor signaling pathway TAS
Traceable Author Statement
more info
 
actin cytoskeleton organization ISS
Inferred from Sequence or Structural Similarity
more info
 
cytoskeleton organization ISS
Inferred from Sequence or Structural Similarity
more info
 
filopodium assembly ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of JUN kinase activity IEA
Inferred from Electronic Annotation
more info
 
positive regulation of apoptotic process TAS
Traceable Author Statement
more info
 
regulation of GTPase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of Rho protein signal transduction IEA
Inferred from Electronic Annotation
more info
 
regulation of cell shape ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of small GTPase mediated signal transduction TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
Golgi apparatus ISS
Inferred from Sequence or Structural Similarity
more info
 
cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
 
cytoskeleton IEA
Inferred from Electronic Annotation
more info
 
cytosol TAS
Traceable Author Statement
more info
 
early endosome membrane IEA
Inferred from Electronic Annotation
more info
 
lamellipodium ISS
Inferred from Sequence or Structural Similarity
more info
 
nucleus IEA
Inferred from Electronic Annotation
more info
 
ruffle ISS
Inferred from Sequence or Structural Similarity
more info
 
ruffle membrane IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
FYVE, RhoGEF and PH domain-containing protein 2
Names
FGD1 family, member 2
FLJ00276 protein
epididymis secretory sperm binding protein
zinc finger FYVE domain-containing protein 4

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_051804.1 RefSeqGene

    Range
    5001..28423
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_173558.4NP_775829.2  FYVE, RhoGEF and PH domain-containing protein 2

    See identical proteins and their annotated locations for NP_775829.2

    Status: REVIEWED

    Source sequence(s)
    AL160264, BC023645, BC053655
    Consensus CDS
    CCDS4829.1
    UniProtKB/Swiss-Prot
    Q7Z6J4
    Related
    ENSP00000274963.8, ENST00000274963.13
    Conserved Domains (5) summary
    cd00160
    Location:104288
    RhoGEF; Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
    cd13236
    Location:538640
    PH2_FGD1-4; FYVE, RhoGEF and PH domain containing/faciogenital dysplasia proteins pleckstrin homology (PH) domain, C-terminus
    cd13386
    Location:320427
    PH1_FGD2; FYVE, RhoGEF and PH domain containing/faciogenital dysplasia protein 2, N-terminal Pleckstrin homology (PH) domain
    cd15741
    Location:453517
    FYVE_FGD1_2_4; FYVE domain found in FYVE, RhoGEF and PH domain-containing protein facio-genital dysplasia FGD1, FGD2, FGD4
    pfam00169
    Location:320417
    PH; PH domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p13 Primary Assembly

    Range
    37005655..37029072
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017010429.2XP_016865918.1  FYVE, RhoGEF and PH domain-containing protein 2 isoform X1

  2. XM_011514372.2XP_011512674.1  FYVE, RhoGEF and PH domain-containing protein 2 isoform X2

    Conserved Domains (2) summary
    cd00160
    Location:104288
    RhoGEF; Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
    cl17171
    Location:320343
    PH-like; Pleckstrin homology-like domain
  3. XM_011514373.2XP_011512675.1  FYVE, RhoGEF and PH domain-containing protein 2 isoform X3

    Conserved Domains (2) summary
    cd00160
    Location:104288
    RhoGEF; Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
    cl17171
    Location:320374
    PH-like; Pleckstrin homology-like domain

RNA

  1. XR_001743243.1 RNA Sequence

  2. XR_001743240.2 RNA Sequence

  3. XR_001743242.2 RNA Sequence

  4. XR_001743241.2 RNA Sequence

  5. XR_001743248.1 RNA Sequence

  6. XR_926106.1 RNA Sequence

  7. XR_001743244.2 RNA Sequence

  8. XR_001743245.2 RNA Sequence

  9. XR_001743246.2 RNA Sequence

  10. XR_001743247.2 RNA Sequence

  11. XR_001743249.2 RNA Sequence

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