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    FGD5 FYVE, RhoGEF and PH domain containing 5 [ Homo sapiens (human) ]

    Gene ID: 152273, updated on 2-Nov-2024

    Summary

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    Official Symbol
    FGD5provided by HGNC
    Official Full Name
    FYVE, RhoGEF and PH domain containing 5provided by HGNC
    Primary source
    HGNC:HGNC:19117
    See related
    Ensembl:ENSG00000154783 MIM:614788; AllianceGenome:HGNC:19117
    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
    ZFYVE23
    Summary
    Predicted to enable guanyl-nucleotide exchange factor activity and small GTPase binding activity. Predicted to be involved in actin cytoskeleton organization; filopodium assembly; and regulation of cell shape. Located in plasma membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in spleen (RPKM 15.9), lung (RPKM 13.8) and 22 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See FGD5 in Genome Data Viewer
    Location:
    3p25.1
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (14810688..14934571)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (14813154..14937021)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (14860469..14976078)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124906215 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:14712491-14713690 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19517 Neighboring gene coiled-coil domain containing 174 Neighboring gene MPRA-validated peak4545 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19518 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19519 Neighboring gene chromosome 3 open reading frame 20 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19520 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19521 Neighboring gene meiotic recombination hotspot H Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:14838036-14838969 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:14845672-14846414 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:14852491-14852991 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:14855464-14855666 Neighboring gene long intergenic non-protein coding RNA 2011 Neighboring gene Sharpr-MPRA regulatory region 8692 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:14905091-14905672 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:14920327-14920828 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:14941355-14942238 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:14942239-14943121 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:14955453-14956275 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:14956276-14957097 Neighboring gene uncharacterized LOC105376963 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:14962633-14963132 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:14963648-14964847 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:14965692-14965871 Neighboring gene Sharpr-MPRA regulatory region 15385 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:14988241-14988930 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14097 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:14989619-14990306 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:14990307-14990994 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19523 Neighboring gene FGD5 antisense RNA 1 Neighboring gene nuclear receptor subfamily 2 group C member 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:15066535-15067034 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19524 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19525 Neighboring gene mitochondrial ribosomal protein S25

    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. Common Variants on FGD5 Increase Hazard of Mortality or Rehospitalization in Patients With Heart Failure From the ASCEND-HF Trial. Gui H, et al. Circ Heart Fail, 2023 Sep. PMID 37725680, Free PMC Article
    2. Characterization of FGD5 Expression in Primary Breast Cancers and Lymph Node Metastases. Valla M, et al. J Histochem Cytochem, 2018 Nov. PMID 30052477, Free PMC Article
    3. Structure and function of the Fgd family of divergent FYVE domain proteins (1). Eitzen G, et al. Biochem Cell Biol, 2019 Jun. PMID 30308128
    4. FGD5 regulates endothelial cell PI3 kinase-β to promote neo-angiogenesis. Azad AK, et al. FASEB J, 2022 Jan. PMID 34882832
    5. FGD5 amplification in breast cancer patients is associated with tumour proliferation and a poorer prognosis. Valla M, et al. Breast Cancer Res Treat, 2017 Apr. PMID 28124285

    See all (34) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Common Variants on FGD5 Increase Hazard of Mortality or Rehospitalization in Patients With Heart Failure From the ASCEND-HF Trial.
      Title: Common Variants on FGD5 Increase Hazard of Mortality or Rehospitalization in Patients With Heart Failure From the ASCEND-HF Trial.
    2. FGD5 regulates endothelial cell PI3 kinase-beta to promote neo-angiogenesis.
      Title: FGD5 regulates endothelial cell PI3 kinase-β to promote neo-angiogenesis.
    3. Faciogenital dysplasia 5 confers the cancer stem cell-like traits of gastric cancer cells through enhancing Sox2 protein stability.
      Title: Faciogenital dysplasia 5 confers the cancer stem cell-like traits of gastric cancer cells through enhancing Sox2 protein stability.
    4. Long non-coding RNA FGD5-AS1 enhances osteosarcoma cell proliferation and migration by targeting miR-506-3p/RAB3D axis.
      Title: Long non-coding RNA FGD5-AS1 enhances osteosarcoma cell proliferation and migration by targeting miR-506-3p/RAB3D axis.
    5. lncRNA FGD5AS1 promotes breast cancer progression by regulating the hsamiR1955p/NUAK2 axis.
      Title: lncRNA FGD5‑AS1 promotes breast cancer progression by regulating the hsa‑miR‑195‑5p/NUAK2 axis.
    6. FGD5 facilitates tumor growth by regulating EGFR ubiquitination in gastric cancer.
      Title: FGD5 facilitates tumor growth by regulating EGFR ubiquitination in gastric cancer.
    7. A high level of lncFGD5-AS1 inhibits epithelial-to-Mesenchymal transition by regulating the miR-196a-5p/SMAD6/BMP axis in gastric Cancer.
      Title: A high level of lncFGD5-AS1 inhibits epithelial-to-Mesenchymal transition by regulating the miR-196a-5p/SMAD6/BMP axis in gastric Cancer.
    8. Faciogenital Dysplasia 5 supports cancer stem cell traits in basal-like breast cancer by enhancing EGFR stability.
      Title: Faciogenital Dysplasia 5 supports cancer stem cell traits in basal-like breast cancer by enhancing EGFR stability.
    9. *FGD5 tyrosine phosphorylation is essential for endothelial junction stabilization.
      Title: VE-PTP inhibition stabilizes endothelial junctions by activating FGD5.
    10. Human FYVE domain containing proteins, those within the faciogenital dysplasia (Fgd) subfamily are particularly divergent and couple with GTPases to exert unique cellular functions.
      Title: Structure and function of the Fgd family of divergent FYVE domain proteins (1).
    Submit: New GeneRIF Correction See all GeneRIFs (18)

    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

    Variation

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    See Variation Viewer (GRCh37.p13)

    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 IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables guanyl-nucleotide exchange factor activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables guanyl-nucleotide exchange factor activity TAS
    Traceable Author Statement
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables small GTPase binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in actin cytoskeleton organization ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in cytoskeleton organization ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in filopodium assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of GTPase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of cell shape ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of small GTPase mediated signal transduction TAS
    Traceable Author Statement
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi apparatus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cytoskeleton IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in early endosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in endoplasmic reticulum IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in lamellipodium ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		  
    located_in ruffle ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in ruffle membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    FYVE, RhoGEF and PH domain-containing protein 5
    Names
    zinc finger FYVE domain-containing protein 23

    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_001320276.2 → NP_001307205.1  FYVE, RhoGEF and PH domain-containing protein 5 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an in-frame exon in the 3' coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AC090937, AW589887, BC144300, DB293373
      UniProtKB/TrEMBL
      B7ZM68
      Related
      ENSP00000445949.1, ENST00000543601.5
      Conserved Domains (5) summary
      cd15792
      Location:1101 → 1223
      PH1_FGD5; FYVE, RhoGEF and PH domain containing/faciogenital dysplasia protein 5, N-terminal Pleckstrin Homology (PH) domain
      cd15742
      Location:1237 → 1303
      FYVE_FGD5; FYVE-like domain found in FYVE, RhoGEF and PH domain-containing protein 5 (FGD5) and similar proteins
      pfam00169
      Location:1116 → 1207
      PH; PH domain
      pfam00621
      Location:896 → 1083
      RhoGEF; RhoGEF domain
      cl17171
      Location:1356 → 1413
      PH-like; Pleckstrin homology-like domain

    2. NM_152536.4 → NP_689749.3  FYVE, RhoGEF and PH domain-containing protein 5 isoform 1

      See identical proteins and their annotated locations for NP_689749.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC087591, AC090937
      Consensus CDS
      CCDS46767.1
      UniProtKB/Swiss-Prot
      B3KVQ3, Q6MZY1, Q6ZNL6, Q7Z303, Q8IYP3, Q8N861, Q8N8G4
      UniProtKB/TrEMBL
      A0A2X0SFF2, A3KMQ0
      Related
      ENSP00000285046.5, ENST00000285046.10
      Conserved Domains (5) summary
      PHA03169
      Location:132 → 323
      PHA03169; hypothetical protein; Provisional
      cd13237
      Location:1366 → 1456
      PH2_FGD5_FGD6; FYVE, RhoGEF and PH domain containing/faciogenital dysplasia proteins 5 and 6 pleckstrin homology (PH) domain, C-terminus
      cd15792
      Location:1101 → 1223
      PH1_FGD5; FYVE, RhoGEF and PH domain containing/faciogenital dysplasia protein 5, N-terminal Pleckstrin Homology (PH) domain
      cd15742
      Location:1237 → 1303
      FYVE_FGD5; FYVE-like domain found in FYVE, RhoGEF and PH domain-containing protein 5 (FGD5) and similar proteins
      pfam00621
      Location:896 → 1082
      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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      14810688..14934571
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011533422.2 → XP_011531724.2  FYVE, RhoGEF and PH domain-containing protein 5 isoform X1

    2. XM_011533423.2 → XP_011531725.2  FYVE, RhoGEF and PH domain-containing protein 5 isoform X3

    3. XM_047447514.1 → XP_047303470.1  FYVE, RhoGEF and PH domain-containing protein 5 isoform X2

    4. XM_047447515.1 → XP_047303471.1  FYVE, RhoGEF and PH domain-containing protein 5 isoform X4

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      14813154..14937021
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054345395.1 → XP_054201370.1  FYVE, RhoGEF and PH domain-containing protein 5 isoform X1

    2. XM_054345396.1 → XP_054201371.1  FYVE, RhoGEF and PH domain-containing protein 5 isoform X2

    3. XM_054345397.1 → XP_054201372.1  FYVE, RhoGEF and PH domain-containing protein 5 isoform X3

    4. XM_054345398.1 → XP_054201373.1  FYVE, RhoGEF and PH domain-containing protein 5 isoform X4

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6ZNL6.3 GenPept UniProtKB/Swiss-Prot:Q6ZNL6

    Gene LinkOut

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

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