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    FGD1 FYVE, RhoGEF and PH domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 2245, updated on 23-Nov-2023

    Summary

    Official Symbol
    FGD1provided by HGNC
    Official Full Name
    FYVE, RhoGEF and PH domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:3663
    See related
    Ensembl:ENSG00000102302 MIM:300546; AllianceGenome:HGNC:3663
    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
    AAS; FGDY; MRXS16; ZFYVE3
    Summary
    This gene encodes a protein that contains Dbl (DH) and pleckstrin (PH) homology domains and is similar to the Rho family of small GTP-binding proteins. The encoded protein specifically binds to the Rho family GTPase Cdc42Hs and can stimulate the GDP-GTP exchange of the isoprenylated form of Cdc42Hs. It also stimulates the mitogen activated protein kinase cascade leading to c-Jun kinase SAPK/JNK1 activation. Defects in this gene are the cause of the faciogenital dysplasia in Aarskog-Scott syndrome and a syndromatic form of X-linked cognitive disability. [provided by RefSeq, Jul 2017]
    Expression
    Ubiquitous expression in endometrium (RPKM 4.2), brain (RPKM 3.6) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See FGD1 in Genome Data Viewer
    Location:
    Xp11.22
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (54445454..54496234, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (53736310..53787092, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (54471887..54522667, complement)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene WNK lysine deficient protein kinase 3 Neighboring gene ribosomal protein L7a pseudogene 71 Neighboring gene MPRA-validated peak7382 silencer Neighboring gene RNA, U6 small nuclear 434, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:54415213-54415877 Neighboring gene MPRA-validated peak7383 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29670 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:54505803-54506356 Neighboring gene TSR2 ribosome maturation factor Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20864 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:54556053-54556573 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29672 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29673 Neighboring gene G protein nucleolar 3 like Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:54665616-54666141 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29675 Neighboring gene phosphoglycerate mutase family member 4 pseudogene 1

    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

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Aarskog syndrome
    MedGen: C0175701 OMIM: 305400 GeneReviews: Not available
    Compare labs

    Copy number response

    Description
    Copy number response
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2021-05-26)

    ClinGen Genome Curation PagePubMed
    Triplosensitivity

    No evidence available (Last evaluated 2021-05-26)

    ClinGen Genome Curation Page

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables guanyl-nucleotide exchange factor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables guanyl-nucleotide exchange factor activity TAS
    Traceable Author Statement
    more info
     
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables small GTPase binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in actin cytoskeleton organization IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in animal organ morphogenesis TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in cytoskeleton organization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in cytoskeleton organization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in filopodium assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in filopodium assembly IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of GTPase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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
     
    involved_in signal transduction TAS
    Traceable Author Statement
    more info
    PubMed 
    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 lamellipodium ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in ruffle ISS
    Inferred from Sequence or Structural Similarity
    more info
     

    General protein information

    Preferred Names
    FYVE, RhoGEF and PH domain-containing protein 1
    Names
    faciogenital dysplasia 1 protein
    rho/Rac GEF
    rho/Rac guanine nucleotide exchange factor FGD1
    zinc finger FYVE domain-containing protein 3

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_008054.1 RefSeqGene

      Range
      4933..55713
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_004463.3NP_004454.2  FYVE, RhoGEF and PH domain-containing protein 1

      See identical proteins and their annotated locations for NP_004454.2

      Status: REVIEWED

      Source sequence(s)
      Z85987
      Consensus CDS
      CCDS14359.1
      UniProtKB/Swiss-Prot
      P98174, Q5H999, Q8N4D9
      UniProtKB/TrEMBL
      A0A2X0SFE1
      Related
      ENSP00000364277.3, ENST00000375135.4
      Conserved Domains (5) summary
      cd00160
      Location:376559
      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:815920
      PH2_FGD1-4; FYVE, RhoGEF and PH domain containing/faciogenital dysplasia proteins pleckstrin homology (PH) domain, C-terminus
      cd01219
      Location:591698
      PH1_FGD1; FYVE, RhoGEF and PH domain containing/faciogenital dysplasia protein 1, N-terminal Pleckstrin homology (PH) domain
      cd15741
      Location:725789
      FYVE_FGD1_2_4; FYVE domain found in FYVE, RhoGEF and PH domain-containing protein facio-genital dysplasia FGD1, FGD2, FGD4
      pfam00169
      Location:591688
      PH; PH domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      54445454..54496234 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      53736310..53787092 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)