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

    Gene ID: 2245, updated on 10-Dec-2024

    Summary

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    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
    mouse all
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    Genomic context

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    See FGD1 in Genome Data Viewer
    Location:
    Xp11.22
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (54445454..54496234, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (53736310..53787092, complement)
    RS_2024_09 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

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Novel truncating variants in FGD1 detected in two Danish families with Aarskog-Scott syndrome and myopathic features. Bayat A, et al. Am J Med Genet A, 2022 Jul. PMID 35388608, Free PMC Article
    2. First case of deletion of the faciogenital dysplasia 1 (FGD1) gene in a patient with Aarskog-Scott syndrome. Bedoyan JK, et al. Eur J Med Genet, 2009 Jul-Aug. PMID 19110080
    3. Familial syndrome resembling Aarskog syndrome. Xu M, et al. Am J Med Genet A, 2010 Aug. PMID 20607856
    4. Unilateral focal polymicrogyria in a patient with classical Aarskog-Scott syndrome due to a novel missense mutation in an evolutionary conserved RhoGEF domain of the faciogenital dysplasia gene FGD1. Bottani A, et al. Am J Med Genet A, 2007 Oct 1. PMID 17847065
    5. Unusually severe expression of craniofacial features in Aarskog-Scott syndrome due to a novel truncating mutation of the FGD1 gene. Orrico A, et al. Am J Med Genet A, 2007 Jan 1. PMID 17152066

    See all (64) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Novel truncating variants in FGD1 detected in two Danish families with Aarskog-Scott syndrome and myopathic features.
      Title: Novel truncating variants in FGD1 detected in two Danish families with Aarskog-Scott syndrome and myopathic features.
    2. Silencing FYVE, RhoGEF, and PH domain containing 1 (FGD1) suppresses melanoma progression by inhibiting PI3K/AKT signaling pathway.
      Title: Silencing FYVE, RhoGEF, and PH domain containing 1 (FGD1) suppresses melanoma progression by inhibiting PI3K/AKT signaling pathway.
    3. A novel truncating variant in the FGD1 gene associated with Aarskog-Scott syndrome in a family previously diagnosed with Tel Hashomer camptodactyly.
      Title: A novel truncating variant in the FGD1 gene associated with Aarskog-Scott syndrome in a family previously diagnosed with Tel Hashomer camptodactyly.
    4. Xp11.22 duplications in four unrelated Chinese families: delineating the genotype-phenotype relationship for HSD17B10 and FGD1.
      Title: Xp11.22 duplications in four unrelated Chinese families: delineating the genotype-phenotype relationship for HSD17B10 and FGD1.
    5. FGD1 promotes tumor progression and regulates tumor immune response in osteosarcoma via inhibiting PTEN activity.
      Title: FGD1 promotes tumor progression and regulates tumor immune response in osteosarcoma via inhibiting PTEN activity.
    6. Intersection of TKS5 and FGD1/CDC42 signaling cascades directs the formation of invadopodia.
      Title: Intersection of TKS5 and FGD1/CDC42 signaling cascades directs the formation of invadopodia.
    7. Sequencing analyses in numerous types of cancer have found missense mutations in the FGD1 gene in metastatic tumors.
      Title: Minireview: Role of genetic changes of faciogenital dysplasia protein 1 in human disease.
    8. A novel variant in FGD1 (a novel hemizygous mutation in FGD1 c.53del (p.Pro18Argfs*106) for which the mother is heterozygous) was found in an Emirati family with two brothers suffering from Aarskog-Scott syndrome. The variant is predicted to be a null mutation, and this is the first report of its kind from the United Arab Emirates.
      Title: A novel, putatively null, FGD1 variant leading to Aarskog-Scott syndrome in a family from UAE.
    9. Splice site mutation of FGD1 gene is associated with Aarskog-Scott syndrome patient with a large anterior fontanel.
      Title: A novel splice site mutation of FGD1 gene in an Aarskog-Scott syndrome patient with a large anterior fontanel.
    10. Results identify a novel mutation of FDG1 in a family with Aarskog syndrome and underscore the phenotypical variability of this condition.
      Title: Aarskog-Scott syndrome: a novel mutation in the FGD1 gene associated with severe craniofacial dysplasia.
    Submit: New GeneRIF Correction See all GeneRIFs (29)

    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

    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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    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 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

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    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)

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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.

    Genomic

    1. NG_008054.1 RefSeqGene

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

    mRNA and Protein(s)

    1. NM_004463.3 → NP_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:376 → 559
      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:815 → 920
      PH2_FGD1-4; FYVE, RhoGEF and PH domain containing/faciogenital dysplasia proteins pleckstrin homology (PH) domain, C-terminus
      cd01219
      Location:591 → 698
      PH1_FGD1; FYVE, RhoGEF and PH domain containing/faciogenital dysplasia protein 1, N-terminal Pleckstrin homology (PH) domain
      cd15741
      Location:725 → 789
      FYVE_FGD1_2_4; FYVE domain found in FYVE, RhoGEF and PH domain-containing protein facio-genital dysplasia FGD1, FGD2, FGD4
      pfam00169
      Location:591 → 688
      PH; PH 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_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)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P98174.2 GenPept UniProtKB/Swiss-Prot:P98174

    Gene LinkOut

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

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