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

Gene ID: 2245, updated on 2-Nov-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
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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: 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. 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
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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

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