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FGD1 Gene(Protein Coding)

FYVE, RhoGEF And PH Domain Containing 1

GCID:
GC0XM054488
GIFtS:
50
Genes Participants
UDN Logo

Aliases for FGD1 Gene

Aliases for FGD1 Gene

  • FYVE, RhoGEF And PH Domain Containing 1 2 3 5
  • Rho/Rac Guanine Nucleotide Exchange Factor FGD1 3 4
  • Zinc Finger FYVE Domain-Containing Protein 3 3 4
  • Faciogenital Dysplasia 1 Protein 3 4
  • Rho/Rac GEF 3 4
  • ZFYVE3 3 4
  • FGDY 3 4
  • Faciogenital Dysplasia (Aarskog-Scott Syndrome) 2
  • FYVE, RhoGEF And PH Domain-Containing Protein 1 3
  • MRXS16 3
  • AAS 3

External Ids for FGD1 Gene

Previous HGNC Symbols for FGD1 Gene

  • FGDY

Previous GeneCards Identifiers for FGD1 Gene

  • GC0XM051323
  • GC0XM052410
  • GC0XM053077
  • GC0XM053438
  • GC0XM054354
  • GC0XM051522

Summaries for FGD1 Gene

Entrez Gene Summary for FGD1 Gene

  • 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]

GeneCards Summary for FGD1 Gene

FGD1 (FYVE, RhoGEF And PH Domain Containing 1) is a Protein Coding gene. Diseases associated with FGD1 include Aarskog-Scott Syndrome and Scott Syndrome. Among its related pathways are p75 NTR receptor-mediated signalling and Actin Nucleation by ARP-WASP Complex. Gene Ontology (GO) annotations related to this gene include guanyl-nucleotide exchange factor activity and small GTPase binding. An important paralog of this gene is FGD4.

UniProtKB/Swiss-Prot for FGD1 Gene

  • Activates CDC42, a member of the Ras-like family of Rho- and Rac proteins, by exchanging bound GDP for free GTP. Plays a role in regulating the actin cytoskeleton and cell shape.

Gene Wiki entry for FGD1 Gene

Additional gene information for FGD1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for FGD1 Gene

Genomics for FGD1 Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for FGD1 Gene

Promoters and enhancers for FGD1 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH0XI054494 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE 550.8 +0.6 563 3.1 ZSCAN5A BCOR ZNF76 ZMYM3 ZNF384 ZNF335 ZFHX2 EGR1 POLR2A ZBTB48 FGD1 PIR39642 GC0XM054327
GH0XI053681 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 11.1 +811.8 811767 6 HDGF PKNOX1 CLOCK SMAD1 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 HUWE1 FAM156B PHF8 KANTR ACTG1P10 ENSG00000233250 TSPYL2 KDM5C FGD1 HSD17B10
GH0XI054042 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 11.1 +451.8 451817 3.9 PKNOX1 CLOCK FOXA2 ARNT NEUROD1 SIN3A FEZF1 DMAP1 ZNF2 YY1 PHF8 KDM5C ACTG1P10 SMC1A KANTR ENSG00000233250 TSPYL2 APEX2 GPR173 MAGED2
GH0XI054539 Enhancer 0.3 ENCODE 12.7 -44.1 -44100 1 CTCF FGD1 GNL3L GC0XM054327
GH0XI054474 Enhancer 0.2 ENCODE 14.6 +21.5 21500 0.9 FGD1 TSR2 GNL3L PIR39642 GC0XM054327
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around FGD1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the FGD1 gene promoter:

Genomic Locations for FGD1 Gene

Genomic Locations for FGD1 Gene
chrX:54,445,454-54,496,166
(GRCh38/hg38)
Size:
50,713 bases
Orientation:
Minus strand
chrX:54,471,887-54,522,599
(GRCh37/hg19)

Genomic View for FGD1 Gene

Genes around FGD1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
FGD1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for FGD1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for FGD1 Gene

Proteins for FGD1 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for FGD1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P98174-FGD1_HUMAN
    Recommended name:
    FYVE, RhoGEF and PH domain-containing protein 1
    Protein Accession:
    P98174
    Secondary Accessions:
    • Q5H999
    • Q8N4D9

    Protein attributes for FGD1 Gene

    Size:
    961 amino acids
    Molecular mass:
    106561 Da
    Quaternary structure:
    • Interacts with DBNL/ABP1 and CTTN. May interact with CCPG1 (By similarity). Binds CDC42.

neXtProt entry for FGD1 Gene

Protein Expression for FGD1 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for FGD1 Gene

No Post-translational modifications

Other Protein References for FGD1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for FGD1 Gene

Domains & Families for FGD1 Gene

Gene Families for FGD1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for FGD1 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for FGD1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P98174

UniProtKB/Swiss-Prot:

FGD1_HUMAN :
  • The DH domain is involved in interaction with CCPG1.
Domain:
  • The DH domain is involved in interaction with CCPG1.
genes like me logo Genes that share domains with FGD1: view

Function for FGD1 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for FGD1 Gene

GENATLAS Biochemistry:
Rho/Rac,CDC42Hs specific (guanine nucleotide exchange factor) 1,involved in signal transduction and mammalian morphogenesis
UniProtKB/Swiss-Prot Function:
Activates CDC42, a member of the Ras-like family of Rho- and Rac proteins, by exchanging bound GDP for free GTP. Plays a role in regulating the actin cytoskeleton and cell shape.

Gene Ontology (GO) - Molecular Function for FGD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005085 guanyl-nucleotide exchange factor activity TAS --
GO:0005089 Rho guanyl-nucleotide exchange factor activity TAS --
GO:0031267 small GTPase binding IDA 8969170
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with FGD1: view
genes like me logo Genes that share phenotypes with FGD1: view

Human Phenotype Ontology for FGD1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Animal Models , Transcription Factor Targets and HOMER Transcription for FGD1 Gene

Localization for FGD1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for FGD1 Gene

Cytoplasm. Cell projection, lamellipodium. Cell projection, ruffle. Cytoplasm, cytoskeleton. Note=Associated with membrane ruffles and lamellipodia. {ECO:0000250}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for FGD1 gene
Compartment Confidence
cytosol 5
golgi apparatus 5
cytoskeleton 4
plasma membrane 3
nucleus 3

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for FGD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001726 ruffle ISS --
GO:0005737 cytoplasm ISS --
GO:0005794 Golgi apparatus IEA,ISS --
GO:0005829 cytosol TAS --
GO:0005856 cytoskeleton IEA --
genes like me logo Genes that share ontologies with FGD1: view

Pathways & Interactions for FGD1 Gene

genes like me logo Genes that share pathways with FGD1: view

Pathways by source for FGD1 Gene

1 KEGG pathway for FGD1 Gene
1 GeneGo (Thomson Reuters) pathway for FGD1 Gene
1 Qiagen pathway for FGD1 Gene

Gene Ontology (GO) - Biological Process for FGD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007010 cytoskeleton organization ISS,IEA --
GO:0007165 signal transduction TAS 8969170
GO:0007186 G-protein coupled receptor signaling pathway TAS --
GO:0007275 multicellular organism development TAS 8969170
GO:0008360 regulation of cell shape ISS,IEA --
genes like me logo Genes that share ontologies with FGD1: view

No data available for SIGNOR curated interactions for FGD1 Gene

Drugs & Compounds for FGD1 Gene

Products:

  1. Drug

(1) Drugs for FGD1 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Guanosine triphosphate Experimental Pharma 0
genes like me logo Genes that share compounds with FGD1: view

Transcripts for FGD1 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for FGD1 Gene

(1) REFSEQ mRNAs :
(4) Additional mRNA sequences :
(75) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for FGD1 Gene

FYVE, RhoGEF and PH domain containing 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for FGD1 Gene

No ASD Table

Relevant External Links for FGD1 Gene

GeneLoc Exon Structure for
FGD1
ECgene alternative splicing isoforms for
FGD1

Expression for FGD1 Gene

Products:

  1. Primer

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for FGD1 Gene

mRNA expression in normal human tissues for FGD1 Gene
mRNA expression by GTEx for FGD1 GenemRNA expression by BioGPS for FGD1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for FGD1 Gene

This gene is overexpressed in Fetal Brain (56.9) and Urine (6.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for FGD1 Gene



Protein tissue co-expression partners for FGD1 Gene

NURSA nuclear receptor signaling pathways regulating expression of FGD1 Gene:

FGD1

SOURCE GeneReport for Unigene cluster for FGD1 Gene:

Hs.709201

mRNA Expression by UniProt/SwissProt for FGD1 Gene:

P98174-FGD1_HUMAN
Tissue specificity: Expressed in fetal heart, brain, lung, kidney and placenta. Less expressed in liver; adult heart, brain, lung, pancreas and skeletal muscle.

Evidence on tissue expression from TISSUES for FGD1 Gene

  • Nervous system(4.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for FGD1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • immune
  • integumentary
  • lymphatic
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Organs:
Head and neck:
  • brain
  • cheek
  • chin
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • mouth
  • neck
  • nose
  • outer ear
  • salivary gland
  • scalp
  • skull
  • tooth
Thorax:
  • breast
  • chest wall
  • clavicle
  • esophagus
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
Abdomen:
  • abdominal wall
  • intestine
  • kidney
  • large intestine
  • liver
  • spleen
Pelvis:
  • anus
  • fallopian tube
  • ovary
  • pelvis
  • penis
  • prostate
  • rectum
  • testicle
  • uterus
  • vagina
  • vas deferens
  • vulva
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • nail
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • blood
  • blood vessel
  • coagulation system
  • hair
  • lymph node
  • lymph vessel
  • peripheral nervous system
  • red blood cell
  • skin
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with FGD1: view

Primer Products

No data available for mRNA differential expression in normal tissues for FGD1 Gene

Orthologs for FGD1 Gene

This gene was present in the common ancestor of animals.

Orthologs for FGD1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia FGD1 34 33
  • 99.03 (n)
 OneToOne
dog
(Canis familiaris)
 Mammalia FGD1 34 33
  • 93.47 (n)
 OneToOne
cow
(Bos Taurus)
 Mammalia FGD1 34 33
  • 93.4 (n)
 OneToOne
rat
(Rattus norvegicus)
 Mammalia Fgd1 33
  • 92.27 (n)
mouse
(Mus musculus)
 Mammalia Fgd1 16 34 33
  • 91.56 (n)
oppossum
(Monodelphis domestica)
 Mammalia FGD1 34
  • 75 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia FGD1 34
  • 56 (a)
 OneToOne
lizard
(Anolis carolinensis)
 Reptilia FGD1 34
  • 68 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia fgd1 33
  • 65.75 (n)
zebrafish
(Danio rerio)
 Actinopterygii fgd1 34 33
  • 70.19 (n)
 OneToOne
fruit fly
(Drosophila melanogaster)
 Insecta RhoGEF4 34
  • 20 (a)
 ManyToMany
worm
(Caenorhabditis elegans)
 Secernentea exc-5 35 34
  • 28 (a)
sea squirt
(Ciona savignyi)
 Ascidiacea CSA.6211 34
  • 38 (a)
 OneToMany
Species where no ortholog for FGD1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for FGD1 Gene

ENSEMBL:
Gene Tree for FGD1 (if available)
TreeFam:
Gene Tree for FGD1 (if available)

Paralogs for FGD1 Gene

Paralogs for FGD1 Gene

(4) SIMAP similar genes for FGD1 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with FGD1: view

Variants for FGD1 Gene

Sequence variations from dbSNP and Humsavar for FGD1 Gene

SNP ID Clin Chr 0X pos Variation AA Info Type
rs137853264 pathogenic, Aarskog syndrome, Aarskog-Scott syndrome (AAS) [MIM:305400] 54,465,522(-) C/T coding_sequence_variant, missense_variant
rs137853265 pathogenic, Aarskog syndrome 54,467,901(-) C/T coding_sequence_variant, missense_variant
rs137853266 pathogenic, Aarskog syndrome 54,467,796(-) C/A coding_sequence_variant, missense_variant
rs137853267 pathogenic, Aarskog syndrome 54,465,797(-) T/C coding_sequence_variant, missense_variant
rs138723423 benign, likely-benign, not specified, not provided 54,470,441(-) C/T coding_sequence_variant, missense_variant

Structural Variations from Database of Genomic Variants (DGV) for FGD1 Gene

Variant ID Type Subtype PubMed ID
esv2740175 CNV deletion 23290073
nsv435891 CNV deletion 17901297

Variation tolerance for FGD1 Gene

Residual Variation Intolerance Score: 7.99% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.41; 42.58% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for FGD1 Gene

Human Gene Mutation Database (HGMD)
FGD1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
FGD1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for FGD1 Gene

Disorders for FGD1 Gene

MalaCards: The human disease database

(7) MalaCards diseases for FGD1 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
aarskog-scott syndrome
  • aas
scott syndrome
  • scts
crane-heise syndrome
  • cleft lip/palate, agenesis of clavicles and cervical vertebrae, and talipes equinovarus
unilateral focal polymicrogyria
global developmental delay, absent or hypoplastic corpus callosum, and dysmorphic facies
  • gdaccf
- elite association - COSMIC cancer census association via MalaCards
Search FGD1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

FGD1_HUMAN
  • Aarskog-Scott syndrome (AAS) [MIM:305400]: A rare multisystemic disorder characterized by disproportionately short stature, and by facial, skeletal and urogenital anomalies. Some patients manifest mental retardation, attention deficit disorder and hyperactivity. {ECO:0000269 PubMed:10930571, ECO:0000269 PubMed:11093277, ECO:0000269 PubMed:14560308}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Note=Defects in FGD1 are found in a patient with non-syndromal X-linked mental retardation. {ECO:0000269 PubMed:11940089}.

Genatlas disease for FGD1 Gene

Aarskog syndrome,faciogenital dysplasia and brachydactyly

Additional Disease Information for FGD1

Genetic Association Database
(GAD)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with FGD1: view

Publications for FGD1 Gene

  1. Phenotypic and molecular characterisation of the Aarskog-Scott syndrome: a survey of the clinical variability in light of FGD1 mutation analysis in 46 patients. (PMID: 14560308) Orrico A … Sorrentino V (European journal of human genetics : EJHG 2004) 3 4 22 44 58
  2. Non-syndromic X-linked mental retardation associated with a missense mutation (P312L) in the FGD1 gene. (PMID: 11940089) Lebel RR … Schwartz CE (Clinical genetics 2002) 3 4 22 44 58
  3. Two novel mutations confirm FGD1 is responsible for the Aarskog syndrome. (PMID: 11093277) Schwartz CE … Neri G (European journal of human genetics : EJHG 2000) 3 4 22 58
  4. A mutation in the pleckstrin homology (PH) domain of the FGD1 gene in an Italian family with faciogenital dysplasia (Aarskog-Scott syndrome). (PMID: 10930571) Orrico A … Sorrentino V (FEBS letters 2000) 3 4 22 58
  5. Isolation and characterization of the faciogenital dysplasia (Aarskog-Scott syndrome) gene: a putative Rho/Rac guanine nucleotide exchange factor. (PMID: 7954831) Pasteris NG … Gorski JL (Cell 1994) 3 4 22 58

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