FGD3 Gene (Protein Coding)

FYVE, RhoGEF And PH Domain Containing 3

GC09P092947
GIFtS:
40
See more...

Aliases for FGD3 Gene

Aliases for FGD3 Gene

  • FYVE, RhoGEF And PH Domain Containing 3 2 3 5
  • ZFYVE5 2 3 4
  • FYVE, RhoGEF And PH Domain-Containing Protein 3 3 4
  • Zinc Finger FYVE Domain-Containing Protein 5 3 4
  • FGD1 Family, Member 3 2 3
  • Faciogenital Dysplasia 3 3
  • FLJ00004 2
  • FGD3 5

External Ids for FGD3 Gene

Previous GeneCards Identifiers for FGD3 Gene

  • GC09P086553
  • GC09P087437
  • GC09P089008
  • GC09P091051
  • GC09P091078
  • GC09P092789
  • GC09P092816
  • GC09P094749
  • GC09P095709
  • GC09P065386

Summaries for FGD3 Gene

GeneCards Summary for FGD3 Gene

FGD3 (FYVE, RhoGEF And PH Domain Containing 3) is a Protein Coding gene. Diseases associated with FGD3 include Aarskog-Scott Syndrome and Charcot-Marie-Tooth Disease, Type 4H. Among its related pathways are Signaling by GPCR and p75 NTR receptor-mediated signalling. 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 FGD1.

UniProtKB/Swiss-Prot Summary for FGD3 Gene

  • Promotes the formation of filopodia. May activate 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 (By similarity).

Gene Wiki entry for FGD3 Gene

Additional gene information for FGD3 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for FGD3 Gene

Genomics for FGD3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for FGD3 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
GH09J092960 Promoter/Enhancer 1.9 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 269.5 +18.7 18652 11.3 SP1 CEBPA POLR2A ZIC2 SIN3A VEZF1 IRF4 TRIM22 SAP130 GABPA FGD3 SUSD3 CENPP SPTLC1 NINJ1 IPPK CARD19 FAM120AOS FAM120A HSALNG0072805
GH09J092946 Promoter/Enhancer 1.6 EPDnew Ensembl ENCODE dbSUPER 263.2 +0.2 178 1.8 NONO ZIC2 ZNF610 SIN3A SP2 ESRRA ZNF571 TARDBP FOXA1 MAZ FGD3 piR-54987-150 PHF2 NOL8 MTND4P15 IARS1 ZNF484 LINC00475 SUSD3 HSALNG0072805
GH09J092972 Promoter/Enhancer 1.1 EPDnew ENCODE dbSUPER 263.1 +27.0 27033 4 ZNF217 ZIC2 TCF7L2 DPF2 SP1 IKZF1 SPI1 IKZF2 EP300 MTA2 FGD3 HSALNG0072805 SUSD3
GH09J092948 Enhancer 0.3 dbSUPER 263.8 +2.0 1966 1.3 HMBOX1 FGD3 SUSD3 HSALNG0072805
GH09J093056 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 18.6 +114.0 114011 9.5 TBP BCL11A SP1 CEBPA NR2C1 MNT IKZF1 SMAD5 POLR2A BHLHE40 SUSD3 NOL8 MTND4P15 FGD3 CARD19 ENSG00000223446 MTCO3P29 IARS1 FAM120A FAM120AOS
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around FGD3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for FGD3

Top Transcription factor binding sites by QIAGEN in the FGD3 gene promoter:
  • c-Myb
  • FOXD1
  • FOXO3
  • FOXO3a
  • FOXO3b
  • PPAR-gamma1
  • PPAR-gamma2
  • Sox5
  • SRY

Genomic Locations for FGD3 Gene

Latest Assembly
chr9:92,947,523-93,036,236
(GRCh38/hg38)
Size:
88,714 bases
Orientation:
Plus strand

Previous Assembly
chr9:95,709,805-95,798,515
(GRCh37/hg19 by Entrez Gene)
Size:
88,711 bases
Orientation:
Plus strand

chr9:95,709,733-95,798,518
(GRCh37/hg19 by Ensembl)
Size:
88,786 bases
Orientation:
Plus strand

Genomic View for FGD3 Gene

Genes around FGD3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
FGD3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for FGD3 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for FGD3 Gene

Proteins for FGD3 Gene

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  3. Assay products for research

  • Protein details for FGD3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5JSP0-FGD3_HUMAN
    Recommended name:
    FYVE, RhoGEF and PH domain-containing protein 3
    Protein Accession:
    Q5JSP0
    Secondary Accessions:
    • F8W7P2
    • Q4VX84
    • Q7Z7D9
    • Q8N5G1

    Protein attributes for FGD3 Gene

    Size:
    725 amino acids
    Molecular mass:
    79401 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for FGD3 Gene

    Alternative splice isoforms for FGD3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for FGD3 Gene

Protein Expression for FGD3 Gene

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

Post-translational modifications for FGD3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for FGD3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for FGD3 Gene

Domains & Families for FGD3 Gene

Gene Families for FGD3 Gene

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

Protein Domains for FGD3 Gene

InterPro:
Blocks:
  • DH domain
  • Zn-finger, FYVE type
ProtoNet:

Suggested Antigen Peptide Sequences for FGD3 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ58637, highly similar to FYVE, RhoGEF and PH domain-containing protein3 (B4DXH4_HUMAN)
  • Zinc finger FYVE domain-containing protein 5 (FGD3_HUMAN)
  • FLJ00004 protein (Q9NXY1_HUMAN)
genes like me logo Genes that share domains with FGD3: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for FGD3 Gene

Function for FGD3 Gene

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  1. Animal Models for research
  2. CRISPR products for research
  3. miRNA products for research
  4. Inhibitory RNAs for research
  5. Clone products for research
  6. Cell Lines for research

Molecular function for FGD3 Gene

UniProtKB/Swiss-Prot Function:
Promotes the formation of filopodia. May activate 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 (By similarity).

Phenotypes From GWAS Catalog for FGD3 Gene

Gene Ontology (GO) - Molecular Function for FGD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005085 guanyl-nucleotide exchange factor activity IBA,ISS --
GO:0031267 small GTPase binding ISS --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with FGD3: view
genes like me logo Genes that share phenotypes with FGD3: view

Animal Models for research

miRNA for FGD3 Gene

miRTarBase miRNAs that target FGD3

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for FGD3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for FGD3 Gene

Localization for FGD3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for FGD3 Gene

Cytoplasm. Cytoplasm, cytoskeleton.

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 FGD3 gene
Compartment Confidence
cytosol 5
cytoskeleton 4
golgi apparatus 4
nucleus 2
plasma membrane 1
extracellular 1

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for FGD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001726 ruffle ISS --
GO:0005737 cytoplasm IBA,ISS --
GO:0005794 Golgi apparatus ISS --
GO:0005829 cytosol TAS --
GO:0005856 cytoskeleton IEA --
genes like me logo Genes that share ontologies with FGD3: view

Pathways & Interactions for FGD3 Gene

genes like me logo Genes that share pathways with FGD3: view

Pathways by source for FGD3 Gene

1 KEGG pathway for FGD3 Gene
1 Qiagen pathway for FGD3 Gene
  • CDC42 Pathway

SIGNOR curated interactions for FGD3 Gene

Activates:

Gene Ontology (GO) - Biological Process for FGD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007010 cytoskeleton organization ISS --
GO:0007186 G protein-coupled receptor signaling pathway TAS --
GO:0008360 regulation of cell shape ISS --
GO:0030036 actin cytoskeleton organization ISS --
GO:0043065 positive regulation of apoptotic process TAS --
genes like me logo Genes that share ontologies with FGD3: view

Drugs & Compounds for FGD3 Gene

Products:

  1. Drug products for research

(1) Drugs for FGD3 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 FGD3: view

Transcripts for FGD3 Gene

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  2. miRNA products for research
  3. Inhibitory RNAs for research
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mRNA/cDNA for FGD3 Gene

5 REFSEQ mRNAs :
12 NCBI additional mRNA sequence :
8 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for FGD3

Alternative Splicing Database (ASD) splice patterns (SP) for FGD3 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14a · 14b ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^
SP1: - -
SP2: - - - -
SP3:
SP4: -
SP5: - - -
SP6:

ExUns: 22a · 22b
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:

Relevant External Links for FGD3 Gene

GeneLoc Exon Structure for
FGD3

Expression for FGD3 Gene

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  1. Primer products for research
  2. Gene Expression Assays for research

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for FGD3 Gene

mRNA expression in normal human tissues for FGD3 Gene
mRNA expression by GTEx for FGD3 GenemRNA expression by BioGPS for FGD3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

  • Thymus (Hematopoietic System)

mRNA differential expression in normal tissues according to GTEx for FGD3 Gene

This gene is overexpressed in Whole Blood (x34.6) and Spleen (x4.2).

Protein differential expression in normal tissues from HIPED for FGD3 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (17.4), Lymph node (14.2), Monocytes (8.7), and NK cells (6.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for FGD3 Gene



Protein tissue co-expression partners for FGD3 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for FGD3

SOURCE GeneReport for Unigene cluster for FGD3 Gene:

Hs.411081

Evidence on tissue expression from TISSUES for FGD3 Gene

  • Blood(4.7)
  • Nervous system(4.4)
genes like me logo Genes that share expression patterns with FGD3: view

Primer products for research

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for FGD3 Gene

Orthologs for FGD3 Gene

This gene was present in the common ancestor of animals.

Orthologs for FGD3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia FGD3 30 31
  • 99.47 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia FGD3 30 31
  • 82 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia FGD3 30 31
  • 80.67 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Fgd3 30 17 31
  • 79.44 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Fgd3 30
  • 79.14 (n)
Platypus
(Ornithorhynchus anatinus)
 Mammalia FGD3 31
  • 49 (a)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia FGD3 31
  • 48 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves FGD3 30 31
  • 65.54 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia FGD3 31
  • 63 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia fgd3 30
  • 68.1 (n)
Zebrafish
(Danio rerio)
 Actinopterygii fgd 30
  • 68.11 (n)
Fruit Fly
(Drosophila melanogaster)
 Insecta RhoGEF4 31
  • 18 (a)
 ManyToMany
Worm
(Caenorhabditis elegans)
 Secernentea exc-5 31 32
  • 21 (a)
 OneToMany
Sea Squirt
(Ciona savignyi)
 Ascidiacea CSA.6211 31
  • 32 (a)
 OneToMany
Species where no ortholog for FGD3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • 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 Vase (Ciona intestinalis)
  • 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 FGD3 Gene

ENSEMBL:
Gene Tree for FGD3 (if available)
TreeFam:
Gene Tree for FGD3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for FGD3: view image

Paralogs for FGD3 Gene

Paralogs for FGD3 Gene

(4) SIMAP similar genes for FGD3 Gene using alignment to 3 proteins:

  • FGD3_HUMAN
  • B4DXH4_HUMAN
  • F8W7P2_HUMAN
genes like me logo Genes that share paralogs with FGD3: view

Variants for FGD3 Gene

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  1. SNP Genotyping and Copy Number Assays for research

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for FGD3 Gene

SNP ID Clinical significance and condition Chr 09 pos Variation AA Info Type
rs113001851 Benign: not provided 93,011,245(+) C/T
NM_001083536.2(FGD3):c.1008C>T (p.Asn336=) 		SYNONYMOUS
rs116496123 Benign: not provided 93,034,624(+) G/T
NM_001083536.2(FGD3):c.1869G>T (p.Val623=) 		SYNONYMOUS
rs3802384 - p.Val275Ile

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for FGD3 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for FGD3 Gene

Variant ID Type Subtype PubMed ID
esv2188240 CNV deletion 18987734
esv2738777 CNV deletion 23290073
esv2738778 CNV deletion 23290073
esv2738779 CNV deletion 23290073
esv3545134 CNV deletion 23714750
esv989428 CNV loss 20482838
nsv1077164 CNV deletion 25765185
nsv1124449 CNV deletion 24896259
nsv1137663 CNV deletion 24896259
nsv521136 CNV loss 19592680
nsv526296 CNV loss 19592680
nsv6617 CNV insertion 18451855
nsv831654 CNV gain 17160897

Variation tolerance for FGD3 Gene

Residual Variation Intolerance Score: 27.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.93; 35.90% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for FGD3 Gene

Human Gene Mutation Database (HGMD)
FGD3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
FGD3

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for FGD3 Gene

Disorders for FGD3 Gene

MalaCards: The human disease database

(2) MalaCards diseases for FGD3 Gene - From: COP

Disorder Aliases PubMed IDs
aarskog-scott syndrome
  • aas
charcot-marie-tooth disease, type 4h
  • cmt4h
- elite association - COSMIC cancer census association via MalaCards
Search FGD3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for FGD3

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with FGD3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for FGD3 Gene

Publications for FGD3 Gene

  1. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 41
  2. Novel insights into FGD3, a putative GEF for Cdc42, that undergoes SCF(FWD1/beta-TrCP)-mediated proteasomal degradation analogous to that of its homologue FGD1 but regulates cell morphology and motility differently from FGD1. (PMID: 18363964) Hayakawa M … Kitagawa M (Genes to cells : devoted to molecular & cellular mechanisms 2008) 3 23
  3. DNA sequence and analysis of human chromosome 9. (PMID: 15164053) Humphray SJ … Dunham I (Nature 2004) 3 4
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  5. Characterization of long cDNA clones from human adult spleen. (PMID: 11214971) Hattori A … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 2000) 2 3

ExternalLinks

View latest publications for FGD3 gene in Mastermind

Products for FGD3 Gene

Sources for FGD3 Gene