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Aliases for FGD4 Gene

Aliases for FGD4 Gene

  • FYVE, RhoGEF And PH Domain Containing 4 2 3 5
  • Zinc Finger FYVE Domain-Containing Protein 6 3 4
  • FGD1-Related F-Actin-Binding Protein 3 4
  • FGD1 Family, Member 4 2 3
  • ZFYVE6 3 4
  • FRABP 3 4
  • FYVE, RhoGEF And PH Domain-Containing Protein 4 3
  • Actin-Filament Binding Protein Frabin 3
  • Actin Filament-Binding Protein Frabin 4
  • CMT4H 3

External Ids for FGD4 Gene

Previous GeneCards Identifiers for FGD4 Gene

  • GC12P032546
  • GC12P032654

Summaries for FGD4 Gene

Entrez Gene Summary for FGD4 Gene

  • This gene encodes a protein that is involved in the regulation of the actin cytoskeleton and cell shape. This protein contains an actin filament-binding domain, which together with its Dbl homology domain and one of its pleckstrin homology domains, can form microspikes. This protein can activate MAPK8 independently of the actin filament-binding domain, and it is also involved in the activation of CDC42 via the exchange of bound GDP for free GTP. The activation of CDC42 also enables this protein to play a role in mediating the cellular invasion of Cryptosporidium parvum, an intracellular parasite that infects the gastrointestinal tract. Mutations in this gene can cause Charcot-Marie-Tooth disease type 4H (CMT4H), a disorder of the peripheral nervous system. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2015]

GeneCards Summary for FGD4 Gene

FGD4 (FYVE, RhoGEF And PH Domain Containing 4) is a Protein Coding gene. Diseases associated with FGD4 include Charcot-Marie-Tooth Disease, Type 4H and Neuropathy, Congenital Hypomyelinating Or Amyelinating, Autosomal Recessive. Among its related pathways are p75 NTR receptor-mediated signalling and Signaling by GPCR. Gene Ontology (GO) annotations related to this gene include actin binding and Rho guanyl-nucleotide exchange factor activity. An important paralog of this gene is FGD1.

UniProtKB/Swiss-Prot for FGD4 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. Activates MAPK8 (By similarity).

Gene Wiki entry for FGD4 Gene

Additional gene information for FGD4 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for FGD4 Gene

Genomics for FGD4 Gene

GeneHancer (GH) Regulatory Elements for FGD4 Gene

Promoters and enhancers for FGD4 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
GH12J032532 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 650.1 +135.1 135116 4.5 FOXA2 ARID4B SIN3A ZNF48 ETS1 YY1 ATF7 FOS NFKBIZ RXRA FGD4 RNU6-494P DNM1L LOC100420981 PIR37592 PIR51402
GH12J032398 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 661.6 +0.4 426 3.3 HDGF PKNOX1 ARID4B SIN3A DMAP1 ZNF2 ZNF143 SP3 NFYC REST FGD4 RNU6-494P
GH12J032500 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE dbSUPER 650.1 +102.8 102798 3.1 ELF3 FOXA2 ARID4B MZF1 SIN3A RAD21 RARA YY1 EGR1 RXRA FGD4 DNM1L LOC100420981 RNU6-494P PIR37592
GH12J032390 Promoter/Enhancer 1.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 656.9 -8.6 -8595 0.9 ELF3 CTCF RNF2 NFATC3 NFYC ZBTB33 BCL6 MAFK FGD4 GC12P032381 ENSG00000207176
GH12J032397 Enhancer 0.4 ENCODE 656.8 -1.7 -1657 0.1 ZNF335 FEZF1 PRDM4 FGD4 ENSG00000207176
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around FGD4 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the FGD4 gene promoter:
  • FOXF2
  • MEF-2A
  • aMEF-2
  • p300
  • E47
  • Tal-1beta
  • Sox9
  • Sox5
  • AML1a
  • AREB6

Genomic Locations for FGD4 Gene

Genomic Locations for FGD4 Gene
chr12:32,399,529-32,646,050
(GRCh38/hg38)
Size:
246,522 bases
Orientation:
Plus strand
chr12:32,552,463-32,798,984
(GRCh37/hg19)
Size:
246,522 bases
Orientation:
Plus strand

Genomic View for FGD4 Gene

Genes around FGD4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
FGD4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for FGD4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for FGD4 Gene

Proteins for FGD4 Gene

  • Protein details for FGD4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96M96-FGD4_HUMAN
    Recommended name:
    FYVE, RhoGEF and PH domain-containing protein 4
    Protein Accession:
    Q96M96
    Secondary Accessions:
    • Q6ULS2
    • Q8TCP6

    Protein attributes for FGD4 Gene

    Size:
    766 amino acids
    Molecular mass:
    86626 Da
    Quaternary structure:
    • Homooligomer.

    Alternative splice isoforms for FGD4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for FGD4 Gene

Post-translational modifications for FGD4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for FGD4 Gene

Domains & Families for FGD4 Gene

Gene Families for FGD4 Gene

Graphical View of Domain Structure for InterPro Entry

Q96M96

UniProtKB/Swiss-Prot:

FGD4_HUMAN :
  • The part of the protein spanning the actin filament-binding domain together with the DH domain and the first PH domain is necessary and sufficient for microspike formation. Activation of MAPK8 requires the presence of all domains with the exception of the actin filament-binding domain (By similarity).
Domain:
  • The part of the protein spanning the actin filament-binding domain together with the DH domain and the first PH domain is necessary and sufficient for microspike formation. Activation of MAPK8 requires the presence of all domains with the exception of the actin filament-binding domain (By similarity).
genes like me logo Genes that share domains with FGD4: view

Function for FGD4 Gene

Molecular function for FGD4 Gene

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. Activates MAPK8 (By similarity).

Phenotypes From GWAS Catalog for FGD4 Gene

Gene Ontology (GO) - Molecular Function for FGD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003779 actin binding IEA --
GO:0005085 guanyl-nucleotide exchange factor activity TAS,IEA --
GO:0005089 Rho guanyl-nucleotide exchange factor activity IEA,TAS --
GO:0031267 small GTPase binding ISS --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with FGD4: view
genes like me logo Genes that share phenotypes with FGD4: view

Human Phenotype Ontology for FGD4 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for FGD4 Gene

MGI Knock Outs for FGD4:
  • Fgd4 Fgd4<tm1.1Ics>

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for FGD4 Gene

Localization for FGD4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for FGD4 Gene

Cytoplasm, cytoskeleton. Cell projection, filopodium. Note=Concentrated in filopodia and poorly detected at lamellipodia. Binds along the sides of actin fibers (By similarity). {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 FGD4 gene
Compartment Confidence
cytosol 5
cytoskeleton 4
golgi apparatus 4
nucleus 2
plasma membrane 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Actin filaments (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for FGD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001726 ruffle ISS --
GO:0005737 cytoplasm ISS --
GO:0005794 Golgi apparatus ISS --
GO:0005829 cytosol TAS --
GO:0005856 cytoskeleton IEA --
genes like me logo Genes that share ontologies with FGD4: view

Pathways & Interactions for FGD4 Gene

genes like me logo Genes that share pathways with FGD4: view

Gene Ontology (GO) - Biological Process for FGD4 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:0030032 lamellipodium assembly IEA --
GO:0030035 microspike assembly IEA --
genes like me logo Genes that share ontologies with FGD4: view

No data available for SIGNOR curated interactions for FGD4 Gene

Drugs & Compounds for FGD4 Gene

(2) Drugs for FGD4 Gene - From: PharmGKB and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Paclitaxel Approved, Vet_approved Pharma Tubulin and Bcl2 inhibitor, Taxanes 3027
Guanosine triphosphate Experimental Pharma 0

(2) Additional Compounds for FGD4 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with FGD4: view

Transcripts for FGD4 Gene

Unigene Clusters for FGD4 Gene

FYVE, RhoGEF and PH domain containing 4:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for FGD4 Gene

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

Relevant External Links for FGD4 Gene

GeneLoc Exon Structure for
FGD4
ECgene alternative splicing isoforms for
FGD4

Expression for FGD4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for FGD4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for FGD4 Gene

This gene is overexpressed in Stomach (15.0), Peripheral blood mononuclear cells (10.3), and Placenta (6.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for FGD4 Gene



Protein tissue co-expression partners for FGD4 Gene

NURSA nuclear receptor signaling pathways regulating expression of FGD4 Gene:

FGD4

SOURCE GeneReport for Unigene cluster for FGD4 Gene:

Hs.117835

mRNA Expression by UniProt/SwissProt for FGD4 Gene:

Q96M96-FGD4_HUMAN
Tissue specificity: Expressed in different tissues, including brain, cerebellum, peripheral nerve, skeletal muscle, heart, uterus, placenta and testis.

Evidence on tissue expression from TISSUES for FGD4 Gene

  • Liver(4.2)
  • Nervous system(3)

Phenotype-based relationships between genes and organs from Gene ORGANizer for FGD4 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • cerebellum
  • head
Thorax:
  • lung
  • rib
  • rib cage
Pelvis:
  • pelvis
Limb:
  • foot
  • lower limb
  • upper limb
General:
  • peripheral nerve
  • peripheral nervous system
  • spinal column
  • spinal cord
  • vertebrae
genes like me logo Genes that share expression patterns with FGD4: view

No data available for mRNA differential expression in normal tissues for FGD4 Gene

Orthologs for FGD4 Gene

This gene was present in the common ancestor of animals.

Orthologs for FGD4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia FGD4 34 33
  • 99.74 (n)
OneToOne
cow
(Bos Taurus)
Mammalia FGD4 34 33
  • 91.37 (n)
OneToOne
dog
(Canis familiaris)
Mammalia FGD4 34 33
  • 91.15 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Fgd4 16 34 33
  • 85.6 (n)
rat
(Rattus norvegicus)
Mammalia Fgd4 33
  • 84.03 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia FGD4 34
  • 78 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia FGD4 34
  • 69 (a)
OneToOne
chicken
(Gallus gallus)
Aves FGD4 34
  • 68 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia FGD4 34
  • 66 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia fgd4 33
  • 69.95 (n)
zebrafish
(Danio rerio)
Actinopterygii fgd4a 34 33
  • 64.28 (n)
OneToMany
CABZ01078314.1 34
  • 62 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta RhoGEF4 34
  • 18 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea exc-5 34
  • 22 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.6211 34
  • 40 (a)
OneToMany
Species where no ortholog for FGD4 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)
  • 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 FGD4 Gene

ENSEMBL:
Gene Tree for FGD4 (if available)
TreeFam:
Gene Tree for FGD4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for FGD4: view image

Paralogs for FGD4 Gene

Paralogs for FGD4 Gene

(6) SIMAP similar genes for FGD4 Gene using alignment to 13 proteins:

  • FGD4_HUMAN
  • B7Z493_HUMAN
  • E9PJX4_HUMAN
  • E9PNX0_HUMAN
  • E9PQT1_HUMAN
  • F8VVF1_HUMAN
  • F8VWL3_HUMAN
  • F8W1R0_HUMAN
  • G3XA97_HUMAN
  • H0YDQ0_HUMAN
  • J3KSS3_HUMAN
  • L8EAP1_HUMAN
  • Q49A55_HUMAN
genes like me logo Genes that share paralogs with FGD4: view

Variants for FGD4 Gene

Sequence variations from dbSNP and Humsavar for FGD4 Gene

SNP ID Clin Chr 12 pos Variation AA Info Type
rs1060501903 uncertain-significance, Charcot-Marie-Tooth disease, type IV 32,611,191(+) A/G coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs1060501904 uncertain-significance, Charcot-Marie-Tooth disease, type IV 32,638,788(+) CCCCCC/CCCCC coding_sequence_variant, frameshift, genic_downstream_transcript_variant
rs10844253 benign, not specified, Charcot-Marie-Tooth, Type 4 32,611,250(+) G/A coding_sequence_variant, non_coding_transcript_variant, synonymous_variant
rs10844268 benign, Charcot-Marie-Tooth, Type 4 32,641,666(+) A/C 3_prime_UTR_variant, genic_downstream_transcript_variant, intron_variant
rs11052033 likely-benign, Charcot-Marie-Tooth, Type 4 32,502,151(+) C/T 5_prime_UTR_variant, genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for FGD4 Gene

Variant ID Type Subtype PubMed ID
esv2751096 CNV gain 17911159
esv3382704 CNV insertion 20981092
esv3581449 CNV gain 25503493
esv3629083 CNV loss 21293372
esv3629084 CNV loss 21293372
esv3629085 CNV gain 21293372
nsv1122716 CNV deletion 24896259
nsv473072 CNV novel sequence insertion 20440878
nsv527786 CNV gain 19592680
nsv951347 CNV duplication 24416366

Variation tolerance for FGD4 Gene

Residual Variation Intolerance Score: 41.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 13.31; 95.33% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for FGD4 Gene

Human Gene Mutation Database (HGMD)
FGD4
SNPedia medical, phenotypic, and genealogical associations of SNPs for
FGD4

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for FGD4 Gene

Disorders for FGD4 Gene

MalaCards: The human disease database

(5) MalaCards diseases for FGD4 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search FGD4 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

FGD4_HUMAN
  • Charcot-Marie-Tooth disease 4H (CMT4H) [MIM:609311]: A recessive demyelinating form of Charcot-Marie-Tooth disease, a disorder of the peripheral nervous system, characterized by progressive weakness and atrophy, initially of the peroneal muscles and later of the distal muscles of the arms. Charcot-Marie-Tooth disease is classified in two main groups on the basis of electrophysiologic properties and histopathology: primary peripheral demyelinating neuropathies (designated CMT1 when they are dominantly inherited) and primary peripheral axonal neuropathies (CMT2). Demyelinating neuropathies are characterized by severely reduced nerve conduction velocities (less than 38 m/sec), segmental demyelination and remyelination with onion bulb formations on nerve biopsy, slowly progressive distal muscle atrophy and weakness, absent deep tendon reflexes, and hollow feet. By convention autosomal recessive forms of demyelinating Charcot-Marie-Tooth disease are designated CMT4. {ECO:0000269 PubMed:17564959, ECO:0000269 PubMed:17564972}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for FGD4

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with FGD4: view

No data available for Genatlas for FGD4 Gene

Publications for FGD4 Gene

  1. Peripheral nerve demyelination caused by a mutant Rho GTPase guanine nucleotide exchange factor, frabin/FGD4. (PMID: 17564972) Stendel C … Senderek J (American journal of human genetics 2007) 3 4 22 58
  2. Phosphatidylinositol 3-kinase and frabin mediate Cryptosporidium parvum cellular invasion via activation of Cdc42. (PMID: 15133042) Chen XM … LaRusso NF (The Journal of biological chemistry 2004) 3 4 22 58
  3. Identification of splicing variants of Frabin with partly different functions and tissue distribution. (PMID: 11527409) Ikeda W … Takai Y (Biochemical and biophysical research communications 2001) 2 3 22 58
  4. 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 44 58
  5. Differential protein expression by dendritic cells from atopic and non-atopic individuals after stimulation by the major house dust mite allergen Der p 1. (PMID: 19494521) Horlock C … Ghaemmaghami AM (International archives of allergy and immunology 2009) 3 22 58

Products for FGD4 Gene

Sources for FGD4 Gene

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