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FGD3 FYVE, RhoGEF and PH domain containing 3 [ Homo sapiens (human) ]

Gene ID: 89846, updated on 2-Nov-2024

Summary

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Official Symbol
FGD3provided by HGNC
Official Full Name
FYVE, RhoGEF and PH domain containing 3provided by HGNC
Primary source
HGNC:HGNC:16027
See related
Ensembl:ENSG00000127084 MIM:617554; AllianceGenome:HGNC:16027
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
ZFYVE5
Summary
Predicted to enable guanyl-nucleotide exchange factor activity and small GTPase binding activity. Predicted to be involved in actin cytoskeleton organization; filopodium assembly; and regulation of cell shape. Predicted to be located in Golgi apparatus; lamellipodium; and ruffle. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Broad expression in spleen (RPKM 16.0), lymph node (RPKM 14.2) and 17 other tissues See more
Orthologs
mouse all
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Genomic context

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See FGD3 in Genome Data Viewer
Location:
9q22.31
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (92947523..93036233)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (105114201..105202903)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (95709805..95798515)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:95656905-95657405 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:95667424-95668065 Neighboring gene sorting nexin 18 pseudogene 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:95674721-95675222 Neighboring gene arachidonate 15-lipoxygenase pseudogene 2 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_109845 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28606 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28607 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28608 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:95727421-95728052 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:95732487-95733178 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:95750216-95750914 Neighboring gene Sharpr-MPRA regulatory region 11306 Neighboring gene uncharacterized LOC101927954 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:95777618-95777854 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:95784152-95785052 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:95786616-95787408 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:95787409-95788200 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:95791809-95792308 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:95791307-95791808 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:95797249-95798042 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:95798869-95799762 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:95811946-95812603 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:95821078-95822058 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:95822059-95823039 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28609 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:95824548-95825115 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28610 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28611 Neighboring gene Sharpr-MPRA regulatory region 12079 Neighboring gene sushi domain containing 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:95844809-95845437 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:95852051-95852551 Neighboring gene uncharacterized LOC101927993 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28612 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20037

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. Expression of FGD3 gene as prognostic factor in young breast cancer patients. Renda I, et al. Sci Rep, 2019 Oct 23. PMID 31645624, Free PMC Article
  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. Hayakawa M, et al. Genes Cells, 2008 Apr. PMID 18363964
  3. Isolation, characterization, and mapping of the mouse Fgd3 gene, a new Faciogenital Dysplasia (FGD1; Aarskog Syndrome) gene homologue. Pasteris NG, et al. Gene, 2000 Jan 25. PMID 10721717
  4. Mutations in FGD4 encoding the Rho GDP/GTP exchange factor FRABIN cause autosomal recessive Charcot-Marie-Tooth type 4H. Delague V, et al. Am J Hum Genet, 2007 Jul. PMID 17564959, Free PMC Article
  5. Characterization of long cDNA clones from human adult spleen. Hattori A, et al. DNA Res, 2000 Dec 31. PMID 11214971

See all (19) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Expression of FGD3 gene as prognostic factor in young breast cancer patients.
    Title: Expression of FGD3 gene as prognostic factor in young breast cancer patients.
  2. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Submit: New GeneRIF Correction

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ00004, MGC117260

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 ISS
Inferred from Sequence or Structural Similarity
more info
  
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 ISS
Inferred from Sequence or Structural Similarity
more info
  
Process Evidence Code Pubs
involved_in actin cytoskeleton organization ISS
Inferred from Sequence or Structural Similarity
more info
  
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 ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of GTPase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
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
  
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 3
Names
FGD1 family, member 3
faciogenital dysplasia 3
zinc finger FYVE domain-containing protein 5

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.

mRNA and Protein(s)

  1. NM_001083536.2 → NP_001077005.1  FYVE, RhoGEF and PH domain-containing protein 3 isoform a

    See identical proteins and their annotated locations for NP_001077005.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a). Variants 1, 2, and 4 all encode the same isoform (a).
    Source sequence(s)
    AL451065, BC032429, BF509875, DA493667
    Consensus CDS
    CCDS43849.1
    UniProtKB/Swiss-Prot
    F8W7P2, Q4VX84, Q5JSP0, Q7Z7D9, Q8N5G1
    UniProtKB/TrEMBL
    A8K9G1
    Related
    ENSP00000364631.3, ENST00000375482.8
    Conserved Domains (4) summary
    cd00160
    Location:160 → 339
    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:598 → 702
    PH2_FGD1-4; FYVE, RhoGEF and PH domain containing/faciogenital dysplasia proteins pleckstrin homology (PH) domain, C-terminus
    cd13387
    Location:371 → 478
    PH1_FGD3; FYVE, RhoGEF and PH domain containing/faciogenital dysplasia protein 3, N-terminal Pleckstrin homology (PH) domain
    cd15740
    Location:531 → 584
    FYVE_FGD3; FYVE-like domain found in FYVE, RhoGEF and PH domain-containing protein 3 (FGD3) and similar proteins

  2. NM_001286993.2 → NP_001273922.1  FYVE, RhoGEF and PH domain-containing protein 3 isoform b

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (b) is 1 aa shorter than isoform a.
    Source sequence(s)
    AK225843, AK292676, AY211386
    Consensus CDS
    CCDS69619.1
    UniProtKB/TrEMBL
    A8K9G1
    Related
    ENSP00000413833.2, ENST00000416701.6
    Conserved Domains (5) summary
    cd13236
    Location:597 → 701
    PH2_FGD1-4; FYVE, RhoGEF and PH domain containing/faciogenital dysplasia proteins pleckstrin homology (PH) domain, C-terminus
    cd13387
    Location:371 → 478
    PH1_FGD3; FYVE, RhoGEF and PH domain containing/faciogenital dysplasia protein 3, N-terminal Pleckstrin homology (PH) domain
    cd15740
    Location:531 → 584
    FYVE_FGD3; FYVE-like domain found in FYVE, RhoGEF and PH domain-containing protein 3 (FGD3) and similar proteins
    pfam00169
    Location:371 → 469
    PH; PH domain
    pfam00621
    Location:161 → 340
    RhoGEF; RhoGEF domain

  3. NM_001369951.1 → NP_001356880.1  FYVE, RhoGEF and PH domain-containing protein 3 isoform a

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4), as well as variants 1 and 2, encodes the longest isoform (a).
    Source sequence(s)
    AL389924, AL451065
    Consensus CDS
    CCDS43849.1
    UniProtKB/Swiss-Prot
    F8W7P2, Q4VX84, Q5JSP0, Q7Z7D9, Q8N5G1
    UniProtKB/TrEMBL
    A8K9G1
    Related
    ENSP00000496819.1, ENST00000468206.6
    Conserved Domains (4) summary
    cd00160
    Location:160 → 339
    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:598 → 702
    PH2_FGD1-4; FYVE, RhoGEF and PH domain containing/faciogenital dysplasia proteins pleckstrin homology (PH) domain, C-terminus
    cd13387
    Location:371 → 478
    PH1_FGD3; FYVE, RhoGEF and PH domain containing/faciogenital dysplasia protein 3, N-terminal Pleckstrin homology (PH) domain
    cd15740
    Location:531 → 584
    FYVE_FGD3; FYVE-like domain found in FYVE, RhoGEF and PH domain-containing protein 3 (FGD3) and similar proteins

  4. NM_001369952.1 → NP_001356881.1  FYVE, RhoGEF and PH domain-containing protein 3 isoform c

    Status: VALIDATED

    Source sequence(s)
    AL389924, AL451065
    UniProtKB/TrEMBL
    A8K9G1
    Conserved Domains (4) summary
    cd00160
    Location:160 → 339
    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:549 → 653
    PH2_FGD1-4; FYVE, RhoGEF and PH domain containing/faciogenital dysplasia proteins pleckstrin homology (PH) domain, C-terminus
    cd15740
    Location:482 → 535
    FYVE_FGD3; FYVE-like domain found in FYVE, RhoGEF and PH domain-containing protein 3 (FGD3) and similar proteins
    cl17171
    Location:345 → 429
    PH-like; Pleckstrin homology-like domain

  5. NM_033086.3 → NP_149077.2  FYVE, RhoGEF and PH domain-containing protein 3 isoform a

    See identical proteins and their annotated locations for NP_149077.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2, and 4 all encode the same isoform (a).
    Source sequence(s)
    AL451065, BC111054, BF509875, DB161711
    Consensus CDS
    CCDS43849.1
    UniProtKB/Swiss-Prot
    F8W7P2, Q4VX84, Q5JSP0, Q7Z7D9, Q8N5G1
    UniProtKB/TrEMBL
    A8K9G1
    Related
    ENSP00000336914.6, ENST00000337352.10
    Conserved Domains (4) summary
    cd00160
    Location:160 → 339
    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:598 → 702
    PH2_FGD1-4; FYVE, RhoGEF and PH domain containing/faciogenital dysplasia proteins pleckstrin homology (PH) domain, C-terminus
    cd13387
    Location:371 → 478
    PH1_FGD3; FYVE, RhoGEF and PH domain containing/faciogenital dysplasia protein 3, N-terminal Pleckstrin homology (PH) domain
    cd15740
    Location:531 → 584
    FYVE_FGD3; FYVE-like domain found in FYVE, RhoGEF and PH domain-containing protein 3 (FGD3) and similar proteins

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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    92947523..93036233
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    105114201..105202903
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5JSP0.1 GenPept UniProtKB/Swiss-Prot:Q5JSP0

Gene LinkOut

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