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

    Gene ID: 89846, updated on 10-Dec-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, Dec 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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 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)

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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