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    FGD2 FYVE, RhoGEF and PH domain containing 2 [ Homo sapiens (human) ]

    Gene ID: 221472, updated on 11-Apr-2024

    Summary

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    Official Symbol
    FGD2provided by HGNC
    Official Full Name
    FYVE, RhoGEF and PH domain containing 2provided by HGNC
    Primary source
    HGNC:HGNC:3664
    See related
    Ensembl:ENSG00000146192 MIM:605091; AllianceGenome:HGNC:3664
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    ZFYVE4
    Summary
    The protein encoded by this gene belongs to a family of guanine nucleotide exchange factors (GEFs) which control cytoskeleton-dependent membrane rearrangements by activating the cell division cycle 42 (CDC42) protein. This gene is expressed in B lymphocytes, macrophages, and dendritic cells. The encoded protein may play a role in leukocyte signaling and vesicle trafficking in antigen-presenting cells in the immune system. [provided by RefSeq, Oct 2016]
    Expression
    Biased expression in spleen (RPKM 19.9), lymph node (RPKM 9.1) and 13 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    6p21.2
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (37005655..37029069)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (36829039..36852622)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (36973431..36996845)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:36926417-36926918 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:36926919-36927418 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:36930796-36931421 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:36931422-36932046 Neighboring gene peptidase inhibitor 16 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:36948504-36949104 Neighboring gene mitochondrial carrier 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:36953526-36954248 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24447 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:36960675-36960875 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:36965399-36966022 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:36966023-36966646 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:36973029-36973191 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24448 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24449 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:36979647-36980146 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:36981577-36982294 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:36992286-36993485 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24450 Neighboring gene CRISPRi-validated cis-regulatory element chr6.2470 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24451 Neighboring gene COX6A1 pseudogene 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:37024071-37024957 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:37025005-37025506 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:37025507-37026006 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17124 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17125 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17126 Neighboring gene Sharpr-MPRA regulatory region 8589 Neighboring gene Sharpr-MPRA regulatory region 8119 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:37045201-37045729 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:37051359-37051859 Neighboring gene ribosomal protein L12 pseudogene 2

    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
    • 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. Characterization of guanine nucleotide exchange activity of DH domain of human FGD2. Chuan J, et al. Protein Expr Purif, 2020 Dec. PMID 32681954
    2. Isolation, characterization, and mapping of the mouse and human Fgd2 genes, faciogenital dysplasia (FGD1; Aarskog syndrome) gene homologues. Pasteris NG, et al. Genomics, 1999 Aug 15. PMID 10458911
    3. FGD2, a CDC42-specific exchange factor expressed by antigen-presenting cells, localizes to early endosomes and active membrane ruffles. Huber C, et al. J Biol Chem, 2008 Dec 5. PMID 18838382, Free PMC Article
    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 (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Characterization of guanine nucleotide exchange activity of DH domain of human FGD2.
      Title: Characterization of guanine nucleotide exchange activity of DH domain of human FGD2.
    2. FGD2 has a role in leukocyte signaling and vesicle trafficking in cells specialized to present antigen in the immune system
      Title: FGD2, a CDC42-specific exchange factor expressed by antigen-presenting cells, localizes to early endosomes and active membrane ruffles.
    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

    EBI GWAS Catalog

    Description
    Genome-wide association study identifies three novel susceptibility loci for severe Acne vulgaris.
    EBI GWAS Catalog

    Variation

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    See Variation Viewer (GRCh37.p13)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ00048, FLJ40929, MGC71330

    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 phosphatidylinositol phosphate binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    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 early endosome membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in lamellipodium ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in ruffle ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in ruffle membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    FYVE, RhoGEF and PH domain-containing protein 2
    Names
    FGD1 family, member 2
    FLJ00276 protein
    epididymis secretory sperm binding protein
    zinc finger FYVE domain-containing protein 4

    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.

    Genomic

    1. NG_051804.1 RefSeqGene

      Range
      5009..28423
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_173558.4 → NP_775829.2  FYVE, RhoGEF and PH domain-containing protein 2

      See identical proteins and their annotated locations for NP_775829.2

      Status: REVIEWED

      Source sequence(s)
      AL160264, BC023645, BC053655
      Consensus CDS
      CCDS4829.1
      UniProtKB/Swiss-Prot
      Q5T8I1, Q6P6A8, Q6ZNL5, Q7Z6J4, Q8IZ32, Q8N868, Q9H7M2
      UniProtKB/TrEMBL
      A0A384NQ05
      Related
      ENSP00000274963.8, ENST00000274963.13
      Conserved Domains (5) summary
      cd00160
      Location:104 → 288
      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:538 → 640
      PH2_FGD1-4; FYVE, RhoGEF and PH domain containing/faciogenital dysplasia proteins pleckstrin homology (PH) domain, C-terminus
      cd13386
      Location:320 → 427
      PH1_FGD2; FYVE, RhoGEF and PH domain containing/faciogenital dysplasia protein 2, N-terminal Pleckstrin homology (PH) domain
      cd15741
      Location:453 → 517
      FYVE_FGD1_2_4; FYVE domain found in FYVE, RhoGEF and PH domain-containing protein facio-genital dysplasia FGD1, FGD2, FGD4
      pfam00169
      Location:320 → 417
      PH; PH domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      37005655..37029069
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047418332.1 → XP_047274288.1  FYVE, RhoGEF and PH domain-containing protein 2 isoform X1

    2. XM_011514372.3 → XP_011512674.1  FYVE, RhoGEF and PH domain-containing protein 2 isoform X3

      Conserved Domains (2) summary
      cd00160
      Location:104 → 288
      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.
      cl17171
      Location:320 → 343
      PH-like; Pleckstrin homology-like domain

    3. XM_011514373.3 → XP_011512675.1  FYVE, RhoGEF and PH domain-containing protein 2 isoform X4

      Conserved Domains (2) summary
      cd00160
      Location:104 → 288
      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.
      cl17171
      Location:320 → 374
      PH-like; Pleckstrin homology-like domain

    4. XM_047418333.1 → XP_047274289.1  FYVE, RhoGEF and PH domain-containing protein 2 isoform X2

    5. XM_047418334.1 → XP_047274290.1  FYVE, RhoGEF and PH domain-containing protein 2 isoform X5

    6. XM_047418335.1 → XP_047274291.1  FYVE, RhoGEF and PH domain-containing protein 2 isoform X6

    RNA

    1. XR_926106.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      36829039..36852622
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054354578.1 → XP_054210553.1  FYVE, RhoGEF and PH domain-containing protein 2 isoform X1

    2. XM_054354580.1 → XP_054210555.1  FYVE, RhoGEF and PH domain-containing protein 2 isoform X3

    3. XM_054354581.1 → XP_054210556.1  FYVE, RhoGEF and PH domain-containing protein 2 isoform X4

    4. XM_054354579.1 → XP_054210554.1  FYVE, RhoGEF and PH domain-containing protein 2 isoform X2

    5. XM_054354582.1 → XP_054210557.1  FYVE, RhoGEF and PH domain-containing protein 2 isoform X5

    6. XM_054354583.1 → XP_054210558.1  FYVE, RhoGEF and PH domain-containing protein 2 isoform X6

    RNA

    1. XR_008487279.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q7Z6J4.1 GenPept UniProtKB/Swiss-Prot:Q7Z6J4

    Gene LinkOut

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

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