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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 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

  • 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

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