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    FGD6 FYVE, RhoGEF and PH domain containing 6 [ Homo sapiens (human) ]

    Gene ID: 55785, updated on 3-Nov-2024

    Summary

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    Official Symbol
    FGD6provided by HGNC
    Official Full Name
    FYVE, RhoGEF and PH domain containing 6provided by HGNC
    Primary source
    HGNC:HGNC:21740
    See related
    Ensembl:ENSG00000180263 MIM:613520; AllianceGenome:HGNC:21740
    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
    ZFYVE24
    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
    Ubiquitous expression in skin (RPKM 3.9), gall bladder (RPKM 3.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See FGD6 in Genome Data Viewer
    Location:
    12q22
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (95076749..95217467, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (95057451..95198262, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (95470525..95611243, complement)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene NANOG hESC enhancer GRCh37_chr12:95383137-95383648 Neighboring gene NADH:ubiquinone oxidoreductase subunit A12 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:95397104-95397731 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:95416774-95417006 Neighboring gene nuclear receptor subfamily 2 group C member 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:95448437-95449289 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:95449290-95450141 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:95466981-95467481 Neighboring gene peroxiredoxin 6 pseudogene Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:95508516-95509249 Neighboring gene MPRA-validated peak1898 silencer Neighboring gene ribosomal protein L14 pseudogene 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4737 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:95591907-95592408 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:95592409-95592908 Neighboring gene Sharpr-MPRA regulatory region 9597 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6807 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:95610907-95611501 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:95611502-95612097 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6809 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:95629839-95630536 Neighboring gene vezatin, adherens junctions transmembrane protein Neighboring gene RNA, U6 small nuclear 808, pseudogene Neighboring gene CBX3 pseudogene 5

    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. A missense variant in FGD6 confers increased risk of polypoidal choroidal vasculopathy. Huang L, et al. Nat Genet, 2016 Jun. PMID 27089177
    2. Genome-wide association study of chemotherapeutic agent-induced severe neutropenia/leucopenia for patients in Biobank Japan. Low SK, et al. Cancer Sci, 2013 Aug. PMID 23648065, Free PMC Article
    3. Selected reaction monitoring mass spectrometry reveals the dynamics of signaling through the GRB2 adaptor. Bisson N, et al. Nat Biotechnol, 2011 Jun 26. PMID 21706016
    4. Prediction of the coding sequences of unidentified human genes. XVI. The complete sequences of 150 new cDNA clones from brain which code for large proteins in vitro. Nagase T, et al. DNA Res, 2000 Feb 28. PMID 10718198
    5. Quantitative study of the interactome of PKCζ involved in the EGF-induced tumor cell chemotaxis. Chen R, et al. J Proteome Res, 2013 Mar 1. PMID 23402259

    See all (31) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. data suggest that oxidized phospholipids and FGD6-Arg329 might act synergistically to increase susceptibility to PCV
      Title: A missense variant in FGD6 confers increased risk of polypoidal choroidal vasculopathy.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide association study of chemotherapeutic agent-induced severe neutropenia/leucopenia for patients in Biobank Japan.
    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)

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of FYVE, RhoGEF and PH domain containing 6 (FGD6) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    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 metal ion 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 ISS
    Inferred from Sequence or Structural Similarity
    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
    		  
    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 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 6
    Names
    zinc finger FYVE domain-containing protein 24

    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_018351.4 → NP_060821.3  FYVE, RhoGEF and PH domain-containing protein 6

      See identical proteins and their annotated locations for NP_060821.3

      Status: VALIDATED

      Source sequence(s)
      AC011598, AC127165, AK124904, AK128492
      Consensus CDS
      CCDS31878.1
      UniProtKB/Swiss-Prot
      Q6ZR53, Q6ZV73, Q7Z2Z7, Q96D44, Q9NUR8, Q9P2I5
      UniProtKB/TrEMBL
      F8VY01
      Related
      ENSP00000344446.4, ENST00000343958.9
      Conserved Domains (5) summary
      cd13237
      Location:1336 → 1424
      PH2_FGD5_FGD6; FYVE, RhoGEF and PH domain containing/faciogenital dysplasia proteins 5 and 6 pleckstrin homology (PH) domain, C-terminus
      cd15793
      Location:1077 → 1199
      PH1_FGD6; FYVE, RhoGEF and PH domain containing/faciogenital dysplasia protein 6, N-terminal Pleckstrin Homology (PH) domain
      cd15743
      Location:1217 → 1277
      FYVE_FGD6; FYVE domain found in FYVE, RhoGEF and PH domain-containing protein 6 (FGD6) and similar proteins
      pfam00169
      Location:1336 → 1426
      PH; PH domain
      pfam00621
      Location:875 → 1059
      RhoGEF; RhoGEF domain

    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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      95076749..95217467 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      95057451..95198262 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6ZV73.2 GenPept UniProtKB/Swiss-Prot:Q6ZV73

    Gene LinkOut

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

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