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

Gene ID: 55785, updated on 11-Apr-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 several processes, including filopodium assembly; regulation of GTPase activity; 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, Apr 2022]
Expression
Ubiquitous expression in skin (RPKM 3.9), gall bladder (RPKM 3.5) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
12q22
Exon count:
21
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (95076749..95217467, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (95057451..95198262, complement)
105.20220307 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
  • 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 (29) 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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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 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)

Genotypes

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 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_2023_10

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

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