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ZFYVE1 zinc finger FYVE-type containing 1 [ Homo sapiens (human) ]

Gene ID: 53349, updated on 27-Nov-2024

Summary

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Official Symbol
ZFYVE1provided by HGNC
Official Full Name
zinc finger FYVE-type containing 1provided by HGNC
Primary source
HGNC:HGNC:13180
See related
Ensembl:ENSG00000165861 MIM:605471; AllianceGenome:HGNC:13180
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
SR3; DFCP1; TAFF1; ZNFN2A1; PPP1R172
Summary
The FYVE domain mediates the recruitment of proteins involved in membrane trafficking and cell signaling to phosphatidylinositol 3-phosphate-containing membranes. This protein contains two zinc-binding FYVE domains in tandem and is reported to localize to the Golgi apparatus. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]
Expression
Ubiquitous expression in thyroid (RPKM 7.4), kidney (RPKM 6.4) and 25 other tissues See more
Orthologs
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Genomic context

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See ZFYVE1 in Genome Data Viewer
Location:
14q24.2
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (72969445..73027106, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (67175059..67232660, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (73436153..73493814, complement)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene tRNA-Cys (anticodon GCA) 8-1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:73437151-73437652 Neighboring gene ribosomal protein S12 pseudogene 1 Neighboring gene MPRA-validated peak2195 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5903 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8692 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:73502840-73503013 Neighboring gene RNA, 7SL, cytoplasmic 586, pseudogene Neighboring gene MED14-independent group 3 enhancer GRCh37_chr14:73524555-73525754 Neighboring gene RBM25 antisense RNA 1 Neighboring gene RNA binding motif protein 25

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. Double FYVE-containing protein 1 (DFCP1): isolation, cloning and characterization of a novel FYVE finger protein from a human bone marrow cDNA library. Derubeis AR, et al. Gene, 2000 Sep 19. PMID 11024279
  2. The role of NSP6 in the biogenesis of the SARS-CoV-2 replication organelle. Ricciardi S, et al. Nature, 2022 Jun. PMID 35551511, Free PMC Article
  3. A subdomain of the endoplasmic reticulum forms a cradle for autophagosome formation. Hayashi-Nishino M, et al. Nat Cell Biol, 2009 Dec. PMID 19898463
  4. Cellular localization and tissue distribution of endogenous DFCP1 protein. Nanao T, et al. Biomed Res, 2015. PMID 25876663
  5. TRIM13 regulates ER stress induced autophagy and clonogenic ability of the cells. Tomar D, et al. Biochim Biophys Acta, 2012 Feb. PMID 22178386

See all (41) citations in PubMed

GeneRIFs: Gene References Into Functions

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)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • KIAA1589

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables 1-phosphatidylinositol binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables 1-phosphatidylinositol binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables phosphatidylinositol-3,4,5-trisphosphate binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables phosphatidylinositol-3,4,5-trisphosphate binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables phosphatidylinositol-3,4-bisphosphate binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables phosphatidylinositol-3,4-bisphosphate binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables phosphatidylinositol-3-phosphate binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables phosphatidylinositol-3-phosphate binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables zinc ion binding NAS
Non-traceable Author Statement
more info
 PubMed 
Process Evidence Code Pubs
involved_in cellular response to starvation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in lipid droplet formation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in lipid droplet formation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in macroautophagy IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation by host of viral genome replication IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in Golgi stack IDA
Inferred from Direct Assay
more info
 PubMed 
located_in autophagosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endoplasmic reticulum IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endoplasmic reticulum membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in extrinsic component of omegasome membrane IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in lipid droplet IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in lipid droplet IDA
Inferred from Direct Assay
more info
 PubMed 
colocalizes_with membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in mitochondria-associated endoplasmic reticulum membrane contact site IDA
Inferred from Direct Assay
more info
 PubMed 
located_in mitochondrion IDA
Inferred from Direct Assay
more info
 PubMed 
located_in omegasome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in perinuclear region of cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in phagophore assembly site IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
zinc finger FYVE domain-containing protein 1
Names
double FYVE-containing protein 1
phosphoinositide-binding protein SR3
protein phosphatase 1, regulatory subunit 172
tandem FYVE fingers-1 protein
zinc finger protein, subfamily 2A, member 1
zinc finger, FYVE domain containing 1

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_001281734.2 → NP_001268663.1  zinc finger FYVE domain-containing protein 1 isoform 3

    See identical proteins and their annotated locations for NP_001268663.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. This results in a shorter protein (isoform 3), compared to isoform 1.
    Source sequence(s)
    AL442663, BC014902, DA324499, DB059103, EL734498
    Consensus CDS
    CCDS61498.1
    UniProtKB/TrEMBL
    G3V5N8
    Related
    ENSP00000326921.5, ENST00000318876.9
    Conserved Domains (3) summary
    cd01851
    Location:174 → 410
    GBP; Guanylate-binding protein (GBP) family (N-terminal domain)
    cd15734
    Location:697 → 757
    FYVE_ZFYV1; FYVE domains found in zinc finger FYVE domain-containing protein 1 (ZFYV1) and similar proteins
    cl22851
    Location:580 → 641
    PHD_SF; PHD finger superfamily

  2. NM_001281735.1 → NP_001268664.1  zinc finger FYVE domain-containing protein 1 isoform 2

    See identical proteins and their annotated locations for NP_001268664.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate 5' exon structure, and thus differs in the 5' UTR and 5' coding region, compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (2) with a shorter N-terminus, compared to isoform 1. Both variants 2 and 4 encode the same isoform (2).
    Source sequence(s)
    AK098542, AL442663, AW070816, BU740588, BX339655, CK005173, HY248287
    Consensus CDS
    CCDS41969.1
    UniProtKB/Swiss-Prot
    Q9HBF4
    Related
    ENSP00000377757.2, ENST00000394207.6
    Conserved Domains (2) summary
    cd15734
    Location:296 → 356
    FYVE_ZFYV1; FYVE domains found in zinc finger FYVE domain-containing protein 1 (ZFYV1) and similar proteins
    cl22851
    Location:179 → 240
    PHD_SF; PHD finger superfamily

  3. NM_021260.4 → NP_067083.1  zinc finger FYVE domain-containing protein 1 isoform 1

    See identical proteins and their annotated locations for NP_067083.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AB046809, BC053520, HY248287
    Consensus CDS
    CCDS9811.1
    UniProtKB/Swiss-Prot
    J3KNL9, Q8WYX7, Q96K57, Q9BXP9, Q9HBF4, Q9HCI3
    UniProtKB/TrEMBL
    G3V5N8
    Related
    ENSP00000450742.1, ENST00000556143.6
    Conserved Domains (3) summary
    cd01851
    Location:174 → 410
    GBP; Guanylate-binding protein (GBP) family (N-terminal domain)
    cd15734
    Location:711 → 771
    FYVE_ZFYV1; FYVE domains found in zinc finger FYVE domain-containing protein 1 (ZFYV1) and similar proteins
    cl28890
    Location:594 → 655
    FYVE_like_SF; FYVE domain like superfamily

  4. NM_178441.2 → NP_848535.1  zinc finger FYVE domain-containing protein 1 isoform 2

    See identical proteins and their annotated locations for NP_848535.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate 5' exon structure, and thus differs in the 5' UTR and 5' coding region, compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (2) with a shorter N-terminus, compared to isoform 1. Both variants 2 and 4 encode the same isoform (2).
    Source sequence(s)
    AF311602, AI073571, AW070816, BX339655, CK005173, HY248287
    Consensus CDS
    CCDS41969.1
    UniProtKB/Swiss-Prot
    Q9HBF4
    Related
    ENSP00000452232.1, ENST00000555072.1
    Conserved Domains (2) summary
    cd15734
    Location:296 → 356
    FYVE_ZFYV1; FYVE domains found in zinc finger FYVE domain-containing protein 1 (ZFYV1) and similar proteins
    cl22851
    Location:179 → 240
    PHD_SF; PHD finger superfamily

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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    72969445..73027106 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047431482.1 → XP_047287438.1  zinc finger FYVE domain-containing protein 1 isoform X2

  2. XM_017021373.2 → XP_016876862.1  zinc finger FYVE domain-containing protein 1 isoform X2

    UniProtKB/Swiss-Prot
    Q9HBF4
    Conserved Domains (2) summary
    cd15734
    Location:296 → 356
    FYVE_ZFYV1; FYVE domains found in zinc finger FYVE domain-containing protein 1 (ZFYV1) and similar proteins
    cl22851
    Location:179 → 240
    PHD_SF; PHD finger superfamily

  3. XM_047431481.1 → XP_047287437.1  zinc finger FYVE domain-containing protein 1 isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    67175059..67232660 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054376226.1 → XP_054232201.1  zinc finger FYVE domain-containing protein 1 isoform X2

  2. XM_054376227.1 → XP_054232202.1  zinc finger FYVE domain-containing protein 1 isoform X2

  3. XM_054376225.1 → XP_054232200.1  zinc finger FYVE domain-containing protein 1 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9HBF4.1 GenPept UniProtKB/Swiss-Prot:Q9HBF4

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