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ZFYVE16 zinc finger FYVE-type containing 16 [ Homo sapiens (human) ]

Gene ID: 9765, updated on 8-Jul-2021

Summary

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Official Symbol
ZFYVE16provided by HGNC
Official Full Name
zinc finger FYVE-type containing 16provided by HGNC
Primary source
HGNC:HGNC:20756
See related
Ensembl:ENSG00000039319 MIM:608880
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
PPP1R69
Summary
This gene encodes an endosomal protein that belongs to the FYVE zinc finger family of proteins. The encoded protein is thought to regulate membrane trafficking in the endosome. This protein functions as a scaffold protein in the transforming growth factor-beta signaling pathway and is involved in positive and negative feedback regulation of the bone morphogenetic protein signaling pathway. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]
Expression
Ubiquitous expression in brain (RPKM 10.1), endometrium (RPKM 9.9) and 25 other tissues See more
Orthologs
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Genomic context

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See ZFYVE16 in Genome Data Viewer
Location:
5q14.1
Exon count:
24
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 5 NC_000005.10 (80407615..80483379)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (79703883..79779198)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene 12 Neighboring gene RNA, U6 small nuclear 211, pseudogene Neighboring gene family with sequence similarity 151 member B Neighboring gene RPS27A pseudogene 9 Neighboring gene ribosomal protein L7 pseudogene 24

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. Genetic Mutation that May Contribute to Failure of Prolapse Surgery in White Women: A Case-Control Study. St Louis S, et al. J Minim Invasive Gynecol, 2016 Jul-Aug. PMID 26944198
  2. EGF-induced tyrosine phosphorylation of Endofin is dependent on PI3K activity and proper localization to endosomes. Toy W, et al. Cell Signal, 2010 Mar. PMID 19887107
  3. Endofin, a FYVE domain protein, interacts with Smad4 and facilitates transforming growth factor-beta signaling. Chen YG, et al. J Biol Chem, 2007 Mar 30. PMID 17272273
  4. Inhibition of transforming growth factor-beta1-induced signaling and epithelial-to-mesenchymal transition by the Smad-binding peptide aptamer Trx-SARA. Zhao BM, et al. Mol Biol Cell, 2006 Sep. PMID 16775010, Free PMC Article
  5. Endofin, an endosomal FYVE domain protein. Seet LF, et al. J Biol Chem, 2001 Nov 9. PMID 11546807

See all (39) citations in PubMed

See citations in PubMed for homologs of this gene provided by HomoloGene

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Two SNPs located near the ZFYVE16 gene on chromosome 5 may have played a role in the early, multicompartment sacrocolpopexy failure.
    Title: Genetic Mutation that May Contribute to Failure of Prolapse Surgery in White Women: A Case-Control Study.
  2. Disruption of proper localization to the endosomes and the Y515 phosphorylation of Endofin enhanced MAPK activation suggesting that Endofin negatively modulates EGFR signaling following receptor endocytosis.
    Title: EGF-induced tyrosine phosphorylation of Endofin is dependent on PI3K activity and proper localization to endosomes.
  3. our study is the first to identify and validate Endofin, DCBLD2, and KIAA0582 as part of a complex EGF phosphotyrosine signaling network
    Title: Phosphoproteomics identified Endofin, DCBLD2, and KIAA0582 as novel tyrosine phosphorylation targets of EGF signaling and Iressa in human cancer cells.
  4. marked recruitment of TOM1 to endosomes was observed in cells overexpressing endofin or its carboxyl-terminal fragment
    Title: Endofin recruits TOM1 to endosomes.
  5. Facilitates TGF-beta signaling as a scaffold protein to promote the R-Smad-Smad4 complex formation by bringing Smad4 to the proximity of the receptor complex.
    Title: Endofin, a FYVE domain protein, interacts with Smad4 and facilitates transforming growth factor-beta signaling.
  6. The key mode of action of Trx-SARA was to reduce the level of Smad2 and Smad3 in complex with Smad4 after TGF-beta1 stimulation.
    Title: Inhibition of transforming growth factor-beta1-induced signaling and epithelial-to-mesenchymal transition by the Smad-binding peptide aptamer Trx-SARA.
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

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

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

  • KIAA0305, DKFZp686E13162

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables 1-phosphatidylinositol binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables phosphatidylinositol-3,4,5-trisphosphate binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in endosomal transport IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
involved_in endosomal transport IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein targeting to lysosome IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
involved_in protein targeting to lysosome IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of endocytosis TAS
Traceable Author Statement
more info
 PubMed 
involved_in signal transduction NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in vesicle organization NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in early endosome IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in early endosome membrane IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
located_in early endosome membrane TAS
Traceable Author Statement
more info
  
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
zinc finger FYVE domain-containing protein 16
Names
endosome-associated FYVE-domain protein
protein phosphatase 1, regulatory subunit 69
zinc finger, FYVE domain containing 16

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_001105251.4 → NP_001098721.2  zinc finger FYVE domain-containing protein 16 isoform a

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3 and 5 encode the same protein (isoform a).
    Source sequence(s)
    AC008771
    Consensus CDS
    CCDS4050.1
    Related
    ENSP00000423663.1, ENST00000510158.5
    Conserved Domains (2) summary
    cd15729
    Location:738 → 804
    FYVE_endofin; FYVE domain found in endofin and similar proteins
    pfam11979
    Location:1167 → 1515
    DUF3480; Domain of unknown function (DUF3480)

  2. NM_001284236.3 → NP_001271165.2  zinc finger FYVE domain-containing protein 16 isoform a

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2 ,3 and 5 encode the same protein (isoform a).
    Source sequence(s)
    AC008771
    Consensus CDS
    CCDS4050.1
    Related
    ENSP00000426848.1, ENST00000505560.5
    Conserved Domains (2) summary
    cd15729
    Location:738 → 804
    FYVE_endofin; FYVE domain found in endofin and similar proteins
    pfam11979
    Location:1167 → 1515
    DUF3480; Domain of unknown function (DUF3480)

  3. NM_001284237.2 → NP_001271166.2  zinc finger FYVE domain-containing protein 16 isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks several exons in the 3' coding region and contains a 3' terminal exon that extends past a splice site that is used in variant 1 resulting in an early stop codon, and a different 3' UTR, compared to variant 1. The encoded protein (isoform b) has a distinct C-terminus and is shorter than isoform a.
    Source sequence(s)
    AC008771
    Related
    ENST00000510995.1
    Conserved Domains (1) summary
    cd15729
    Location:738 → 804
    FYVE_endofin; FYVE domain found in endofin and similar proteins

  4. NM_001349434.2 → NP_001336363.2  zinc finger FYVE domain-containing protein 16 isoform a

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3 and 5 encode the same protein (isoform a).
    Source sequence(s)
    AC008771
    Consensus CDS
    CCDS4050.1
    Conserved Domains (2) summary
    cd15729
    Location:738 → 804
    FYVE_endofin; FYVE domain found in endofin and similar proteins
    pfam11979
    Location:1167 → 1515
    DUF3480; Domain of unknown function (DUF3480)

  5. NM_014733.6 → NP_055548.4  zinc finger FYVE domain-containing protein 16 isoform a

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (a). Variants 1, 2, 3 and 5 encode the same protein (isoform a).
    Source sequence(s)
    AC008771
    Consensus CDS
    CCDS4050.1
    Related
    ENSP00000337159.5, ENST00000338008.9
    Conserved Domains (2) summary
    cd15729
    Location:738 → 804
    FYVE_endofin; FYVE domain found in endofin and similar proteins
    pfam11979
    Location:1167 → 1515
    DUF3480; Domain of unknown function (DUF3480)

RNA

  1. NR_146172.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) contains three alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC008771

  2. NR_146173.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) contains two alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC008771

  3. NR_146174.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) contains two alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC008771

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p13 Primary Assembly

    Range
    80407615..80483379
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005248632.4 → XP_005248689.1  zinc finger FYVE domain-containing protein 16 isoform X1

    See identical proteins and their annotated locations for XP_005248689.1

    UniProtKB/Swiss-Prot
    Q7Z3T8
    Conserved Domains (2) summary
    cd15729
    Location:738 → 804
    FYVE_endofin; FYVE domain found in endofin and similar proteins
    pfam11979
    Location:1167 → 1515
    DUF3480; Domain of unknown function (DUF3480)

  2. XM_017010092.2 → XP_016865581.1  zinc finger FYVE domain-containing protein 16 isoform X1

    UniProtKB/Swiss-Prot
    Q7Z3T8
    Conserved Domains (2) summary
    cd15729
    Location:738 → 804
    FYVE_endofin; FYVE domain found in endofin and similar proteins
    pfam11979
    Location:1167 → 1515
    DUF3480; Domain of unknown function (DUF3480)

  3. XM_017010091.1 → XP_016865580.1  zinc finger FYVE domain-containing protein 16 isoform X1

    UniProtKB/Swiss-Prot
    Q7Z3T8
    Conserved Domains (2) summary
    cd15729
    Location:738 → 804
    FYVE_endofin; FYVE domain found in endofin and similar proteins
    pfam11979
    Location:1167 → 1515
    DUF3480; Domain of unknown function (DUF3480)

  4. XM_024446270.1 → XP_024302038.1  zinc finger FYVE domain-containing protein 16 isoform X1

    Conserved Domains (2) summary
    cd15729
    Location:738 → 804
    FYVE_endofin; FYVE domain found in endofin and similar proteins
    pfam11979
    Location:1167 → 1515
    DUF3480; Domain of unknown function (DUF3480)

  5. XM_024446273.1 → XP_024302041.1  zinc finger FYVE domain-containing protein 16 isoform X2

    Conserved Domains (1) summary
    pfam11979
    Location:355 → 703
    DUF3480; Domain of unknown function (DUF3480)

  6. XM_024446271.1 → XP_024302039.1  zinc finger FYVE domain-containing protein 16 isoform X2

    Conserved Domains (1) summary
    pfam11979
    Location:355 → 703
    DUF3480; Domain of unknown function (DUF3480)

  7. XM_024446272.1 → XP_024302040.1  zinc finger FYVE domain-containing protein 16 isoform X2

    Conserved Domains (1) summary
    pfam11979
    Location:355 → 703
    DUF3480; Domain of unknown function (DUF3480)

  8. XM_017010096.1 → XP_016865585.1  zinc finger FYVE domain-containing protein 16 isoform X3

    Related
    ENST00000511829.5

RNA

  1. XR_001742375.1 RNA Sequence

  2. XR_001742377.2 RNA Sequence

  3. XR_001742376.2 RNA Sequence

  4. XR_001742380.2 RNA Sequence

  5. XR_001742373.1 RNA Sequence

  6. XR_001742382.2 RNA Sequence

  7. XR_001742379.2 RNA Sequence

  8. XR_001742384.1 RNA Sequence

  9. XR_001742381.1 RNA Sequence

  10. XR_002956199.1 RNA Sequence

  11. XR_001742378.2 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q7Z3T8.3 GenPept UniProtKB/Swiss-Prot:Q7Z3T8

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