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ZFYVE9 zinc finger FYVE-type containing 9 [ Homo sapiens (human) ]

Gene ID: 9372, updated on 17-Jun-2019

Summary

Official Symbol
ZFYVE9provided by HGNC
Official Full Name
zinc finger FYVE-type containing 9provided by HGNC
Primary source
HGNC:HGNC:6775
See related
Ensembl:ENSG00000157077 MIM:603755
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
NSP; SARA; MADHIP; SMADIP; PPP1R173
Summary
This gene encodes a double zinc finger motif-containing protein that participates in the transforming growth factor-beta (TGFB) signalling pathway. The encoded protein interacts directly with SMAD2 and SMAD3, and recruits SMAD2 to the TGFB receptor. There are multiple pseudogenes for this gene on chromosomes 2, 15, and X. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2013]
Expression
Ubiquitous expression in brain (RPKM 8.0), thyroid (RPKM 7.9) and 25 other tissues See more
Orthologs

Genomic context

See ZFYVE9 in Genome Data Viewer
Location:
1p32.3
Exon count:
21
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (52142001..52348664)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (52607678..52812358)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene basic transcription factor 3 like 4 Neighboring gene uncharacterized LOC107984956 Neighboring gene alcohol dehydrogenase 5 (class III), chi polypeptide pseudogene Neighboring gene RNA, 7SL, cytoplasmic 788, pseudogene Neighboring gene TRA2A pseudogene Neighboring gene PDCL3 pseudogene 6 Neighboring gene ribosomal protein L9 pseudogene 12 Neighboring gene DnaJ heat shock protein family (Hsp40) member C19 pseudogene 7 Neighboring gene anaphase promoting complex subunit 10 pseudogene 1 Neighboring gene coiled-coil and C2 domain containing 1B Neighboring gene phospholipase A2 group XIIA pseudogene 1 Neighboring gene origin recognition complex subunit 1

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Nef nef Genome-wide shRNA screening identifies ZFYVE9, which is required for HIV-1 Nef-induced downregulation of CD4 in HeLa CD4+ cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Disease, organism-specific biosystem (from REACTOME)
    Disease, organism-specific biosystemBiological processes are captured in Reactome by identifying the molecules (DNA, RNA, protein, small molecules) involved in them and describing the details of their interactions. From this molecular ...
  • Diseases of signal transduction, organism-specific biosystem (from REACTOME)
    Diseases of signal transduction, organism-specific biosystemSignaling processes are central to human physiology (e.g., Pires-da Silva & Sommer 2003), and their disruption by either germ-line and somatic mutation can lead to serious disease. Here, the molecula...
  • Downregulation of TGF-beta receptor signaling, organism-specific biosystem (from REACTOME)
    Downregulation of TGF-beta receptor signaling, organism-specific biosystemTGF-beta receptor signaling is downregulated by proteasome and lysosome-mediated degradation of ubiquitinated TGFBR1, SMAD2 and SMAD3, as well as by dephosphorylation of TGFBR1, SMAD2 and SMAD3. In t...
  • Endocytosis, organism-specific biosystem (from KEGG)
    Endocytosis, organism-specific biosystemEndocytosis is a mechanism for cells to remove ligands, nutrients, and plasma membrane (PM) proteins, and lipids from the cell surface, bringing them into the cell interior. Transmembrane proteins en...
  • Endocytosis, conserved biosystem (from KEGG)
    Endocytosis, conserved biosystemEndocytosis is a mechanism for cells to remove ligands, nutrients, and plasma membrane (PM) proteins, and lipids from the cell surface, bringing them into the cell interior. Transmembrane proteins en...
  • Loss of Function of SMAD2/3 in Cancer, organism-specific biosystem (from REACTOME)
    Loss of Function of SMAD2/3 in Cancer, organism-specific biosystemLoss-of-function of SMAD2 and SMAD3 in cancer occurs less frequently than the loss of SMAD4 function and was studied in most detail in colorectal cancer (Fleming et al. 2013). Similarly to SMAD4, cod...
  • Loss of Function of TGFBR1 in Cancer, organism-specific biosystem (from REACTOME)
    Loss of Function of TGFBR1 in Cancer, organism-specific biosystemTGF-beta receptor 1 (TGFBR1) loss-of-function is a less frequent mechanism for inactivation of TGF-beta signaling in cancer compared to SMAD4 and TGFBR2 inactivation. Genomic deletion of TGFBR1 locus...
  • SMAD2/3 MH2 Domain Mutants in Cancer, organism-specific biosystem (from REACTOME)
    SMAD2/3 MH2 Domain Mutants in Cancer, organism-specific biosystemMutations in the MH2 domain of SMAD2 and SMAD3 affect their ability to form heterotrimers with SMAD4, thereby impairing TGF-beta signaling (Fleming et al. 2013).The SMAD2 and SMAD3 MH2 domain residue...
  • SMAD2/3 Phosphorylation Motif Mutants in Cancer, organism-specific biosystem (from REACTOME)
    SMAD2/3 Phosphorylation Motif Mutants in Cancer, organism-specific biosystemThe conserved phosphorylation motif Ser-Ser-X-Ser at the C-terminus of SMAD2 and SMAD3 is subject to disruptive mutations in cancer. The last two serine residues in this conserved motif, namely Ser46...
  • Signal Transduction, organism-specific biosystem (from REACTOME)
    Signal Transduction, organism-specific biosystemSignal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such a...
  • Signaling by TGF-beta Receptor Complex, organism-specific biosystem (from REACTOME)
    Signaling by TGF-beta Receptor Complex, organism-specific biosystemThe TGF-beta/BMP pathway incorporates several signaling pathways that share most, but not all, components of a central signal transduction engine. The general signaling scheme is rather simple: upon ...
  • Signaling by TGF-beta Receptor Complex in Cancer, organism-specific biosystem (from REACTOME)
    Signaling by TGF-beta Receptor Complex in Cancer, organism-specific biosystemSignaling by the TGF-beta receptor complex is tumor suppressive, as it inhibits cell growth and promotes cell differentiation and apoptosis (Shipley et al. 1986, Hannon et al. 1994, Datto et al. 1995...
  • TGF-beta Receptor Signaling, organism-specific biosystem (from WikiPathways)
    TGF-beta Receptor Signaling, organism-specific biosystemThe Transforming growth factor beta (TGFβ) signaling pathway is involved in many cellular processes in both the adult organism and the developing embryo including cell growth, cell differentiat...
  • TGF-beta Signaling Pathway, organism-specific biosystem (from WikiPathways)
    TGF-beta Signaling Pathway, organism-specific biosystemThe signal transduction mechanisms underlying the pathophysiological activities of transforming growth factor-? (TGF-?) have been extensively studied since its discovery nearly 30 years ago. TGF-? li...
  • TGF-beta receptor signaling, organism-specific biosystem (from Pathway Interaction Database)
    TGF-beta receptor signaling, organism-specific biosystem
    TGF-beta receptor signaling
  • TGF-beta receptor signaling activates SMADs, organism-specific biosystem (from REACTOME)
    TGF-beta receptor signaling activates SMADs, organism-specific biosystemBinding of transforming growth factor beta 1 (TGF beta 1, i.e. TGFB1) to TGF beta receptor type 2 (TGFBR2) activates TGF beta receptor signaling cascade. TGFB1 is posttranslationally processed by fur...
  • TGF-beta signaling pathway, organism-specific biosystem (from KEGG)
    TGF-beta signaling pathway, organism-specific biosystemThe transforming growth factor-beta (TGF-beta) family members, which include TGF-betas, activins and bone morphogenetic proteins (BMPs), are structurally related secreted cytokines found in species r...
  • TGF-beta signaling pathway, conserved biosystem (from KEGG)
    TGF-beta signaling pathway, conserved biosystemThe transforming growth factor-beta (TGF-beta) family members, which include TGF-betas, activins and bone morphogenetic proteins (BMPs), are structurally related secreted cytokines found in species r...
  • TGFBR1 KD Mutants in Cancer, organism-specific biosystem (from REACTOME)
    TGFBR1 KD Mutants in Cancer, organism-specific biosystemMutations in the kinase domain (KD) of TGF-beta receptor 1 (TGFBR1) have been found in Ferguson-Smith tumor i.e. multiple self-healing squamous epithelioma - MSSE (Goudie et al. 2011), breast cancer ...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
1-phosphatidylinositol binding IDA
Inferred from Direct Assay
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein domain specific binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
endocytosis NAS
Non-traceable Author Statement
more info
PubMed 
endosomal transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
transforming growth factor beta receptor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
transforming growth factor beta receptor signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
transforming growth factor beta receptor signaling pathway NAS
Non-traceable Author Statement
more info
PubMed 
transforming growth factor beta receptor signaling pathway TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
cytosol IDA
Inferred from Direct Assay
more info
 
early endosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
early endosome NAS
Non-traceable Author Statement
more info
PubMed 
early endosome membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
early endosome membrane IDA
Inferred from Direct Assay
more info
PubMed 
early endosome membrane TAS
Traceable Author Statement
more info
 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
protein-containing complex IMP
Inferred from Mutant Phenotype
more info
PubMed 

General protein information

Preferred Names
zinc finger FYVE domain-containing protein 9
Names
MAD, mothers against decapentaplegic homolog interacting protein, receptor activation anchor
MADH-interacting protein
novel serine protease
protein phosphatase 1, regulatory subunit 173
smad anchor for receptor activation
zinc finger, FYVE domain containing 9

NCBI Reference Sequences (RefSeq)

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_004799.3NP_004790.2  zinc finger FYVE domain-containing protein 9 isoform 3

    See identical proteins and their annotated locations for NP_004790.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) represents the longer transcript and encodes the longer isoform (3).
    Source sequence(s)
    AF130419, AL139156, BC032680, DR005493
    Consensus CDS
    CCDS563.1
    UniProtKB/Swiss-Prot
    O95405
    Related
    ENSP00000287727.3, ENST00000287727.7
    Conserved Domains (3) summary
    cd15729
    Location:690757
    FYVE_endofin; FYVE domain found in endofin and similar proteins
    pfam11409
    Location:773811
    SARA; Smad anchor for receptor activation (SARA)
    pfam11979
    Location:10481400
    DUF3480; Domain of unknown function (DUF3480)
  2. NM_007324.4NP_015563.2  zinc finger FYVE domain-containing protein 9 isoform 1

    See identical proteins and their annotated locations for NP_015563.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) lacks an in-frame exon, compared to variant 3. The encoded isoform (1) is shorter than isoform 3.
    Source sequence(s)
    AF130419, AL139156, BC032680, DR005493
    Consensus CDS
    CCDS564.1
    UniProtKB/Swiss-Prot
    O95405
    Related
    ENSP00000349737.2, ENST00000357206.6
    Conserved Domains (2) summary
    cd15729
    Location:690757
    FYVE_endofin; FYVE domain found in endofin and similar proteins
    pfam11979
    Location:9891341
    DUF3480; Domain of unknown function (DUF3480)

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    52142001..52348664
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017002845.1XP_016858334.1  zinc finger FYVE domain-containing protein 9 isoform X2

  2. XM_011542437.2XP_011540739.1  zinc finger FYVE domain-containing protein 9 isoform X1

    See identical proteins and their annotated locations for XP_011540739.1

    UniProtKB/Swiss-Prot
    O95405
    Conserved Domains (3) summary
    cd15729
    Location:690757
    FYVE_endofin; FYVE domain found in endofin and similar proteins
    pfam11409
    Location:773811
    SARA; Smad anchor for receptor activation (SARA)
    pfam11979
    Location:10481400
    DUF3480; Domain of unknown function (DUF3480)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_007323.1: Suppressed sequence

    Description
    NM_007323.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
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