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

    Gene ID: 9372, updated on 28-Oct-2024

    Summary

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    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; AllianceGenome:HGNC:6775
    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
    mouse all
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    Genomic context

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    See ZFYVE9 in Genome Data Viewer
    Location:
    1p32.3
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (52142089..52346634)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (52023594..52228099)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (52607761..52812306)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene thioredoxin domain containing 12 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:52520887-52521291 Neighboring gene TXNDC12 antisense RNA 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:52521457-52522170 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:52522171-52522882 Neighboring gene basic transcription factor 3 like 4 Neighboring gene collagen alpha-2(I) chain-like Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 885 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:52613533-52614066 Neighboring gene alcohol dehydrogenase 5 (class III), chi polypeptide pseudogene Neighboring gene RNA, 7SL, cytoplasmic 788, pseudogene Neighboring gene TRA2A pseudogene Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:52647543-52648512 Neighboring gene MPRA-validated peak225 silencer Neighboring gene PDCL3 pseudogene 6 Neighboring gene ribosomal protein L9 pseudogene 12 Neighboring gene MPRA-validated peak226 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr1:52683789-52683961 Neighboring gene DnaJ heat shock protein family (Hsp40) member C19 pseudogene 7 Neighboring gene anaphase promoting complex subunit 10 pseudogene 1 Neighboring gene NANOG-H3K27ac hESC enhancers GRCh37_chr1:52815874-52816848 and GRCh37_chr1:52816849-52817822 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:52822843-52823344 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 886 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 887 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1031 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 888 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 889 Neighboring gene phospholipase A2 group XIIA pseudogene 1 Neighboring gene coiled-coil and C2 domain containing 1B

    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. Identification of a novel serine protease-like molecule in human brain. Meckelein B, et al. Brain Res Mol Brain Res, 1998 Apr. PMID 9582421
    2. Smad anchor for receptor activation (SARA) in TGF-beta signaling. Tang WB, et al. Front Biosci (Elite Ed), 2010 Jun 1. PMID 20515759
    3. [SARA expression in high glucose induced epithelium to mesenchymal transition of proximal tubule cells]. Tang W, et al. Zhong Nan Da Xue Xue Bao Yi Xue Ban, 2010 Dec. PMID 21200089
    4. Expression, purification, and functional characterization of recombinant PTD-SARA. Huang C, et al. Acta Biochim Biophys Sin (Shanghai), 2011 Feb. PMID 21266541
    5. Longitudinal changes of SARA scale in Friedreich ataxia: Strong influence of baseline score and age at onset. Porcu L, et al. Ann Clin Transl Neurol, 2023 Nov. PMID 37641437, Free PMC Article

    See all (69) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Longitudinal changes of SARA scale in Friedreich ataxia: Strong influence of baseline score and age at onset.
      Title: Longitudinal changes of SARA scale in Friedreich ataxia: Strong influence of baseline score and age at onset.
    2. SMURF2 and SMAD7 induce SARA degradation via the proteasome.
      Title: SMURF2 and SMAD7 induce SARA degradation via the proteasome.
    3. SARA expression was significantly upregulated in the temporal cortex of patients with temporal lobe epilepsy.
      Title: Smad Anchor for Receptor Activation and Phospho-Smad3 Were Upregulated in Patients with Temporal Lobe Epilepsy.
    4. we have identified endofin as an important signalling component required for basal and BMP-induced hepcidin expression.
      Title: Endofin, a novel BMP-SMAD regulator of the iron-regulatory hormone, hepcidin.
    5. SARA may serve as a potential novel target in pre-Epithelial-mesenchymal transition states for the amelioration renal fibrosis seen in chronic kidney diseases
      Title: Smad Anchor for Receptor Activation Regulates High Glucose-Induced EMT via Modulation of Smad2 and Smad3 Activities in Renal Tubular Epithelial Cells.
    6. PI3K-C2a was also required for TGFb receptor-mediated formation of SARA-Smad2/3 complex
      Title: Phosphatidylinositol 3-kinase class II α-isoform PI3K-C2α is required for transforming growth factor β-induced Smad signaling in endothelial cells.
    7. The negative influence that perturbation of RNF11 and SARA levels exerts on the lysosomal degradation of EGFRs could underscore the significance of overexpression of RNF11 in certain cancers.
      Title: SARA and RNF11 interact with each other and ESCRT-0 core proteins and regulate degradative EGFR trafficking.
    8. TGF-beta1 can induce epithelial-to-mesenchymal transition through reduction in SARA expression, SARA is also basally regulated by its interaction with PI3K.
      Title: Phosphatidylinositol 3-kinase and Rab5 GTPase inversely regulate the Smad anchor for receptor activation (SARA) protein independently of transforming growth factor-β1.
    9. no correlation between SARA expression and the levels of TGF-beta1-induced phosphorylation of Smads in various B-cell lymphomas
      Title: SARA is dispensable for functional TGF-β signaling.
    10. SARA binds to ERBIN using a new domain, which we have called the ERBID (ERBIN-binding domain)
      Title: ERBIN is a new SARA-interacting protein: competition between SARA and SMAD2 and SMAD3 for binding to ERBIN.
    Submit: New GeneRIF Correction See all GeneRIFs (18)

    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

    HIV-1 interactions

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    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 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

    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 protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein domain specific binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in endocytosis NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in endosomal transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in transforming growth factor beta receptor signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in transforming growth factor beta receptor signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in transforming growth factor beta receptor signaling pathway 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 NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    is_active_in early endosome membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in early endosome membrane IDA
    Inferred from Direct Assay
    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
    		  
    part_of protein-containing complex IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 

    General protein information

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    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)

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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_004799.4 → NP_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, Q5T0F6, Q5T0F7, Q9UNE1, Q9Y5R7
      UniProtKB/TrEMBL
      Q59GI4
      Related
      ENSP00000287727.3, ENST00000287727.8
      Conserved Domains (3) summary
      cd15729
      Location:690 → 757
      FYVE_endofin; FYVE domain found in endofin and similar proteins
      pfam11409
      Location:773 → 811
      SARA; Smad anchor for receptor activation (SARA)
      pfam11979
      Location:1048 → 1400
      DUF3480; Domain of unknown function (DUF3480)

    2. NM_007324.5 → NP_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/TrEMBL
      Q59GI4
      Related
      ENSP00000349737.2, ENST00000357206.6
      Conserved Domains (2) summary
      cd15729
      Location:690 → 757
      FYVE_endofin; FYVE domain found in endofin and similar proteins
      pfam11979
      Location:989 → 1341
      DUF3480; Domain of unknown function (DUF3480)

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      52142089..52346634
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047434682.1 → XP_047290638.1  zinc finger FYVE domain-containing protein 9 isoform X3

    2. XM_047434674.1 → XP_047290630.1  zinc finger FYVE domain-containing protein 9 isoform X2

    3. XM_011542437.3 → XP_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, Q5T0F6, Q5T0F7, Q9UNE1, Q9Y5R7
      UniProtKB/TrEMBL
      Q59GI4
      Related
      ENSP00000360647.1, ENST00000371591.2
      Conserved Domains (3) summary
      cd15729
      Location:690 → 757
      FYVE_endofin; FYVE domain found in endofin and similar proteins
      pfam11409
      Location:773 → 811
      SARA; Smad anchor for receptor activation (SARA)
      pfam11979
      Location:1048 → 1400
      DUF3480; Domain of unknown function (DUF3480)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      52023594..52228099
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054339675.1 → XP_054195650.1  zinc finger FYVE domain-containing protein 9 isoform X3

    2. XM_054339673.1 → XP_054195648.1  zinc finger FYVE domain-containing protein 9 isoform X1

      UniProtKB/Swiss-Prot
      O95405, Q5T0F6, Q5T0F7, Q9UNE1, Q9Y5R7

    3. XM_054339674.1 → XP_054195649.1  zinc finger FYVE domain-containing protein 9 isoform X2

    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.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O95405.2 GenPept UniProtKB/Swiss-Prot:O95405

    Gene LinkOut

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

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