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    MTMR4 myotubularin related protein 4 [ Homo sapiens (human) ]

    Gene ID: 9110, updated on 2-Nov-2024

    Summary

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    Official Symbol
    MTMR4provided by HGNC
    Official Full Name
    myotubularin related protein 4provided by HGNC
    Primary source
    HGNC:HGNC:7452
    See related
    Ensembl:ENSG00000108389 MIM:603559; AllianceGenome:HGNC:7452
    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
    ZFYVE11; FYVE-DSP2
    Summary
    Enables several functions, including R-SMAD binding activity; phosphatidylinositol phosphate phosphatase activity; and protein phosphatase binding activity. Involved in several processes, including midbody abscission; negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway; and phosphatidylinositol dephosphorylation. Located in early endosome membrane; late endosome membrane; and recycling endosome membrane. Is active in early phagosome membrane and endosome membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in testis (RPKM 12.1), brain (RPKM 10.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See MTMR4 in Genome Data Viewer
    Location:
    17q22
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (58489537..58519047, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (59357413..59386918, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (56566898..56595241, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene TSPOAP1, SUPT4H1 and RNF43 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8768 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr17:56430343-56430878 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12482 Neighboring gene ring finger protein 43 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:56471542-56472741 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr17:56475825-56476680 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr17:56523372-56523966 Neighboring gene heat shock transcription factor 5 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8769 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8770 Neighboring gene SET pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12483 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8771 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:56595757-56596502 Neighboring gene SEPTIN4 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:56606301-56606801 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:56608575-56609075 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8772 Neighboring gene septin 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12485 Neighboring gene MPRA-validated peak2918 silencer Neighboring gene uncharacterized LOC107985048 Neighboring gene testis expressed 14, intercellular bridge forming factor

    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. Crystallization and preliminary X-ray crystallographic analysis of the PH-GRAM domain of human MTMR4. Lee JU, et al. Acta Crystallogr F Struct Biol Commun, 2014 Sep. PMID 25195910, Free PMC Article
    2. MTMR4 Is Required for the Stability of the Salmonella-Containing Vacuole. Teo WX, et al. Front Cell Infect Microbiol, 2016. PMID 27625994, Free PMC Article
    3. MTMR4, a phosphoinositide-specific 3'-phosphatase, regulates TFEB activity and the endocytic and autophagic pathways. Pham HQ, et al. Genes Cells, 2018 Jul 2. PMID 29962048
    4. Genome-wide association scan for childhood caries implicates novel genes. Shaffer JR, et al. J Dent Res, 2011 Dec. PMID 21940522, Free PMC Article
    5. The myotubularin phosphatase MTMR4 regulates sorting from early endosomes. Naughtin MJ, et al. J Cell Sci, 2010 Sep 15. PMID 20736309

    See all (43) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. MTMR4 SNVs modulate ion channel degradation and clinical severity in congenital long QT syndrome: insights in the mechanism of action of protective modifier genes.
      Title: MTMR4 SNVs modulate ion channel degradation and clinical severity in congenital long QT syndrome: insights in the mechanism of action of protective modifier genes.
    2. Here the authors demonstrate that green fluorescent protein-tagged MTMR4 is recruited to the Salmonella-containing vacuole and infection of cells depleted of endogenous MTMR4 results in a decrease in viable intracellular Salmonella.
      Title: MTMR4 Is Required for the Stability of the Salmonella-Containing Vacuole.
    3. myotubularin-related protein 3 and myotubularin-related protein 4 may act as a bridge between CEP55 and polo-like kinase 1, ensuring proper CEP55 phosphorylation and regulating CEP55 recruitment to the midbody.
      Title: Myotubularin-related proteins 3 and 4 interact with polo-like kinase 1 and centrosomal protein of 55 kDa to ensure proper abscission.
    4. the PH-GRAM domain of human MTMR4 was cloned, overexpressed in Escherichia coli, purified and crystallized by the vapour-diffusion method
      Title: Crystallization and preliminary X-ray crystallographic analysis of the PH-GRAM domain of human MTMR4.
    5. MTMR4 is a necessary negative modulator for the homeostasis of BMP/Dpp signaling
      Title: Myotubularin-related protein 4 (MTMR4) attenuates BMP/Dpp signaling by dephosphorylation of Smad proteins.
    6. MTMR4 localizes at the interface of early and recycling endosomes to regulate trafficking.
      Title: The myotubularin phosphatase MTMR4 regulates sorting from early endosomes.
    7. MTMR4 belongs to the myotubularin family of phosphoinositides phosphatases
      Title: Characterization of the myotubularin dual specificity phosphatase gene family from yeast to human.
    8. MTMR4 plays an important role in preventing the overactivation of TGFbeta signaling by dephosphorylating activated R-Smads that have been trafficked to early endosomes
      Title: MTMR4 attenuates transforming growth factor beta (TGFbeta) signaling by dephosphorylating R-Smads in endosomes.
    9. Observational study of gene-disease association. (HuGE Navigator)
      Title: Phosphoinositide cycle gene polymorphisms affect the plasma lipid profile in the Quebec Family Study.
    10. Data found that hMTMR4 (human MTMR4) and Nedd4 co-immunoprecipitated and co-localized to late endosomes.
      Title: The inositol phosphatase MTMR4 is a novel target of the ubiquitin ligase Nedd4.
    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 scan for childhood caries implicates novel genes.
    EBI GWAS Catalog
    Genome-wide association study of vitamin D levels in children: replication in the Western Australian Pregnancy Cohort (Raine) study.
    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

    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

    • KIAA0647

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables R-SMAD binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables molecular adaptor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity TAS
    Traceable Author Statement
    more info
    		  
    enables phosphatidylinositol-3-phosphate phosphatase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables phosphatidylinositol-3-phosphate phosphatase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables phosphatidylinositol-3-phosphate phosphatase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables phosphatidylinositol-3-phosphate phosphatase activity TAS
    Traceable Author Statement
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein phosphatase binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein phosphatase binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein serine/threonine phosphatase activity TAS
    Traceable Author Statement
    more info
    		  
    enables protein tyrosine phosphatase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in midbody abscission IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of BMP signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of endocytic recycling IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of transforming growth factor beta receptor signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of transforming growth factor beta receptor signaling pathway TAS
    Traceable Author Statement
    more info
    		  
    involved_in phagosome maturation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in phosphatidylinositol biosynthetic process TAS
    Traceable Author Statement
    more info
    		  
    involved_in phosphatidylinositol dephosphorylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in phosphatidylinositol dephosphorylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in phosphatidylinositol dephosphorylation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of autophagy IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    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
    		  
    is_active_in early phagosome membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in endosome membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in extracellular space HDA PubMed 
    located_in late endosome membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in recycling endosome membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    phosphatidylinositol-3,5-bisphosphate 3-phosphatase MTMR4; myotubularin-related protein 4
    Names
    FYVE domain-containing dual specificity protein phosphatase 2
    phosphatidylinositol-3,5-bisphosphate 3-phosphatase
    zinc finger FYVE domain-containing protein 11
    zinc finger, FYVE domain containing 11
    NP_001364995.1
    NP_001364996.1
    NP_004678.3
    XP_005257843.1
    XP_006722231.1
    XP_011523762.1
    XP_047292975.1
    XP_054173704.1
    XP_054173705.1
    XP_054173706.1
    XP_054173707.1
    XP_054173708.1

    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_001378066.1 → NP_001364995.1  phosphatidylinositol-3,5-bisphosphate 3-phosphatase MTMR4 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC005666
      UniProtKB/TrEMBL
      J3QR65
      Conserved Domains (3) summary
      cd13342
      Location:27 → 140
      PH-GRAM_MTMR4; Myotubularian (MTM) related 4 protein (MTMR4) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain
      cd15733
      Location:1115 → 1174
      FYVE_MTMR4; FYVE domain found in myotubularin-related protein 4 (MTMR4) and similar proteins
      cd14587
      Location:176 → 483
      PTP-MTMR4; protein tyrosine phosphatase-like domain of myotubularin related phosphoinositide phosphatase 4

    2. NM_001378067.1 → NP_001364996.1  phosphatidylinositol-3,5-bisphosphate 3-phosphatase MTMR4 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC005666
      Consensus CDS
      CCDS92367.1
      UniProtKB/TrEMBL
      A0A804HJV7, J3QR65
      Related
      ENSP00000507664.1, ENST00000682306.1
      Conserved Domains (3) summary
      cd13342
      Location:37 → 150
      PH-GRAM_MTMR4; Myotubularian (MTM) related 4 protein (MTMR4) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain
      cd15733
      Location:1125 → 1184
      FYVE_MTMR4; FYVE domain found in myotubularin-related protein 4 (MTMR4) and similar proteins
      cd14587
      Location:186 → 493
      PTP-MTMR4; protein tyrosine phosphatase-like domain of myotubularin related phosphoinositide phosphatase 4

    3. NM_004687.5 → NP_004678.3  phosphatidylinositol-3,5-bisphosphate 3-phosphatase MTMR4 isoform 1

      See identical proteins and their annotated locations for NP_004678.3

      Status: VALIDATED

      Source sequence(s)
      AB014547, BC035609, DR003190
      Consensus CDS
      CCDS11608.1
      UniProtKB/Swiss-Prot
      D3DTZ6, Q8IV27, Q9NYA4, Q9Y4D5
      UniProtKB/TrEMBL
      J3QR65
      Related
      ENSP00000325285.5, ENST00000323456.9
      Conserved Domains (3) summary
      cd13342
      Location:23 → 136
      PH-GRAM_MTMR4; Myotubularian (MTM) related 4 protein (MTMR4) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain
      cd15733
      Location:1111 → 1170
      FYVE_MTMR4; FYVE domain found in myotubularin-related protein 4 (MTMR4) and similar proteins
      pfam06602
      Location:127 → 519
      Myotub-related; Myotubularin-like phosphatase domain

    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_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      58489537..58519047 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006722168.5 → XP_006722231.1  myotubularin-related protein 4 isoform X2

      See identical proteins and their annotated locations for XP_006722231.1

      UniProtKB/Swiss-Prot
      D3DTZ6, Q8IV27, Q9NYA4, Q9Y4D5
      UniProtKB/TrEMBL
      J3QR65
      Conserved Domains (3) summary
      cd13342
      Location:23 → 136
      PH-GRAM_MTMR4; Myotubularian (MTM) related 4 protein (MTMR4) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain
      cd15733
      Location:1111 → 1170
      FYVE_MTMR4; FYVE domain found in myotubularin-related protein 4 (MTMR4) and similar proteins
      pfam06602
      Location:127 → 519
      Myotub-related; Myotubularin-like phosphatase domain

    2. XM_047437019.1 → XP_047292975.1  myotubularin-related protein 4 isoform X2

      UniProtKB/Swiss-Prot
      D3DTZ6, Q8IV27, Q9NYA4, Q9Y4D5

    3. XM_005257786.6 → XP_005257843.1  myotubularin-related protein 4 isoform X2

      See identical proteins and their annotated locations for XP_005257843.1

      UniProtKB/Swiss-Prot
      D3DTZ6, Q8IV27, Q9NYA4, Q9Y4D5
      UniProtKB/TrEMBL
      J3QR65
      Conserved Domains (3) summary
      cd13342
      Location:23 → 136
      PH-GRAM_MTMR4; Myotubularian (MTM) related 4 protein (MTMR4) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain
      cd15733
      Location:1111 → 1170
      FYVE_MTMR4; FYVE domain found in myotubularin-related protein 4 (MTMR4) and similar proteins
      pfam06602
      Location:127 → 519
      Myotub-related; Myotubularin-like phosphatase domain

    4. XM_011525460.4 → XP_011523762.1  myotubularin-related protein 4 isoform X1

      See identical proteins and their annotated locations for XP_011523762.1

      UniProtKB/TrEMBL
      J3QR65
      Conserved Domains (3) summary
      cd13342
      Location:27 → 140
      PH-GRAM_MTMR4; Myotubularian (MTM) related 4 protein (MTMR4) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain
      cd15733
      Location:1115 → 1174
      FYVE_MTMR4; FYVE domain found in myotubularin-related protein 4 (MTMR4) and similar proteins
      cd14587
      Location:176 → 483
      PTP-MTMR4; protein tyrosine phosphatase-like domain of myotubularin related phosphoinositide phosphatase 4

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      59357413..59386918 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054317732.1 → XP_054173707.1  myotubularin-related protein 4 isoform X2

    2. XM_054317731.1 → XP_054173706.1  myotubularin-related protein 4 isoform X2

    3. XM_054317733.1 → XP_054173708.1  myotubularin-related protein 4 isoform X2

    4. XM_054317729.1 → XP_054173704.1  myotubularin-related protein 4 isoform X1

    5. XM_054317730.1 → XP_054173705.1  myotubularin-related protein 4 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NYA4.2 GenPept UniProtKB/Swiss-Prot:Q9NYA4

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