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    MTMR3 myotubularin related protein 3 [ Homo sapiens (human) ]

    Gene ID: 8897, updated on 5-Mar-2024

    Summary

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    Official Symbol
    MTMR3provided by HGNC
    Official Full Name
    myotubularin related protein 3provided by HGNC
    Primary source
    HGNC:HGNC:7451
    See related
    Ensembl:ENSG00000100330 MIM:603558; AllianceGenome:HGNC:7451
    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
    ZFYVE10; FYVE-DSP1
    Summary
    This gene encodes a member of the myotubularin dual specificity protein phosphatase gene family. The encoded protein is structurally similar to myotubularin but in addition contains a FYVE domain and an N-terminal PH-GRAM domain. The protein can self-associate and also form heteromers with another myotubularin related protein. The protein binds to phosphoinositide lipids through the PH-GRAM domain, and can hydrolyze phosphatidylinositol(3)-phosphate and phosphatidylinositol(3,5)-biphosphate in vitro. The encoded protein has been observed to have a perinuclear, possibly membrane-bound, distribution in cells, but it has also been found free in the cytoplasm. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in bone marrow (RPKM 20.3), testis (RPKM 13.1) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    22q12.2
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (29883174..30030868)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (30346548..30494210)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (30279163..30426857)

    Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:30162881-30163530 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:30179115-30179288 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:30194678-30195178 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:30195179-30195679 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:30196571-30197566 Neighboring gene ubiquinol-cytochrome c reductase, complex III subunit X Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18820 Neighboring gene Sharpr-MPRA regulatory region 3108 Neighboring gene activating signal cointegrator 1 complex subunit 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18822 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13597 Neighboring gene Sharpr-MPRA regulatory region 2042 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30302705-30303206 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30303207-30303706 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:30308572-30309554 Neighboring gene RNA, U6 small nuclear 331, pseudogene Neighboring gene RNA, U5F small nuclear 5, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18823 Neighboring gene NANOG hESC enhancer GRCh37_chr22:30338137-30338638 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18824 Neighboring gene HORMAD2 and MTMR3 antisense RNA 1 Neighboring gene microRNA 6818 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13600 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18825 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:30475909-30476606 Neighboring gene calponin 2 pseudogene 1 Neighboring gene HORMA domain containing 2 Neighboring gene ribosomal protein L36 pseudogene 17

    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. MTMR3 is upregulated in patients with breast cancer and regulates proliferation, cell cycle progression and autophagy in breast cancer cells. Wang Z, et al. Oncol Rep, 2019 Nov. PMID 31485632, Free PMC Article
    2. Myotubularin-related phosphatase 3 promotes growth of colorectal cancer cells. Zheng B, et al. ScientificWorldJournal, 2014. PMID 25215329, Free PMC Article
    3. Expression, purification, crystallization and preliminary crystallographic analysis of human myotubularin-related protein 3. Son JY, et al. Acta Crystallogr F Struct Biol Commun, 2014 Sep. PMID 25195900, Free PMC Article
    4. Brief Report: identification of MTMR3 as a novel susceptibility gene for lupus nephritis in northern Han Chinese by shared-gene analysis with IgA nephropathy. Zhou XJ, et al. Arthritis Rheumatol, 2014 Oct. PMID 24943867, Free PMC Article
    5. Modulation of local PtdIns3P levels by the PI phosphatase MTMR3 regulates constitutive autophagy. Taguchi-Atarashi N, et al. Traffic, 2010 Apr. PMID 20059746

    See all (72) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Breast cancer risk is associated with the HULC rs7763881, MTMR3 rs12537 polymorphisms, and serum levels of HULC and MTMR3 in Egyptian patients.
      Title: Breast cancer risk is associated with the HULC rs7763881, MTMR3 rs12537 polymorphisms, and serum levels of HULC and MTMR3 in Egyptian patients.
    2. MTMR3 risk alleles enhance Toll Like Receptor 9-induced IgA immunity in IgA nephropathy.
      Title: MTMR3 risk alleles enhance Toll Like Receptor 9-induced IgA immunity in IgA nephropathy.
    3. miR-100-5p is upregulated in multiple myeloma and involves in the pathogenesis of multiple myeloma through targeting MTMR3.
      Title: miR-100-5p is upregulated in multiple myeloma and involves in the pathogenesis of multiple myeloma through targeting MTMR3.
    4. Circular RNA MCTP2 inhibits cisplatin resistance in gastric cancer by miR-99a-5p-mediated induction of MTMR3 expression.
      Title: Circular RNA MCTP2 inhibits cisplatin resistance in gastric cancer by miR-99a-5p-mediated induction of MTMR3 expression.
    5. Exosomal miR-1910-3p promotes proliferation, metastasis, and autophagy of breast cancer cells by targeting MTMR3 and activating the NF-kappaB signaling pathway.
      Title: Exosomal miR-1910-3p promotes proliferation, metastasis, and autophagy of breast cancer cells by targeting MTMR3 and activating the NF-ÎşB signaling pathway.
    6. Three SNPs of FCRL3 and one SNP of MTMR3 are associated with immunoglobulin A nephropathy risk.
      Title: Three SNPs of FCRL3 and one SNP of MTMR3 are associated with immunoglobulin A nephropathy risk.
    7. Association of MTMR3 rs12537 at miR-181a binding site with rheumatoid arthritis and systemic lupus erythematosus risk in Egyptian patients.
      Title: Association of MTMR3 rs12537 at miR-181a binding site with rheumatoid arthritis and systemic lupus erythematosus risk in Egyptian patients.
    8. Study demonstrated that high levels of MTMR3 were associated with relapsefree survival and the triplenegative breast cancer subtype, as well as with a protumorigenic function in human breast cancer cells. Its knockdown suppressed proliferation and colony formation through cell cycle arrest and autophagy in MDAMB231 cells. These results provided novel insights into the pathological mechanism of breast cancer.
      Title: MTMR3 is upregulated in patients with breast cancer and regulates proliferation, cell cycle progression and autophagy in breast cancer cells.
    9. Data suggest MTMR3 has multiple functions in regulation of autophagy; one mechanism appears to be direct interaction between MTMR3 and mTORC1 (MTOR, mLST8, raptor) which inhibits phosphorylation activity of mTORC1; MTMR3 is localized to Golgi apparatus.
      Title: The PtdIns3-phosphatase MTMR3 interacts with mTORC1 and suppresses its activity.
    10. the rs713875 IBD risk polymorphism increases MTMR3 expression, which modulates pattern recognition receptor (PRR)-induced outcomes, including increased induced caspase-1 activation
      Title: MTMR3 risk allele enhances innate receptor-induced signaling and cytokines by decreasing autophagy and increasing caspase-1 activation.
    Submit: New GeneRIF Correction See all GeneRIFs (22)

    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
    A genome-wide association study identifies two new lung cancer susceptibility loci at 13q12.12 and 22q12.2 in Han Chinese.
    EBI GWAS Catalog
    A genome-wide association study in Han Chinese identifies multiple susceptibility loci for IgA nephropathy.
    EBI GWAS Catalog
    Common variants at five new loci associated with early-onset inflammatory bowel disease.
    EBI GWAS Catalog
    Discovery and refinement of loci associated with lipid levels.
    EBI GWAS Catalog
    Genome-wide association study identifies susceptibility loci for IgA nephropathy.
    EBI GWAS Catalog
    Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.
    EBI GWAS Catalog
    Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
    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

    • FLJ32333, KIAA0371

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein serine/threonine phosphatase activity TAS
    Traceable Author Statement
    more info
    		  
    enables protein tyrosine phosphatase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein tyrosine/serine/threonine phosphatase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cellular response to glucose starvation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in macroautophagy TAS
    Traceable Author Statement
    more info
    		  
    involved_in phosphatidylinositol 5-phosphate metabolic process IDA
    Inferred from Direct Assay
    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 protein dephosphorylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of autophagosome assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of autophagy IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of phosphatidylinositol dephosphorylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    myotubularin-related protein 3
    Names
    FYVE (Fab1 YGLO23 Vsp27 EEA1 domain) dual-specificity protein phosphatase
    FYVE domain-containing dual specificity protein phosphatase 1
    phosphatidylinositol-3,5-bisphosphate 3-phosphatase
    phosphatidylinositol-3-phosphate phosphatase
    zinc finger FYVE domain-containing protein 10
    zinc finger, FYVE domain containing 10
    NP_066576.1
    NP_694690.1
    NP_694691.1

    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_021090.4 → NP_066576.1  myotubularin-related protein 3 isoform c

      See identical proteins and their annotated locations for NP_066576.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) is the longest transcript and encodes the longest isoform (c).
      Source sequence(s)
      AB002369, AC003071, BU733010, DA126318
      Consensus CDS
      CCDS13870.1
      UniProtKB/Swiss-Prot
      A5PL26, A7MD32, Q13615, Q9NYN5, Q9NYN6, Q9UDX6, Q9UEG3
      UniProtKB/TrEMBL
      A7E2W2, A8K0L6
      Related
      ENSP00000384651.3, ENST00000401950.7
      Conserved Domains (3) summary
      cd13341
      Location:23 → 116
      PH-GRAM_MTMR3; Myotubularian (MTM) related 3 protein (MTMR3) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain
      cd15732
      Location:1115 → 1175
      FYVE_MTMR3; FYVE domain found in myotubularin-related protein 3 (MTMR3) and similar proteins
      pfam06602
      Location:127 → 523
      Myotub-related; Myotubularin-like phosphatase domain

    2. NM_153050.3 → NP_694690.1  myotubularin-related protein 3 isoform a

      See identical proteins and their annotated locations for NP_694690.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) includes an alternate in-frame exon and lacks another alternate in-frame exon compared to variant 3, resulting in a protein (isoform a) that is shorter than isoform c.
      Source sequence(s)
      AB002369, AC003071, AF233436, BU733010, DA126318
      Consensus CDS
      CCDS13871.1
      UniProtKB/TrEMBL
      A7E2W2, A8K0L6
      Related
      ENSP00000331649.3, ENST00000333027.7
      Conserved Domains (3) summary
      cd13341
      Location:23 → 116
      PH-GRAM_MTMR3; Myotubularian (MTM) related 3 protein (MTMR3) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain
      cd15732
      Location:1078 → 1147
      FYVE_MTMR3; FYVE domain found in myotubularin-related protein 3 (MTMR3) and similar proteins
      pfam06602
      Location:127 → 523
      Myotub-related; Myotubularin-like phosphatase domain

    3. NM_153051.3 → NP_694691.1  myotubularin-related protein 3 isoform b

      See identical proteins and their annotated locations for NP_694691.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 3, resulting in a protein (isoform b) that is shorter than isoform c.
      Source sequence(s)
      AB002369, AC003071, AF233437, BU733010, DA126318
      Consensus CDS
      CCDS46682.1
      UniProtKB/TrEMBL
      A7E2W2, A8K0L6
      Related
      ENSP00000307271.6, ENST00000351488.7
      Conserved Domains (3) summary
      cd13341
      Location:23 → 116
      PH-GRAM_MTMR3; Myotubularian (MTM) related 3 protein (MTMR3) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain
      cd15732
      Location:1078 → 1138
      FYVE_MTMR3; FYVE domain found in myotubularin-related protein 3 (MTMR3) and similar proteins
      pfam06602
      Location:127 → 523
      Myotub-related; Myotubularin-like phosphatase domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000022.11 Reference GRCh38.p14 Primary Assembly

      Range
      29883174..30030868
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060946.1 Alternate T2T-CHM13v2.0

      Range
      30346548..30494210
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001013676.1: Suppressed sequence

      Description
      NM_001013676.1: This RefSeq was permanently suppressed because it is entirely UTR sequence.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q13615.3 GenPept UniProtKB/Swiss-Prot:Q13615

    Gene LinkOut

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