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    MTM1 myotubularin 1 [ Homo sapiens (human) ]

    Gene ID: 4534, updated on 27-Aug-2024

    Summary

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    Official Symbol
    MTM1provided by HGNC
    Official Full Name
    myotubularin 1provided by HGNC
    Primary source
    HGNC:HGNC:7448
    See related
    Ensembl:ENSG00000171100 MIM:300415; AllianceGenome:HGNC:7448
    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
    CNM; CNMX; MTMX; XLMTM
    Summary
    This gene encodes a dual-specificity phosphatase that acts on both phosphotyrosine and phosphoserine. It is required for muscle cell differentiation and mutations in this gene have been identified as being responsible for X-linked myotubular myopathy. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in colon (RPKM 4.7), testis (RPKM 3.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    Xq28
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (150562653..150673143)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (148830768..148940792)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (149737071..149841616)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:149406763-149407264 Neighboring gene X-ray repair cross complementing 6 pseudogene 2 Neighboring gene mastermind like domain containing 1 Neighboring gene uncharacterized LOC124905223 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:149733744-149734666 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:149734667-149735588 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21050 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30021 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30022 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21051 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30024 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30023 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21052 Neighboring gene myotubularin related protein 1 Neighboring gene cytochrome P450 family 2 subfamily C member 64, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21053 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:149940339-149940886 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:149940887-149941432 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:149946045-149946676 Neighboring gene uncharacterized LOC124905294 Neighboring gene CD99 molecule like 2

    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. X-linked myotubular myopathy mimics hereditary spastic paraplegia in two female manifesting carriers of pathogenic MTM1 variant. Kraatari M, et al. Eur J Med Genet, 2020 Nov. PMID 32805447
    2. Adult MTM1-related myopathy carriers: Classification based on deep phenotyping. Cocanougher BT, et al. Neurology, 2019 Oct 15. PMID 31541013, Free PMC Article
    3. Three novel MTM1 pathogenic variants identified in Japanese patients with X-linked myotubular myopathy. Nishikawa A, et al. Mol Genet Genomic Med, 2019 May. PMID 30884204, Free PMC Article
    4. Using exome sequencing to decipher family history in a healthy individual: Comparison of pathogenic and population MTM1 variants. Penon M, et al. Mol Genet Genomic Med, 2018 Sep. PMID 30047259, Free PMC Article
    5. Novel findings associated with MTM1 suggest a higher number of female symptomatic carriers. Savarese M, et al. Neuromuscul Disord, 2016 Apr-May. PMID 27017278, Free PMC Article

    See all (94) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. BIN1, Myotubularin, and Dynamin-2 Coordinate T-Tubule Growth in Cardiomyocytes.
      Title: BIN1, Myotubularin, and Dynamin-2 Coordinate T-Tubule Growth in Cardiomyocytes.
    2. Circ_FURIN knockdown assuages Testosterone-induced human ovarian granulosa-like tumor cell disorders by sponging miR-423-5p to reduce MTM1 expression in polycystic ovary syndrome.
      Title: Circ_FURIN knockdown assuages Testosterone-induced human ovarian granulosa-like tumor cell disorders by sponging miR-423-5p to reduce MTM1 expression in polycystic ovary syndrome.
    3. X-linked myotubular myopathy mimics hereditary spastic paraplegia in two female manifesting carriers of pathogenic MTM1 variant.
      Title: X-linked myotubular myopathy mimics hereditary spastic paraplegia in two female manifesting carriers of pathogenic MTM1 variant.
    4. MTM1 mutation is related to myopathy
      Title: Adult MTM1-related myopathy carriers: Classification based on deep phenotyping.
    5. Three novel mutations in the second cluster of PTP domain in MTM1 were identified in 3 patients with X-linked myotubular myopathy.
      Title: Three novel MTM1 pathogenic variants identified in Japanese patients with X-linked myotubular myopathy.
    6. our data highlight a safeguarding function of the MTM1-UBQLN2 complex that ensures cytoskeletal integrity to avoid proteotoxic aggregate formation
      Title: The MTM1-UBQLN2-HSP complex mediates degradation of misfolded intermediate filaments in skeletal muscle.
    7. This study found in the centronuclear myopathies have mutation in MTM1.
      Title: Characterization and genetic diagnosis of centronuclear myopathies in seven Chinese patients.
    8. Using exome sequencing to decipher family history in a healthy individual: Comparison of pathogenic and population MTM1 variants.
      Title: Using exome sequencing to decipher family history in a healthy individual: Comparison of pathogenic and population MTM1 variants.
    9. Expression of several MTMR2 isoforms ameliorates the myopathic phenotype owing to MTM1 loss, with increased muscle force, reduced myofiber atrophy, and reduction of the intracellular disorganization hallmarks associated with myotubular myopathy.
      Title: Expression of the neuropathy-associated MTMR2 gene rescues MTM1-associated myopathy.
    10. level of myotubes MTM1 mutations do not dramatically affect calcium homeostasis and calcium release mediated through the ryanodine receptor 1, though they do affect myotube size and nuclear content..mature muscles such as those obtained from patient muscle biopsies exhibit a significant decrease in expression of the ryanodine receptor 1, a decrease in muscle-specific microRNAs and a considerable up-regulation of HDAC4.
      Title: Cellular, biochemical and molecular changes in muscles from patients with X-linked myotubular myopathy due to MTM1 mutations.
    Submit: New GeneRIF Correction See all GeneRIFs (54)

    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

    Associated conditions

    Description Tests
    Severe X-linked myotubular myopathy
    MedGen: C0410203 OMIM: 310400 GeneReviews: X-Linked Myotubular Myopathy
    		Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2021-01-11)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2021-01-11)

    ClinGen Genome Curation PagePubMed

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    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 intermediate filament binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables phosphatidylinositol binding 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 TAS
    Traceable Author Statement
    more info
    		  
    enables phosphoprotein phosphatase activity 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 TOR signaling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in autophagosome assembly IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in endosome to lysosome transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in intermediate filament organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in mitochondrion distribution IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mitochondrion distribution IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in mitochondrion organization IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in muscle cell cellular homeostasis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of TOR signaling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of autophagosome assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of proteasomal ubiquitin-dependent protein catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in phosphatidylinositol 3-kinase/protein kinase B signal transduction IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 positive regulation of skeletal muscle tissue growth IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in proteasome-mediated ubiquitin-dependent protein catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein dephosphorylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of vacuole organization IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in skeletal muscle tissue growth IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in I band IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 IDA
    Inferred from Direct Assay
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in filopodium IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in late endosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in ruffle IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    myotubularin
    Names
    phosphatidylinositol-3,5-bisphosphate 3-phosphatase
    phosphatidylinositol-3-phosphate phosphatase
    NP_000243.1
    NP_001363835.1
    NP_001363836.1
    NP_001363837.1
    XP_011529473.1
    XP_011529474.1
    XP_016885036.1
    XP_016885037.1
    XP_016885040.1
    XP_047298088.1
    XP_047298089.1
    XP_047298090.1
    XP_047298091.1
    XP_047298092.1
    XP_047298093.1
    XP_054183086.1
    XP_054183087.1
    XP_054183088.1
    XP_054183089.1
    XP_054183090.1
    XP_054183091.1
    XP_054183092.1
    XP_054183093.1
    XP_054183094.1
    XP_054183095.1
    XP_054183096.1

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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.

    Genomic

    1. NG_008199.1 RefSeqGene

      Range
      5001..109570
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_839

    mRNA and Protein(s)

    1. NM_000252.3 → NP_000243.1  myotubularin isoform 1

      See identical proteins and their annotated locations for NP_000243.1

      Status: REVIEWED

      Source sequence(s)
      BC030779, BQ002481, DC418907, U46024
      Consensus CDS
      CCDS14694.1
      UniProtKB/Swiss-Prot
      A6NDB1, B7Z491, F2Z330, Q13496, Q8NEL1
      UniProtKB/TrEMBL
      A8K6P5
      Related
      ENSP00000359423.3, ENST00000370396.7
      Conserved Domains (2) summary
      cd13355
      Location:44 → 143
      PH-GRAM_MTM1; Myotubularian 1 protein (MTM1) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain
      pfam06602
      Location:162 → 489
      Myotub-related; Myotubularin-like phosphatase domain

    2. NM_001376906.1 → NP_001363835.1  myotubularin isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC136957, AF002223
      UniProtKB/TrEMBL
      A8K6P5
      Conserved Domains (2) summary
      cd13355
      Location:44 → 143
      PH-GRAM_MTM1; Myotubularian 1 protein (MTM1) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain
      pfam06602
      Location:162 → 489
      Myotub-related; Myotubularin-like phosphatase domain

    3. NM_001376907.1 → NP_001363836.1  myotubularin isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC136957, AF002223
      UniProtKB/TrEMBL
      A0A8I5QJV9
      Related
      ENSP00000510634.1, ENST00000692015.1
      Conserved Domains (2) summary
      pfam06602
      Location:113 → 451
      Myotub-related; Myotubularin-like phosphatase domain
      cl17171
      Location:44 → 106
      PH-like; Pleckstrin homology-like domain

    4. NM_001376908.1 → NP_001363837.1  myotubularin isoform 1

      Status: REVIEWED

      Source sequence(s)
      AC136957, AF002223
      Consensus CDS
      CCDS14694.1
      UniProtKB/Swiss-Prot
      A6NDB1, B7Z491, F2Z330, Q13496, Q8NEL1
      UniProtKB/TrEMBL
      A8K6P5
      Related
      ENSP00000508718.1, ENST00000689694.1
      Conserved Domains (2) summary
      cd13355
      Location:44 → 143
      PH-GRAM_MTM1; Myotubularian 1 protein (MTM1) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain
      pfam06602
      Location:162 → 489
      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_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      150562653..150673143
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047442132.1 → XP_047298088.1  myotubularin isoform X1

      UniProtKB/TrEMBL
      A8K6P5

    2. XM_011531172.2 → XP_011529474.1  myotubularin isoform X3

      See identical proteins and their annotated locations for XP_011529474.1

      UniProtKB/TrEMBL
      A0A8I5KZ76, A8K6P5
      Conserved Domains (2) summary
      pfam06602
      Location:165 → 498
      Myotub-related; Myotubularin-like phosphatase domain
      cl17171
      Location:44 → 158
      PH-like; Pleckstrin homology-like domain

    3. XM_047442133.1 → XP_047298089.1  myotubularin isoform X1

      UniProtKB/TrEMBL
      A8K6P5

    4. XM_047442134.1 → XP_047298090.1  myotubularin isoform X4

      UniProtKB/TrEMBL
      A8K6P5

    5. XM_017029548.2 → XP_016885037.1  myotubularin isoform X3

      UniProtKB/TrEMBL
      A0A8I5KZ76, A8K6P5
      Conserved Domains (2) summary
      pfam06602
      Location:165 → 498
      Myotub-related; Myotubularin-like phosphatase domain
      cl17171
      Location:44 → 158
      PH-like; Pleckstrin homology-like domain

    6. XM_011531171.2 → XP_011529473.1  myotubularin isoform X3

      See identical proteins and their annotated locations for XP_011529473.1

      UniProtKB/TrEMBL
      A0A8I5KZ76, A8K6P5
      Related
      ENSP00000510607.1, ENST00000689314.1
      Conserved Domains (2) summary
      pfam06602
      Location:165 → 498
      Myotub-related; Myotubularin-like phosphatase domain
      cl17171
      Location:44 → 158
      PH-like; Pleckstrin homology-like domain

    7. XM_047442137.1 → XP_047298093.1  myotubularin isoform X6

      UniProtKB/TrEMBL
      A0A8I5QJV9
      Related
      ENST00000306167.11

    8. XM_047442135.1 → XP_047298091.1  myotubularin isoform X4

      UniProtKB/TrEMBL
      A8K6P5

    9. XM_047442136.1 → XP_047298092.1  myotubularin isoform X5

      UniProtKB/TrEMBL
      A8K6P5

    10. XM_017029547.1 → XP_016885036.1  myotubularin isoform X2

      UniProtKB/TrEMBL
      A8K6P5

    11. XM_017029551.3 → XP_016885040.1  myotubularin isoform X7

      UniProtKB/TrEMBL
      A0A8I5KQR6
      Related
      ENSP00000509809.1, ENST00000690282.1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      148830768..148940792
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054327111.1 → XP_054183086.1  myotubularin isoform X1

      UniProtKB/TrEMBL
      A8K6P5

    2. XM_054327115.1 → XP_054183090.1  myotubularin isoform X3

      UniProtKB/TrEMBL
      A0A8I5KZ76, A8K6P5

    3. XM_054327112.1 → XP_054183087.1  myotubularin isoform X1

      UniProtKB/TrEMBL
      A8K6P5

    4. XM_054327117.1 → XP_054183092.1  myotubularin isoform X4

      UniProtKB/TrEMBL
      A8K6P5

    5. XM_054327116.1 → XP_054183091.1  myotubularin isoform X3

      UniProtKB/TrEMBL
      A0A8I5KZ76, A8K6P5

    6. XM_054327114.1 → XP_054183089.1  myotubularin isoform X3

      UniProtKB/TrEMBL
      A0A8I5KZ76, A8K6P5

    7. XM_054327120.1 → XP_054183095.1  myotubularin isoform X6

      UniProtKB/TrEMBL
      A0A8I5QJV9

    8. XM_054327118.1 → XP_054183093.1  myotubularin isoform X4

      UniProtKB/TrEMBL
      A8K6P5

    9. XM_054327119.1 → XP_054183094.1  myotubularin isoform X5

      UniProtKB/TrEMBL
      A8K6P5

    10. XM_054327113.1 → XP_054183088.1  myotubularin isoform X2

      UniProtKB/TrEMBL
      A8K6P5

    11. XM_054327121.1 → XP_054183096.1  myotubularin isoform X7

      UniProtKB/TrEMBL
      A0A8I5KQR6
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q13496.2 GenPept UniProtKB/Swiss-Prot:Q13496

    Gene LinkOut

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