MTM1

gene
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Summary

MTM1 (myotubularin 1, HGNC:7448) is a protein-coding gene on chromosome Xq28, encoding Myotubularin (Q13496). Lipid phosphatase which dephosphorylates phosphatidylinositol 3-monophosphate (PI3P) and phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2). It is haploinsufficient (ClinGen: sufficient evidence).

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.

Source: NCBI Gene 4534 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): X-linked myotubular myopathy (Definitive, ClinGen)
  • Clinical variants (ClinVar): 947 total — 183 pathogenic, 84 likely-pathogenic
  • Phenotypes (HPO): 63
  • Dosage sensitivity (ClinGen): haploinsufficiency sufficient evidence, triplosensitivity no evidence
  • MANE Select transcript: NM_000252

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:7448
Approved symbolMTM1
Namemyotubularin 1
LocationXq28
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000171100
Ensembl biotypeprotein_coding
OMIM300415
Entrez4534

Gene structure

Transcript identifiers

Ensembl transcripts: 58 — 44 protein_coding, 7 nonsense_mediated_decay, 5 retained_intron, 2 protein_coding_CDS_not_defined

ENST00000306167, ENST00000370393, ENST00000370396, ENST00000490530, ENST00000684910, ENST00000685439, ENST00000685944, ENST00000686212, ENST00000687215, ENST00000687365, ENST00000688152, ENST00000688403, ENST00000689314, ENST00000689694, ENST00000689810, ENST00000690282, ENST00000690351, ENST00000691232, ENST00000691482, ENST00000691686, ENST00000691851, ENST00000692015, ENST00000692638, ENST00000692852, ENST00000692915, ENST00000693422, ENST00000866457, ENST00000866458, ENST00000866459, ENST00000866460, ENST00000866461, ENST00000866462, ENST00000866463, ENST00000866464, ENST00000866465, ENST00000866466, ENST00000866467, ENST00000866468, ENST00000866469, ENST00000866470, ENST00000866471, ENST00000866472, ENST00000866473, ENST00000866474, ENST00000866475, ENST00000866476, ENST00000866477, ENST00000866478, ENST00000866479, ENST00000924084, ENST00000924085, ENST00000924086, ENST00000949259, ENST00000949260, ENST00000949261, ENST00000949262, ENST00000949263, ENST00000949264

RefSeq mRNA: 4 — MANE Select: NM_000252 NM_000252, NM_001376906, NM_001376907, NM_001376908

CCDS: CCDS14694

Canonical transcript exons

ENST00000370396 — 15 exons

ExonStartEnd
ENSE00001209472150568621150568662
ENSE00001209481150598592150598686
ENSE00001452583150671428150673143
ENSE00003471580150659664150659756
ENSE00003480949150614589150614699
ENSE00003515670150657821150658027
ENSE00003566589150645683150645871
ENSE00003580713150660371150660484
ENSE00003623254150638943150639026
ENSE00003638194150663433150663609
ENSE00003647417150649716150649901
ENSE00003647423150592605150592677
ENSE00003648599150641269150641418
ENSE00003672204150596498150596570
ENSE00003684863150619038150619139

Expression profiles

Bgee: expression breadth ubiquitous, 281 present calls, max score 92.40.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.3255 / max 72.6903, expressed in 1714 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
1979688.32551714

Top tissues by expression

293 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
secondary oocyteCL:000065592.40gold quality
rectumUBERON:000105288.77gold quality
germinal epithelium of ovaryUBERON:000130487.84gold quality
monocyteCL:000057687.12gold quality
colonic mucosaUBERON:000031786.99gold quality
mononuclear cellCL:000084286.66gold quality
mucosa of sigmoid colonUBERON:000499386.36gold quality
leukocyteCL:000073886.35gold quality
jejunal mucosaUBERON:000039985.54gold quality
colonic epitheliumUBERON:000039785.46gold quality
calcaneal tendonUBERON:000370185.22gold quality
bone marrow cellCL:000209285.19gold quality
epithelium of nasopharynxUBERON:000195184.07gold quality
mucosa of transverse colonUBERON:000499184.03gold quality
transverse colonUBERON:000115783.99gold quality
right adrenal glandUBERON:000123383.81gold quality
right adrenal gland cortexUBERON:003582783.81gold quality
oocyteCL:000002383.74gold quality
mucosa of paranasal sinusUBERON:000503083.53gold quality
left adrenal glandUBERON:000123483.06gold quality
left adrenal gland cortexUBERON:003582582.73gold quality
hair follicleUBERON:000207382.29gold quality
choroid plexus epitheliumUBERON:000391182.21gold quality
adrenal glandUBERON:000236982.17gold quality
large intestineUBERON:000005982.12gold quality
seminal vesicleUBERON:000099882.00gold quality
muscle of legUBERON:000138381.97gold quality
colonUBERON:000115581.96gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047381.91gold quality
gastrocnemiusUBERON:000138881.87gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes5.67

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

126 targeting MTM1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-3646100.0073.565283
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-5692A100.0074.406850
HSA-MIR-3163100.0077.238605
HSA-MIR-4776-3P100.0068.731340
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-3924100.0072.092394
HSA-MIR-223-3P99.9970.141140
HSA-MIR-428299.9975.366408
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-1213699.9872.815713
HSA-MIR-485-3P99.9870.681585
HSA-MIR-539-3P99.9870.741616
HSA-MIR-3692-3P99.9870.272139
HSA-MIR-548N99.9871.944170
HSA-MIR-570-3P99.9672.414910
HSA-MIR-548AA99.9670.643753
HSA-MIR-548AP-3P99.9670.643753
HSA-MIR-548T-3P99.9670.643753
HSA-MIR-448799.9664.581252
HSA-MIR-23A-3P99.9574.243163
HSA-MIR-23B-3P99.9574.243163
HSA-MIR-23C99.9573.923192
HSA-MIR-548AB99.9571.313488
HSA-MIR-55999.9572.283609
HSA-MIR-548A-5P99.9471.273482
HSA-MIR-548AD-5P99.9471.233502
HSA-MIR-548AE-5P99.9471.233502

Functional genomics

ClinGen dosage: haploinsufficiency 3 (sufficient evidence), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 40)

  • Myotubularin is the 2nd member of the PTP superfamily to utilize an inositol lipid as its physiologic substrate and activity toward PI(3)P may be common to all myotubularin family enzymes. Loss of PI(3)P phosphatase activity correlates with human disease. (PMID:10900271)
  • Expression of human myotubularin inhibited growth of S. pombe and induced a vacuolar phenotype similar to mutants of VPS34, a phosphatidylinositol 3-kinase (PI3K). Myotubularin directly dephosphorylates phosphatidylinositol 3-monophosphate (PtdIns3P) (PMID:11001925)
  • Shows that most MTM1 mutations including missense lead to a strong decrease in protein level : the associated myotubular myopathy is most probably due to total loss-of-function (PMID:11456308)
  • Heterozygous female carriers of MTM1 mutations who develop myopathic symptoms may present with limb girdle and facial weakness and may manifest a skewed pattern of X-chromosome inactivation. (PMID:11552027)
  • mutations in fifty patients with X-linked myotubular myopathy in the United States (PMID:11793470)
  • The phosphatase activity of myotubularin MTM1 towards the 3-position of phosphatidylinositol 3-phosphate is conserved in homologous proteins MTMR2 and MTMR3 (PMID:11846405)
  • Localization to Rac1-induced cell membrane ruffles is dependent on the presence of a domain highly conserved in the myotubularin family. Myotubularin may dephosphorylate a subpool of PtdIns3P at the plasma membrane. (PMID:12118066)
  • Knocking-out MTM1 in mouse reproduces a myotubular myopathy phenotype and suggests a role for myotubularin in structural organization of muscle fibers (PMID:12391329)
  • REVIEW: the cellular mechanisms of PTEN and MTMR function and their role in the etiology of cancer and other human diseases (PMID:12495846)
  • 192 different mutations in the MTM1 gene have been described in 328 families. (PMID:12522554)
  • investigation of MTM1 and MTMR6 and finding that they use PtdIns(3,5)P2 in addition to PtdIns3P as a substrate in vitro (PMID:12646134)
  • Identification of myotubularin as the lipid phosphatase catalytic subunit associated with the 3-phosphatase adapter protein, 3-PAP. (PMID:12847286)
  • REVIEW: Myotubularin defines a large family of cooperating catalytically active and inactive phosphatases, conserved from yeast to human. Myotubularin homologs, MTMR2 and MTMR13, are mutated in autosomal recessive Charcot-Marie-Tooth neuropathies. (PMID:12925573)
  • Myotubularin MTM1 is implicated in intracellular trafficking of the glucose receptor GLUT4 (PMID:14500759)
  • role of MTM1 in the production of phosphatidylinositol 5-phosphate in mammalian cells suggesting the lack of transformation of phosphatidylinositol 3,5-bisphosphate into PtdIns(5)P might be an important component in the etiology of myotubular myopathy (PMID:14660569)
  • myotubularin phosphatase physiologically functions in late endosomal trafficking and vacuolar morphology through interaction with PtdIns(3,5)P(2). (PMID:14722070)
  • We newly identified 26 unrelated Japanese patients with MTM1 mutations by genomic DNA and transcript analysis, including 12 novel mutations. (PMID:15725586)
  • Two families had a myopathy affecting only women, with asymmetric weakness, skeletal asymmetry, and an elevated hemidiaphragm. One family had a myotubularin stop codon mutation in exon 9; the other had a splice site mutation in exon 13. (PMID:15883335)
  • Patients with MTM1 missense mutations had larger myofiber diameters than those with truncation/deletion mutations. These data indicate that differences in myofiber size correlate with MTM1 mutation type and patient outcome. (PMID:17537630)
  • X-linked myotubular myopathy of baby boy has new mutation of mtm1. (PMID:17621527)
  • The diagnosis of myotubular myopathy was confirmed by genetic analysis revealing a novel frameshift mutation (1314-1315insT) of the myotubularin-coding MTM1 gene. (PMID:17827085)
  • REVIEW : MTM1 and homologous proteins are mutated in several neuromuscular diseases (PMID:18429927)
  • A phylogenetic study revealing co-evolution of myotubularins with PI 3-kinase class III complex (PMID:18774718)
  • Data show that an atypical, late-onset form of MTM1-related centronuclear myopathy has a new histological marker “Necklace fibers”. (PMID:19084976)
  • A base pair change was detected in exon 11 of the MTM1 gene: c.1160C>A, which caused an amino acid change, p.S387Y. The father’s gene was normal but the mother had the same mutation as her son and was thus a carrier. (PMID:19129059)
  • Disruption of MTM1 in mouse leads to defects in triad structure, a proposed mechanism for the related muscle disease (PMID:19846786)
  • Myotubularin MTM1 forms cytosolic needle-like structures upon stress (PMID:20140253)
  • hemizygous mutations in the MTM1 gene including c.1261-10A>G in case, 1, c.70C>T (R24X) in case 2, and a previously unreported mutation, c.924_926delCTT(p. F308del), in case 3 (PMID:20358311)
  • Novel MTM1 antibodies for molecular diagnosis, and identification of novel deep intronic mutations (PMID:20434914)
  • Sequence analysis of the entire coding region of the MTM1 gene identified a hemizygous deletion of the T nucleotide at position 431 in exon 6 (c.431delT [p.Leu144fs]), which results in frameshift at codon 144. (PMID:20500434)
  • mutations in MTM1 disrupted the MTM1-desmin complex, resulting in abnormal intermediate filament assembly and architecture in muscle cells (PMID:21135508)
  • Myotubularin regulates Akt-dependent survival signaling via phosphatidylinositol 3-phosphate. (PMID:21478156)
  • A nonsense mutation Arg486STOP was identified in exon 7 of the MTM1 gene. (PMID:21488203)
  • data explain the basis for phenotypic variability among human patients with MTM1 p.R69C mutations and establish the Mtm1 p.R69C mouse as a valuable model for the disease, as its less severe phenotype will expand the scope of testable preclinical therapies (PMID:22068590)
  • The patients of Myopathy had a novel heterozygous splice site mutation in the myotubularin gene, MTM1 (c.867+1G>T). Analysis of MTM1 cDNA revealed that the mutation resulted in aberrant splicing with variable exon skipping. (PMID:22101172)
  • Mutations in specific myotubularins such as MTM1 result in myotubular myopathy and Charcot-Marie-Tooth peripheral neuropathy. (Review) (PMID:22403079)
  • Large duplications in MTM1 may account for a number of Centronuclear myopathy cases that have remained genetically unresolved. (PMID:22968136)
  • Analysis of human XLMTM patient myotubes showed that mutations that disrupt the interaction between myotubularin and MTMR12 proteins result in reduction of both myotubularin and MTMR12 (PMID:23818870)
  • mutations in SPEG cause a centronuclear myopathy phenotype as a result of its interaction with MTM1. (PMID:25087613)
  • This study demonistrated that MTM1 mutation releated to Centronuclear myopathy. (PMID:25957634)

Cross-species orthologs

15 orthologs

OrganismSymbolGene ID
danio_reriomtm1ENSDARG00000037560
mus_musculusMtm1ENSMUSG00000031337
rattus_norvegicusMtm1ENSRNOG00000002516
drosophila_melanogastermtmFBGN0025742
drosophila_melanogasterSbfFBGN0025802
drosophila_melanogasterMtmr6FBGN0028497
drosophila_melanogasterCG14411FBGN0030582
drosophila_melanogasterCG3632FBGN0030735
drosophila_melanogasterCG5026FBGN0035945
caenorhabditis_elegansmtm-1WBGENE00003475
caenorhabditis_elegansWBGENE00003476
caenorhabditis_elegansWBGENE00003477
caenorhabditis_elegansWBGENE00003478
caenorhabditis_elegansWBGENE00003479
caenorhabditis_elegansmtm-10WBGENE00021683

Paralogs (13): MTMR7 (ENSG00000003987), MTMR11 (ENSG00000014914), MTMR1 (ENSG00000063601), MTMR2 (ENSG00000087053), SBF1 (ENSG00000100241), MTMR3 (ENSG00000100330), MTMR8 (ENSG00000102043), MTMR9 (ENSG00000104643), MTMR4 (ENSG00000108389), SBF2 (ENSG00000133812), MTMR6 (ENSG00000139505), MTMR12 (ENSG00000150712), MTMR10 (ENSG00000166912)

Protein

Protein identifiers

MyotubularinQ13496 (reviewed: Q13496)

Alternative names: Phosphatidylinositol-3,5-bisphosphate 3-phosphatase, Phosphatidylinositol-3-phosphate phosphatase

All UniProt accessions (15): A0A8I5KNI6, A0A8I5KQR6, A0A8I5KRS4, A0A8I5KT87, A0A8I5KVB1, A0A8I5KVR9, A0A8I5KW93, A0A8I5KYA6, A0A8I5KYJ1, A0A8I5KZ76, A0A8I5KZ85, A0A8I5QJL1, A0A8I5QJV9, B7Z499, Q13496

UniProt curated annotations — full annotation on UniProt →

Function. Lipid phosphatase which dephosphorylates phosphatidylinositol 3-monophosphate (PI3P) and phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2). Has also been shown to dephosphorylate phosphotyrosine- and phosphoserine-containing peptides. Negatively regulates EGFR degradation through regulation of EGFR trafficking from the late endosome to the lysosome. Plays a role in vacuolar formation and morphology. Regulates desmin intermediate filament assembly and architecture. Plays a role in mitochondrial morphology and positioning. Required for skeletal muscle maintenance but not for myogenesis. In skeletal muscles, stabilizes MTMR12 protein levels.

Subunit / interactions. Heterodimer with MTMR12. Interacts with KMT2A/MLL1 (via SET domain). Interacts with DES in skeletal muscle but not in cardiac muscle. Interacts with SPEG.

Subcellular location. Cytoplasm. Cell membrane. Cell projection. Filopodium. Ruffle. Late endosome. Myofibril. Sarcomere.

Disease relevance. Myopathy, centronuclear, X-linked (CNMX) [MIM:310400] A congenital muscle disorder characterized by progressive muscular weakness and wasting involving mainly limb girdle, trunk, and neck muscles. It may also affect distal muscles. Weakness may be present during childhood or adolescence or may not become evident until the third decade of life. Ptosis is a frequent clinical feature. The most prominent histopathologic features include high frequency of centrally located nuclei in muscle fibers not secondary to regeneration, radial arrangement of sarcoplasmic strands around the central nuclei, and predominance and hypotrophy of type 1 fibers. The disease is caused by variants affecting the gene represented in this entry.

Activity regulation. Allosterically activated by phosphatidylinositol 5-phosphate (PI5P).

Domain organisation. The GRAM domain mediates binding to PI(3,5)P2 and, with lower affinity, to other phosphoinositides.

Similarity. Belongs to the protein-tyrosine phosphatase family. Non-receptor class myotubularin subfamily.

Isoforms (2)

UniProt IDNamesCanonical?
Q13496-11yes
Q13496-22

RefSeq proteins (4): NP_000243, NP_001363835, NP_001363836, NP_001363837 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000387Tyr_Pase_domDomain
IPR003595Tyr_Pase_catDomain
IPR004182GRAMDomain
IPR010569Myotubularin-like_Pase_domDomain
IPR011993PH-like_dom_sfHomologous_superfamily
IPR016130Tyr_Pase_ASActive_site
IPR029021Prot-tyrosine_phosphatase-likeHomologous_superfamily
IPR030564MyotubularinFamily

Pfam: PF02893, PF06602

Enzyme classification (BRENDA):

  • EC 3.1.3.64 — phosphatidylinositol-3-phosphatase (BRENDA: 10 organisms, 32 substrates, 7 inhibitors, 2 Km, 0 kcat entries)
  • EC 3.1.3.95 — phosphatidylinositol-3,5-bisphosphate 3-phosphatase (BRENDA: 2 organisms, 16 substrates, 1 inhibitors, 0 Km, 0 kcat entries)

Substrate kinetics (BRENDA)

1 substrates with measured Km, best-characterized 1. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
INOSITOL 1,3-BISPHOSPHATE0.0008–0.00372

Catalyzed reactions (Rhea), 5 shown:

  • a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol-3-phosphate) + H2O = a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol) + phosphate (RHEA:12316)
  • a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol-3,5-bisphosphate) + H2O = a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol-5-phosphate) + phosphate (RHEA:39019)
  • 1,2-dioctanoyl-sn-glycero-3-phospho-(1-D-myo-inositol-3-phosphate) + H2O = 1,2-dioctanoyl-sn-glycero-3-phospho-(1D-myo-inositol) + phosphate (RHEA:42328)
  • 1,2-dioctanoyl-sn-glycero-3-phospho-(1D-myo-inositol-3,5-bisphosphate) + H2O = 1,2-dioctanoyl-sn-glycero-3-phospho-(1D-myo-inositol-5-phosphate) + phosphate (RHEA:45632)
  • 1,2-dihexadecanoyl-sn-glycero-3-phospho-(1D-myo-inositol-3,5-bisphosphate) + H2O = 1,2-dihexadecanoyl-sn-glycero-3-phospho-(1D-myo-inositol-5-phosphate) + phosphate (RHEA:45636)

UniProt features (114 total): sequence variant 61, binding site 21, mutagenesis site 18, modified residue 4, domain 2, region of interest 2, compositionally biased region 2, chain 1, sequence conflict 1, splice variant 1, active site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q13496-F190.100.80

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (1): 375 (phosphocysteine intermediate)

Ligand- & substrate-binding residues (21): 313; 313; 314; 314; 376; 376; 377; 377; 378; 378; 379; 379

Post-translational modifications (4): 13, 18, 495, 588

Mutagenesis-validated functional residues (18):

PositionPhenotype
255disrupts interaction with des.
257no effect on subcellular location.
269disrupts interaction with des. does not affect lipid phosphatase activity.
278localizes to plasma membrane extensions. does not affect interaction with des.
375no effect on subcellular location.
375lacks activity toward pi3p. does not affect interaction with des or mtmr12.
377no effect on subcellular location.
380does not affect interaction with des.
394produces an unstable protein.
410produces an unstable protein.
420does not affect interaction with des.
443produces an unstable protein.
474–603reduces mtmr12 protein levels in myotubes.
114reduced response to pi5p.
181disrupts interaction with des. does not affect lipid phosphatase activity.
206disrupts interaction with des. does not affect lipid phosphatase activity.
209disrupts interaction with des. does not affect lipid phosphatase activity.
220loss of activity.

Function

Pathways and Gene Ontology

Reactome pathways

7 pathways

IDPathway
R-HSA-1660499Synthesis of PIPs at the plasma membrane
R-HSA-1660516Synthesis of PIPs at the early endosome membrane
R-HSA-1660517Synthesis of PIPs at the late endosome membrane
R-HSA-1430728Metabolism
R-HSA-1483255PI Metabolism
R-HSA-1483257Phospholipid metabolism
R-HSA-556833Metabolism of lipids

MSigDB gene sets: 0 (showing top):

GO Biological Process (22): autophagosome assembly (GO:0000045), protein dephosphorylation (GO:0006470), phosphatidylinositol biosynthetic process (GO:0006661), mitochondrion organization (GO:0007005), endosome to lysosome transport (GO:0008333), protein transport (GO:0015031), TOR signaling (GO:0031929), negative regulation of TOR signaling (GO:0032007), negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435), proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161), phosphatidylinositol 3-kinase/protein kinase B signal transduction (GO:0043491), regulation of vacuole organization (GO:0044088), intermediate filament organization (GO:0045109), muscle cell cellular homeostasis (GO:0046716), phosphatidylinositol dephosphorylation (GO:0046856), mitochondrion distribution (GO:0048311), skeletal muscle tissue growth (GO:0048630), positive regulation of skeletal muscle tissue growth (GO:0048633), negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction (GO:0051898), negative regulation of autophagosome assembly (GO:1902902), lipid metabolic process (GO:0006629), dephosphorylation (GO:0016311)

GO Molecular Function (7): phosphatidylinositol-3-phosphate phosphatase activity (GO:0004438), phosphoprotein phosphatase activity (GO:0004721), intermediate filament binding (GO:0019215), phosphatidylinositol binding (GO:0035091), phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity (GO:0052629), protein binding (GO:0005515), hydrolase activity (GO:0016787)

GO Cellular Component (12): ruffle (GO:0001726), cytoplasm (GO:0005737), late endosome (GO:0005770), cytosol (GO:0005829), plasma membrane (GO:0005886), membrane (GO:0016020), filopodium (GO:0030175), I band (GO:0031674), endosome (GO:0005768), endomembrane system (GO:0012505), sarcomere (GO:0030017), cell projection (GO:0042995)

Reactome top-level categories

Rollup of top-4 pathways:

CategoryPathways
PI Metabolism3
Phospholipid metabolism1
Metabolism of lipids1
Metabolism1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure7
phosphatidylinositol metabolic process2
negative regulation of intracellular signal transduction2
binding2
Atg12 activating enzyme activity1
protein-phosphatidylethanolamide deconjugating activity1
Atg12 conjugating enzyme activity1
Atg12 ligase activity1
organelle assembly1
Atg1/ULK1 kinase complex assembly1
autophagosome organization1
dephosphorylation1
protein modification process1
biosynthetic process1
organelle organization1
lysosomal transport1
intercellular transport1
vesicle-mediated transport1
transport1
intracellular protein localization1
establishment of protein localization1
intracellular signal transduction1
TOR signaling1
regulation of TOR signaling1
regulation of proteasomal ubiquitin-dependent protein catabolic process1
proteasome-mediated ubiquitin-dependent protein catabolic process1
negative regulation of proteasomal protein catabolic process1
negative regulation of ubiquitin-dependent protein catabolic process1
ubiquitin-dependent protein catabolic process1
proteasomal protein catabolic process1
intracellular signaling cassette1
vacuole organization1
regulation of organelle organization1
intermediate filament cytoskeleton organization1
supramolecular fiber organization1
cellular homeostasis1
phospholipid dephosphorylation1
mitochondrion localization1
skeletal muscle tissue development1
developmental growth1

Protein interactions and networks

STRING

1276 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
MTM1MTMR14Q8NCE2949
MTM1PIK3C3Q8NEB9939
MTM1DNM2P50570926
MTM1MAMLD1Q13495908
MTM1HACD1B0YJ81862
MTM1RYR1P21817842
MTM1PIK3R4Q99570815
MTM1BIN1O00499761
MTM1SPEGQ15772702
MTM1FIG4Q92562604
MTM1CCDC78A2IDD5596
MTM1CMTM1Q8IZ96578
MTM1DYSFO75923570
MTM1PLEK2Q9NYT0562
MTM1CACNA1SQ13698561

IntAct

47 interactions, top by confidence:

ABTypeScore
DESMTM1psi-mi:“MI:0915”(physical association)0.710
MTM1DESpsi-mi:“MI:0407”(direct interaction)0.710
MTM1DESpsi-mi:“MI:0915”(physical association)0.710
DESMTM1psi-mi:“MI:0403”(colocalization)0.710
DESMTM1psi-mi:“MI:0407”(direct interaction)0.710
DESDESpsi-mi:“MI:0915”(physical association)0.710
YWHAHPLEKHG3psi-mi:“MI:0914”(association)0.610
MTM1BIN1psi-mi:“MI:0915”(physical association)0.600
BIN1MTM1psi-mi:“MI:0915”(physical association)0.600
MTM1BIN1psi-mi:“MI:0407”(direct interaction)0.600
MTM1MTMR12psi-mi:“MI:0915”(physical association)0.570
MTMR12MTM1psi-mi:“MI:0915”(physical association)0.570
MTM1MTMR12psi-mi:“MI:0407”(direct interaction)0.570
MTM1MTMR12psi-mi:“MI:0403”(colocalization)0.570
TRIML2SRGAP2psi-mi:“MI:0914”(association)0.530
Pip4k2aMTM1psi-mi:“MI:0914”(association)0.500
Pip4k2aMTM1psi-mi:“MI:0915”(physical association)0.500
NRASESYT2psi-mi:“MI:2364”(proximity)0.480
MTM1Despsi-mi:“MI:0915”(physical association)0.460

BioGRID (92): MTM1 (Reconstituted Complex), MTM1 (Affinity Capture-Western), BIN1 (Affinity Capture-Western), CUL4A (Co-fractionation), HLA-C (Affinity Capture-MS), KIAA1468 (Affinity Capture-MS), KRT2 (Affinity Capture-MS), KRT5 (Affinity Capture-MS), SNX17 (Affinity Capture-MS), MTM1 (Affinity Capture-MS), MTM1 (Affinity Capture-MS), MTFR1 (Affinity Capture-MS), SAMM50 (Affinity Capture-MS), CALU (Affinity Capture-MS), CIAO1 (Affinity Capture-MS)

ESM2 similar proteins: A0A0G2JXT6, A0JMF6, A0JMK5, A2ALK8, A2BGG1, A6QLT4, A7MB43, G5ED68, O13819, O14830, P26045, P33402, P51432, Q09M05, Q13496, Q13613, Q15111, Q3USB7, Q4KWH5, Q4R6N0, Q4U2V3, Q52KU6, Q5EB32, Q5F452, Q5R6F6, Q5R9S3, Q5U581, Q62688, Q6AXQ4, Q6NU08, Q6TEL0, Q6XPS3, Q7TPM9, Q7ZXF1, Q8K394, Q8NCE2, Q8VE11, Q8VEL2, Q96EF0, Q96MI9

Diamond homologs: A0A0G2JXT6, A0JMK5, A2BGG1, A4FU01, A6QLT2, A6QLT4, A7MB43, E9PXF8, F4J3T8, F4JWB3, G5ED68, O13819, P47147, Q13496, Q13613, Q13614, Q13615, Q22712, Q2KJ24, Q3V1L6, Q52KU6, Q54GQ1, Q55E58, Q5EB32, Q5F452, Q5PQT2, Q5R6F6, Q5R9S3, Q5REB9, Q5U581, Q5ZIV1, Q6AXQ4, Q6NTN5, Q6NU08, Q6TEL0, Q7TPM9, Q7ZXF1, Q80TA6, Q8K296, Q8VE11

SIGNOR signaling

1 interactions.

AEffectBMechanism
TFEB“up-regulates quantity by expression”MTM1“transcriptional regulation”

Disease & clinical

Clinical variants and AI predictions

ClinVar

947 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic183
Likely pathogenic84
Uncertain significance192
Likely benign267
Benign64

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1071778NM_000252.3(MTM1):c.339T>A (p.Cys113Ter)Pathogenic
1072286NM_000252.3(MTM1):c.1546A>T (p.Lys516Ter)Pathogenic
1074917NM_000252.3(MTM1):c.1459G>T (p.Glu487Ter)Pathogenic
1075319NM_000252.3(MTM1):c.1447G>T (p.Glu483Ter)Pathogenic
11054NM_000252.3(MTM1):c.1190A>G (p.Tyr397Cys)Pathogenic
11055NM_000252.3(MTM1):c.205C>T (p.Arg69Cys)Pathogenic
11057NM_000252.3(MTM1):c.141_144delPathogenic
11059NM_000252.3(MTM1):c.721C>T (p.Arg241Cys)Pathogenic
11060NM_000252.3(MTM1):c.670C>T (p.Arg224Ter)Pathogenic
11061NM_000252.3(MTM1):c.605del (p.Leu202fs)Pathogenic
1172673NM_000252.3(MTM1):c.1400del (p.Leu467fs)Pathogenic
1301887NM_000252.3(MTM1):c.63+1G>TPathogenic
1338243NM_000252.3(MTM1):c.1109C>G (p.Ser370Ter)Pathogenic
1338304NM_000252.3(MTM1):c.197C>T (p.Thr66Ile)Pathogenic
1338336NM_000252.3(MTM1):c.1228G>T (p.Glu410Ter)Pathogenic
1360711NM_000252.3(MTM1):c.310G>T (p.Glu104Ter)Pathogenic
1371544NM_000252.3(MTM1):c.819_820dup (p.Leu274fs)Pathogenic
1379211NM_000252.3(MTM1):c.548G>A (p.Trp183Ter)Pathogenic
1457292NC_000023.10:g.(?149761067)(149761149_?)delPathogenic
1458095NM_000252.3(MTM1):c.1008_1009dup (p.Trp337fs)Pathogenic
1459032NM_000252.3(MTM1):c.590C>T (p.Thr197Ile)Pathogenic
158893NM_000252.3(MTM1):c.1053+1G>CPathogenic
158894NM_000252.3(MTM1):c.1088_1089del (p.Lys363fs)Pathogenic
158895NM_000252.3(MTM1):c.109C>T (p.Arg37Ter)Pathogenic
158896NM_000252.3(MTM1):c.1120C>G (p.His374Asp)Pathogenic
158898NM_000252.3(MTM1):c.1136G>A (p.Trp379Ter)Pathogenic
158899NM_000252.3(MTM1):c.1137G>A (p.Trp379Ter)Pathogenic
158900NM_000252.3(MTM1):c.1139A>T (p.Asp380Val)Pathogenic
158901NM_000252.3(MTM1):c.1160C>A (p.Ser387Tyr)Pathogenic
158903NM_000252.3(MTM1):c.1191T>G (p.Tyr397Ter)Pathogenic

SpliceAI

2959 predictions. Top by Δscore:

VariantEffectΔscore
X:150596489:T:Aacceptor_gain1.0000
X:150596493:TCTA:Tacceptor_loss1.0000
X:150596494:CTA:Cacceptor_loss1.0000
X:150596495:TA:Tacceptor_loss1.0000
X:150596496:A:AGacceptor_gain1.0000
X:150596496:AGAC:Aacceptor_gain1.0000
X:150596497:G:GTacceptor_gain1.0000
X:150596497:GA:Gacceptor_gain1.0000
X:150596497:GAC:Gacceptor_gain1.0000
X:150596497:GACG:Gacceptor_gain1.0000
X:150596497:GACGT:Gacceptor_gain1.0000
X:150596568:CTG:Cdonor_gain1.0000
X:150596568:CTGGT:Cdonor_loss1.0000
X:150596569:TGGT:Tdonor_loss1.0000
X:150596571:G:GCdonor_loss1.0000
X:150596571:G:GGdonor_gain1.0000
X:150596572:T:Gdonor_loss1.0000
X:150614695:GTAAA:Gdonor_gain1.0000
X:150614700:G:GGdonor_gain1.0000
X:150638938:TCTA:Tacceptor_loss1.0000
X:150638939:CTA:Cacceptor_loss1.0000
X:150638940:TAGCC:Tacceptor_loss1.0000
X:150638941:A:AGacceptor_gain1.0000
X:150638941:A:Gacceptor_loss1.0000
X:150638942:G:GGacceptor_gain1.0000
X:150638942:G:GTacceptor_loss1.0000
X:150638942:GC:Gacceptor_gain1.0000
X:150638942:GCC:Gacceptor_gain1.0000
X:150638942:GCCA:Gacceptor_gain1.0000
X:150638942:GCCAT:Gacceptor_gain1.0000

AlphaMissense

3988 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
X:150641399:G:CR220T1.000
X:150641399:G:TR220M1.000
X:150641400:G:CR220S1.000
X:150641400:G:TR220S1.000
X:150645843:G:CR280T1.000
X:150645864:C:AA287D1.000
X:150649791:C:GH315D1.000
X:150649801:G:CR318P1.000
X:150649884:T:AW346R1.000
X:150649884:T:CW346R1.000
X:150657890:T:CC375R1.000
X:150657892:C:GC375W1.000
X:150657899:G:AG378R1.000
X:150657899:G:CG378R1.000
X:150657900:G:AG378E1.000
X:150657900:G:TG378V1.000
X:150657902:T:AW379R1.000
X:150657902:T:CW379R1.000
X:150657905:G:CD380H1.000
X:150657906:A:CD380A1.000
X:150657906:A:TD380V1.000
X:150657909:G:CR381T1.000
X:150657909:G:TR381M1.000
X:150657910:G:CR381S1.000
X:150657910:G:TR381S1.000
X:150657960:G:TR398M1.000
X:150657998:T:AW411R1.000
X:150657998:T:CW411R1.000
X:150663565:T:AW534R1.000
X:150663565:T:CW534R1.000

dbSNP variants (sampled 300 via entrez): RS1000012678 (X:150581154 C>G), RS1000053320 (X:150633646 A>G), RS1000125314 (X:150622699 T>C), RS1000202607 (X:150639072 A>G), RS1000258369 (X:150565662 C>A), RS1000308493 (X:150665443 C>A), RS1000320606 (X:150655227 A>C), RS1000546466 (X:150662754 A>G), RS1000773581 (X:150641628 C>A,G,T), RS1000810666 (X:150612857 G>T), RS1000944585 (X:150613411 A>G), RS1001053801 (X:150673242 C>T), RS1001059710 (X:150604011 G>T), RS1001113695 (X:150593553 G>C), RS1001191466 (X:150567383 A>G)

Disease associations

OMIM: gene MIM:300415 | disease phenotypes: MIM:310400, MIM:160150, MIM:134610, MIM:614408

GenCC curated gene-disease

DiseaseClassificationInheritance
X-linked myotubular myopathyDefinitiveX-linked

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
X-linked myotubular myopathyDefinitiveXL

Mondo (7): X-linked myotubular myopathy (MONDO:0010683), centronuclear myopathy (MONDO:0018947), neurodevelopmental disorder (MONDO:0700092), congenital fiber-type disproportion myopathy (MONDO:0009711), familial Mediterranean fever, autosomal dominant (MONDO:0007601), autosomal dominant centronuclear myopathy (MONDO:0008048), myopathy (MONDO:0005336)

Orphanet (6): X-linked centronuclear myopathy (Orphanet:596), Centronuclear myopathy (Orphanet:595), Congenital fiber-type disproportion myopathy (Orphanet:2020), Familial Mediterranean fever (Orphanet:342), Qualitative or quantitative defects of myotubularin (Orphanet:207110), Autosomal dominant centronuclear myopathy (Orphanet:169189)

HPO phenotypes

63 total (30 of 63 shown, HPO-id order):

HPOTerm
HP:0000028Cryptorchidism
HP:0000048Bifid scrotum
HP:0000054Micropenis
HP:0000218High palate
HP:0000238Hydrocephalus
HP:0000256Macrocephaly
HP:0000268Dolichocephaly
HP:0000275Narrow face
HP:0000276Long face
HP:0000278Retrognathia
HP:0000348High forehead
HP:0000467Neck muscle weakness
HP:0000478Abnormality of the eye
HP:0000544External ophthalmoplegia
HP:0000689Dental malocclusion
HP:0000807Glanular hypospadias
HP:0000808Penoscrotal hypospadias
HP:0000883Thin ribs
HP:0001166Arachnodactyly
HP:0001270Motor delay
HP:0001284Areflexia
HP:0001290Generalized hypotonia
HP:0001305Dandy-Walker malformation
HP:0001319Neonatal hypotonia
HP:0001371Flexion contracture
HP:0001382Joint hypermobility
HP:0001419X-linked recessive inheritance
HP:0001558Decreased fetal movement
HP:0001561Polyhydramnios
HP:0001622Premature birth

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

DescriptorNameTree numbers
D065886Neurodevelopmental DisordersF03.625

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

40 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
potassium chromate(VI)affects cotreatment, decreases expression2
FR900359affects phosphorylation1
dicrotophosdecreases expression1
2,4,6-tribromophenoldecreases expression1
methylmercuric chloridedecreases expression1
triphenyl phosphateaffects expression1
decabromobiphenyl etherdecreases expression1
trichostatin Adecreases expression1
arseniteaffects binding, decreases reaction1
sodium arsenitedecreases expression1
manganese chloridedecreases expression1
gossypol acetic acidincreases expression1
epigallocatechin gallateaffects cotreatment, decreases expression1
di-n-butylphosphoric acidaffects expression1
chromium hexavalent iondecreases expression1
2-palmitoylglycerolincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamidedecreases expression, affects cotreatment1
2,2’,4,4’-tetrabromodiphenyl etherdecreases expression1
dorsomorphinaffects cotreatment, decreases expression1
pentabrominated diphenyl ether 100decreases expression1
hexabrominated diphenyl ether 153decreases expression1
3-(2-hydroxy-4-(2-methylnonan-2-yl)phenyl)cyclohexan-1-olincreases expression1
Resveratrolaffects cotreatment, increases expression1
Sunitinibincreases expression1
Vorinostatdecreases expression, affects cotreatment1
Air Pollutantsdecreases expression, increases abundance1
Benzo(a)pyreneaffects methylation1
Caffeineaffects phosphorylation1
Manganesedecreases expression1
Methotrexateincreases expression1

Cellosaurus cell lines

15 cell lines: 7 induced pluripotent stem cell, 3 finite cell line, 3 cancer cell line, 2 transformed cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_A3JYHPS2882Induced pluripotent stem cellMale
CVCL_A3JZHPS2883Induced pluripotent stem cellMale
CVCL_A3KAHPS2884Induced pluripotent stem cellMale
CVCL_A3KBHPS2885Induced pluripotent stem cellMale
CVCL_A3KCHPS2886Induced pluripotent stem cellMale
CVCL_A3KDHPS2887Induced pluripotent stem cellMale
CVCL_AD70GM06813Finite cell lineMale
CVCL_AD71GM10680Transformed cell lineMale
CVCL_AD85GM23984Transformed cell lineMale
CVCL_AD86GM24346Finite cell lineMale

Clinical trials (associated diseases)

268 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT04586348PHASE4UNKNOWNPrenatal Iodine Supplementation and Early Childhood Neurodevelopment
NCT04873115PHASE4UNKNOWNDouble-blind, Placebo-controlled, Randomized Clinical Trial Comparing the Efficacy and Safety of Sialanar Plus orAl rehabiLitation Against Placebo Plus Oral Rehabilitation for chIldren and Adolescents With seVere Sialorrhoea and Neurodisabilties,
NCT00120055PHASE4COMPLETEDAssociation Between Systemic Exposure of Atorvastatin and Metabolites and Atorvastatin-induced Myotoxicity
NCT03633565PHASE4UNKNOWNComparative Study of Strategies for Management of Duchenne Myopathy (DM)
NCT02559102PHASE3COMPLETEDDexmedetomidine Sedation Versus General Anaesthesia for Inguinal Hernia Surgery in Infants
NCT02757079PHASE3COMPLETEDStudy of the Efficacy and Safety of NPC-15 for Sleep Disorders of Children With Neurodevelopmental Disorders
NCT06915480PHASE3RECRUITINGReducing Missed Appointments
NCT07377032PHASE3RECRUITINGTAP-GRIN: Interventional Study on Patients With GRIN-related Neurodevelopmental Disorders
NCT01225614PHASE3UNKNOWNEfficacy and Tolerance of Early Launching of Nocturnal Non Invasive
NCT02909959PHASE2COMPLETEDSulforaphane for the Treatment of Young Men With Autism Spectrum Disorder
NCT06081348PHASE2RECRUITINGSertraline vs. Placebo in the Treatment of Anxiety in Children and AdoLescents With NeurodevelopMental Disorders
NCT06352372PHASE2COMPLETEDSafety and Efficacy of tPBM for Epileptiform Activity in Autism
NCT00503191PHASE1COMPLETEDNeuroModulation Technique Treatment of Autism
NCT04475848PHASE1COMPLETEDA Study to Investigate the Safety, Tolerability, Pharmacokinetics, Pharmacodynamics and Food Effect of RO6953958 in Healthy Participants
NCT06300398PHASE1COMPLETEDIAMA-6 Oral Dose Study in Healthy Adults
NCT00278564PHASE1TERMINATEDStem Cell Transplantation in Idiopathic Inflammatory Myopathy Diseases
NCT03199469PHASE2/PHASE3ACTIVE_NOT_RECRUITINGA Study of AT132 in Young Children With X-Linked Myotubular Myopathy (XLMTM)
NCT04915846PHASE1/PHASE2TERMINATEDTamoxifen Therapy for Myotubular Myopathy
NCT07052929PHASE1/PHASE2RECRUITINGStudy of ASP2957 in Male Participants With X-linked Myotubular Myopathy Who Need Ventilators
NCT01840657Not specifiedCOMPLETEDMyotubular Myopathy Event Study
NCT02453152Not specifiedCOMPLETEDRespiratory Muscle Function in Untreated X-Linked Myotubular Myopathy (XLMTM)
NCT02704273Not specifiedCOMPLETEDA Clinical Assessment Study in X-Linked Myotubular Myopathy (XLMTM) Subjects
NCT04064307Not specifiedRECRUITINGMyotubular and Centronuclear Myopathy Patient Registry
NCT05711771Not specifiedWITHDRAWNMedication Therapy Management (MTM) for a Medicaid Managed Care Population Within Patient-Centered Medical Homes
NCT06581146Not specifiedRECRUITINGA Study to Check Liver Health in Boys With XLMTM, a Serious Genetic Muscle Condition
NCT04033159PHASE1/PHASE2TERMINATEDEarly Phase Human Drug Trial to Investigate Dynamin 101 (DYN101) in Patients ≥ 16 Years With Centronuclear Myopathies
NCT04743557PHASE1/PHASE2WITHDRAWNEarly Phase Human Drug Trial to Investigate DYN101 in Participants 2 to 17 Years With Centronuclear Myopathies
NCT00272883Not specifiedRECRUITINGMolecular and Genetic Studies of Congenital Myopathies
NCT03351270Not specifiedCOMPLETEDProspective Natural History Study of Patients With Myotubular Myopathy and Other CentroNuclear Myopathies
NCT04977648Not specifiedWITHDRAWNNatural History Study of Patients With Centronuclear Myopathies
NCT05099107Not specifiedCOMPLETEDChanges of Motor Function Tests in Congenital Myopathy Subjects Treated With Oral Salbutamol as Compared to no Treatment
NCT05982119Not specifiedRECRUITINGAssessments in Patients With Muscular Pathology and in Control Subjects : The ActiLiège Next Study
NCT06157268Not specifiedRECRUITINGThe Natural History and Muscle Fatigability of Patients With Congenital Myopathies.
NCT06791369Not specifiedNOT_YET_RECRUITINGThe Prevalence of RYR1-related Disease
NCT07021820Not specifiedRECRUITINGMultispectral Optoacoustic Tomography for Advanced Imaging of Centronuclear Myopathy
NCT07478172Not specifiedRECRUITINGEffects of Whole-body Electrical Muscle Stimulation Exercise on Adults With Neuromuscular Disease
NCT01783041PHASE2/PHASE3COMPLETEDEffect of Early L-Carnitine Supplementation on Neurodevelopmental Outcomes in Very Preterm Infants
NCT05767385PHASE2/PHASE3RECRUITINGFetal Cerebrovascular Autoregulation in Congenital Heart Disease and Association With Neonatal Neurobehavior
NCT05675098EARLY_PHASE1NOT_YET_RECRUITINGCentral Nervous System Stimulants and Physical Function in Children With Cerebral Palsy
NCT00783783Not specifiedCOMPLETEDCYP2D6 Pharmacogenetics in Risperidone-Treated Children