MTM1 myotubularin 1 [Homo sapiens (human)] - Gene

Summary

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

Location:: Xq28

Exon count:: 19

Annotation release	Status	Assembly	Chr	Location
RS_2023_03	current	GRCh38.p14 (GCF_000001405.40)	X	NC_000023.11 (150562653..150673143)
RS_2023_03	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_000023.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
MTM1 mutation is related to myopathy
Title: Adult MTM1-related myopathy carriers: Classification based on deep phenotyping.
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.
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.
This study found in the centronuclear myopathies have mutation in MTM1.
Title: Characterization and genetic diagnosis of centronuclear myopathies in seven Chinese patients.
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.
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.
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.
In platelets, MTM1 is a highly active 3-phosphatase mainly associated to membranes and found on the dense granules and to a lesser extent on alpha-granules.
Title: Expression of myotubularins in blood platelets: Characterization and potential diagnostic of X-linked myotubular myopathy.

Submit: New GeneRIF Correction See all GeneRIFs (53)

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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH17874 (e-PCR)
- UniSTS:69445

SHGC-34459 (e-PCR)
- UniSTS:56160

DXS1345 (e-PCR)
- UniSTS:99430

WI-10395 (e-PCR)
- UniSTS:18548

WI-15352 (e-PCR)
- UniSTS:13015

DXS8150 (e-PCR)
- UniSTS:63461

Homology

Homologs of the MTM1 gene: The MTM1 gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, C.elegans, and frog.
Orthologs from Annotation Pipeline: 484 organisms have orthologs with human gene MTM1
Orthologs

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	PubMed
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	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	PubMed
involved_in mitochondrion distribution	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mitochondrion morphogenesis	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in mitochondrion morphogenesis	IDA Inferred from Direct Assay more info	PubMed
involved_in muscle cell cellular homeostasis	IBA Inferred from Biological aspect of Ancestor more info	PubMed
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	PubMed
involved_in negative regulation of proteasomal ubiquitin-dependent protein catabolic process	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of protein kinase B signaling	IEA Inferred from Electronic Annotation more info
involved_in phosphatidylinositol biosynthetic process	TAS Traceable Author Statement 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 kinase B signaling	IEA Inferred from Electronic Annotation more info
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
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 plasma membrane	IBA Inferred from Biological aspect of Ancestor more info	PubMed
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

EC 3.1.3.64

EC 3.1.3.95

NP_001363835.1

EC 3.1.3.64

EC 3.1.3.95

NP_001363836.1

EC 3.1.3.64

EC 3.1.3.95

NP_001363837.1

EC 3.1.3.64

EC 3.1.3.95

XP_011529473.1

EC 3.1.3.64

EC 3.1.3.95

XP_011529474.1

EC 3.1.3.64

EC 3.1.3.95

XP_016885036.1

EC 3.1.3.64

EC 3.1.3.95

XP_016885037.1

EC 3.1.3.64

EC 3.1.3.95

XP_016885040.1

EC 3.1.3.64

EC 3.1.3.95

XP_047298088.1

EC 3.1.3.64

EC 3.1.3.95

XP_047298089.1

EC 3.1.3.64

EC 3.1.3.95

XP_047298090.1

EC 3.1.3.64

EC 3.1.3.95

XP_047298091.1

EC 3.1.3.64

EC 3.1.3.95

XP_047298092.1

EC 3.1.3.64

EC 3.1.3.95

XP_047298093.1

EC 3.1.3.64

EC 3.1.3.95

XP_054183086.1

EC 3.1.3.64

EC 3.1.3.95

XP_054183087.1

EC 3.1.3.64

EC 3.1.3.95

XP_054183088.1

EC 3.1.3.64

EC 3.1.3.95

XP_054183089.1

EC 3.1.3.64

EC 3.1.3.95

XP_054183090.1

EC 3.1.3.64

EC 3.1.3.95

XP_054183091.1

EC 3.1.3.64

EC 3.1.3.95

XP_054183092.1

EC 3.1.3.64

EC 3.1.3.95

XP_054183093.1

EC 3.1.3.64

EC 3.1.3.95

XP_054183094.1

EC 3.1.3.64

EC 3.1.3.95

XP_054183095.1

EC 3.1.3.64

EC 3.1.3.95

XP_054183096.1

EC 3.1.3.64

EC 3.1.3.95

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.

Genomic

NG_008199.1 RefSeqGene

Range

5001..109570

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_839

mRNA and Protein(s)

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

Q13496, Q8NEL1

UniProtKB/TrEMBL

A0A024RC06

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
NM_001376906.1 → NP_001363835.1 myotubularin isoform 2

Status: REVIEWED

Source sequence(s)

AC136957, AF002223

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
NM_001376907.1 → NP_001363836.1 myotubularin isoform 3

Status: REVIEWED

Source sequence(s)

AC136957, AF002223

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
NM_001376908.1 → NP_001363837.1 myotubularin isoform 1

Status: REVIEWED

Source sequence(s)

AC136957, AF002223

Consensus CDS

CCDS14694.1

UniProtKB/Swiss-Prot

Q8NEL1

UniProtKB/TrEMBL

A0A024RC06

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