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

Summary

Official Symbol: MTMR4provided by HGNC
Official Full Name: myotubularin related protein 4provided by HGNC
Primary source: HGNC:HGNC:7452
See related: Ensembl:ENSG00000108389 MIM:603559; AllianceGenome:HGNC:7452
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: ZFYVE11; FYVE-DSP2
Summary: Enables several functions, including R-SMAD binding activity; phosphatidylinositol phosphate phosphatase activity; and protein phosphatase binding activity. Involved in several processes, including midbody abscission; negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway; and phosphatidylinositol dephosphorylation. Located in early endosome membrane; late endosome membrane; and recycling endosome membrane. Is active in early phagosome membrane and endosome membrane. [provided by Alliance of Genome Resources, Dec 2024]
Expression: Ubiquitous expression in testis (RPKM 12.1), brain (RPKM 10.5) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 17q22

Exon count:: 23

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (58489537..58519047, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (59357413..59386918, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (56566898..56595241, complement)

Chromosome 17 - NC_000017.11 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?

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

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association scan for childhood caries implicates novel genes. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of vitamin D levels in children: replication in the Western Australian Pregnancy Cohort (Raine) study. EBI GWAS Catalog EBI GWAS CatalogPubMed

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

SHGC-78927 (e-PCR)
- UniSTS:95744

D17S1363E (e-PCR)
- UniSTS:27972

D17S1780 (e-PCR)
- UniSTS:154192

G06215 (e-PCR)
- UniSTS:42848

WI-12688 (e-PCR)
- UniSTS:43388

D17S2030 (e-PCR)
- UniSTS:31616

G42216 (e-PCR)
- UniSTS:93319

AA596759 (e-PCR), detects polymorphism
- UniSTS:143030

STS-H68355 (e-PCR)
- UniSTS:43997

A002V09 (e-PCR)
- UniSTS:12008

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables R-SMAD binding	IDA Inferred from Direct Assay more info	PubMed
enables histone H2AXY142 phosphatase activity	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables molecular adaptor activity	IDA Inferred from Direct Assay more info	PubMed
enables non-membrane spanning protein tyrosine phosphatase activity	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	IMP Inferred from Mutant Phenotype more info	PubMed
enables phosphatidylinositol-3-phosphate phosphatase activity	TAS Traceable Author Statement more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein phosphatase binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein phosphatase binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein serine/threonine phosphatase activity	TAS Traceable Author Statement more info
enables protein tyrosine phosphatase activity, metal-dependent	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in midbody abscission	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of BMP signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of endocytic recycling	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transforming growth factor beta receptor signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transforming growth factor beta receptor signaling pathway	TAS Traceable Author Statement more info
involved_in phagosome maturation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in phosphatidylinositol biosynthetic process	TAS Traceable Author Statement more info
involved_in phosphatidylinositol dephosphorylation	IBA Inferred from Biological aspect of Ancestor more info
involved_in phosphatidylinositol dephosphorylation	IDA Inferred from Direct Assay more info	PubMed
involved_in phosphatidylinositol dephosphorylation	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	TAS Traceable Author Statement more info
located_in early endosome membrane	IDA Inferred from Direct Assay more info	PubMed
located_in early endosome membrane	TAS Traceable Author Statement more info
is_active_in early phagosome membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in endosome membrane	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular space	HDA more info	PubMed
located_in late endosome membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in membrane	IDA Inferred from Direct Assay more info	PubMed
located_in recycling endosome membrane	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: phosphatidylinositol-3,5-bisphosphate 3-phosphatase MTMR4; myotubularin-related protein 4

Names: FYVE domain-containing dual specificity protein phosphatase 2; phosphatidylinositol-3,5-bisphosphate 3-phosphatase; zinc finger FYVE domain-containing protein 11; zinc finger, FYVE domain containing 11

NP_001364995.1

EC 3.1.3.95

NP_001364996.1

EC 3.1.3.95

NP_004678.3

EC 3.1.3.95

XP_005257843.1

EC 3.1.3.95

XP_006722231.1

EC 3.1.3.95

XP_011523762.1

EC 3.1.3.95

XP_047292975.1

EC 3.1.3.95

XP_054173704.1

EC 3.1.3.95

XP_054173705.1

EC 3.1.3.95

XP_054173706.1

EC 3.1.3.95

XP_054173707.1

EC 3.1.3.95

XP_054173708.1

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.

mRNA and Protein(s)

NM_001378066.1 → NP_001364995.1 phosphatidylinositol-3,5-bisphosphate 3-phosphatase MTMR4 isoform 2

Status: VALIDATED

Source sequence(s)

AC005666

UniProtKB/TrEMBL

J3QR65

Conserved Domains (3) summary

cd13342
Location:27 → 140

PH-GRAM_MTMR4; Myotubularian (MTM) related 4 protein (MTMR4) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain

cd15733
Location:1115 → 1174

FYVE_MTMR4; FYVE domain found in myotubularin-related protein 4 (MTMR4) and similar proteins

cd14587
Location:176 → 483

PTP-MTMR4; protein tyrosine phosphatase-like domain of myotubularin related phosphoinositide phosphatase 4
NM_001378067.1 → NP_001364996.1 phosphatidylinositol-3,5-bisphosphate 3-phosphatase MTMR4 isoform 3

Status: VALIDATED

Source sequence(s)

AC005666

Consensus CDS

CCDS92367.1

UniProtKB/TrEMBL

A0A804HJV7, J3QR65

Related

ENSP00000507664.1, ENST00000682306.1

Conserved Domains (3) summary

cd13342
Location:37 → 150

PH-GRAM_MTMR4; Myotubularian (MTM) related 4 protein (MTMR4) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain

cd15733
Location:1125 → 1184

FYVE_MTMR4; FYVE domain found in myotubularin-related protein 4 (MTMR4) and similar proteins

cd14587
Location:186 → 493

PTP-MTMR4; protein tyrosine phosphatase-like domain of myotubularin related phosphoinositide phosphatase 4
NM_004687.5 → NP_004678.3 phosphatidylinositol-3,5-bisphosphate 3-phosphatase MTMR4 isoform 1

See identical proteins and their annotated locations for NP_004678.3

Status: VALIDATED

Source sequence(s)

AB014547, BC035609, DR003190

Consensus CDS

CCDS11608.1

UniProtKB/Swiss-Prot

D3DTZ6, Q8IV27, Q9NYA4, Q9Y4D5

UniProtKB/TrEMBL

J3QR65

Related

ENSP00000325285.5, ENST00000323456.9

Conserved Domains (3) summary

cd13342
Location:23 → 136

PH-GRAM_MTMR4; Myotubularian (MTM) related 4 protein (MTMR4) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain

cd15733
Location:1111 → 1170

FYVE_MTMR4; FYVE domain found in myotubularin-related protein 4 (MTMR4) and similar proteins

pfam06602
Location:127 → 519

Myotub-related; Myotubularin-like phosphatase domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000017.11 Reference GRCh38.p14 Primary Assembly

Range

58489537..58519047 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

See identical proteins and their annotated locations for XP_006722231.1

UniProtKB/Swiss-Prot

D3DTZ6, Q8IV27, Q9NYA4, Q9Y4D5

UniProtKB/TrEMBL

J3QR65

Conserved Domains (3) summary

cd13342
Location:23 → 136

PH-GRAM_MTMR4; Myotubularian (MTM) related 4 protein (MTMR4) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain

cd15733
Location:1111 → 1170

FYVE_MTMR4; FYVE domain found in myotubularin-related protein 4 (MTMR4) and similar proteins

pfam06602
Location:127 → 519

Myotub-related; Myotubularin-like phosphatase domain
XM_047437019.1 → XP_047292975.1 myotubularin-related protein 4 isoform X2

UniProtKB/Swiss-Prot

D3DTZ6, Q8IV27, Q9NYA4, Q9Y4D5

UniProtKB/TrEMBL

J3QR65
XM_005257786.6 → XP_005257843.1 myotubularin-related protein 4 isoform X2

See identical proteins and their annotated locations for XP_005257843.1

UniProtKB/Swiss-Prot

D3DTZ6, Q8IV27, Q9NYA4, Q9Y4D5

UniProtKB/TrEMBL

J3QR65

Conserved Domains (3) summary

cd13342
Location:23 → 136

PH-GRAM_MTMR4; Myotubularian (MTM) related 4 protein (MTMR4) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain

cd15733
Location:1111 → 1170

FYVE_MTMR4; FYVE domain found in myotubularin-related protein 4 (MTMR4) and similar proteins

pfam06602
Location:127 → 519

Myotub-related; Myotubularin-like phosphatase domain
XM_011525460.4 → XP_011523762.1 myotubularin-related protein 4 isoform X1

See identical proteins and their annotated locations for XP_011523762.1

UniProtKB/TrEMBL

J3QR65

Conserved Domains (3) summary

cd13342
Location:27 → 140

PH-GRAM_MTMR4; Myotubularian (MTM) related 4 protein (MTMR4) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain

cd15733
Location:1115 → 1174

FYVE_MTMR4; FYVE domain found in myotubularin-related protein 4 (MTMR4) and similar proteins

cd14587
Location:176 → 483

PTP-MTMR4; protein tyrosine phosphatase-like domain of myotubularin related phosphoinositide phosphatase 4

Alternate T2T-CHM13v2.0

Genomic

NC_060941.1 Alternate T2T-CHM13v2.0

Range

59357413..59386918 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

J3QR65
XM_054317731.1 → XP_054173706.1 myotubularin-related protein 4 isoform X2

UniProtKB/TrEMBL

J3QR65
XM_054317733.1 → XP_054173708.1 myotubularin-related protein 4 isoform X2

UniProtKB/TrEMBL

J3QR65
XM_054317729.1 → XP_054173704.1 myotubularin-related protein 4 isoform X1

UniProtKB/TrEMBL

J3QR65
XM_054317730.1 → XP_054173705.1 myotubularin-related protein 4 isoform X2

UniProtKB/TrEMBL

J3QR65