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

Gene ID: 8897, updated on 27-Nov-2024

Summary

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

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See MTMR3 in Genome Data Viewer
Location:
22q12.2
Exon count:
21
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (29883174..30030868)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (30346548..30494210)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (30279163..30426857)

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

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. MTMR3 is upregulated in patients with breast cancer and regulates proliferation, cell cycle progression and autophagy in breast cancer cells. Wang Z, et al. Oncol Rep, 2019 Nov. PMID 31485632, Free PMC Article
  2. Myotubularin-related phosphatase 3 promotes growth of colorectal cancer cells. Zheng B, et al. ScientificWorldJournal, 2014. PMID 25215329, Free PMC Article
  3. Expression, purification, crystallization and preliminary crystallographic analysis of human myotubularin-related protein 3. Son JY, et al. Acta Crystallogr F Struct Biol Commun, 2014 Sep. PMID 25195900, Free PMC Article
  4. Analysis of phosphoinositide binding domain properties within the myotubularin-related protein MTMR3. Lorenzo O, et al. J Cell Sci, 2005 May 1. PMID 15840652
  5. Modulation of local PtdIns3P levels by the PI phosphatase MTMR3 regulates constitutive autophagy. Taguchi-Atarashi N, et al. Traffic, 2010 Apr. PMID 20059746

See all (78) citations in PubMed

GeneRIFs: Gene References Into Functions

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

Phenotypes

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

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ32333, KIAA0371

Gene Ontology Provided by GOA

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

General protein information

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Preferred Names
phosphatidylinositol-3,5-bisphosphate 3-phosphatase MTMR3
Names
FYVE (Fab1 YGLO23 Vsp27 EEA1 domain) dual-specificity protein phosphatase
FYVE domain-containing dual specificity protein phosphatase 1
phosphatidylinositol-3,5-bisphosphate 3-phosphatase
phosphatidylinositol-3-phosphate phosphatase
zinc finger FYVE domain-containing protein 10
zinc finger, FYVE domain containing 10
NP_066576.1
NP_694690.1
NP_694691.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_021090.4 → NP_066576.1  phosphatidylinositol-3,5-bisphosphate 3-phosphatase MTMR3 isoform c

    See identical proteins and their annotated locations for NP_066576.1

    Status: REVIEWED

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

  2. NM_153050.3 → NP_694690.1  phosphatidylinositol-3,5-bisphosphate 3-phosphatase MTMR3 isoform a

    See identical proteins and their annotated locations for NP_694690.1

    Status: REVIEWED

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

  3. NM_153051.3 → NP_694691.1  phosphatidylinositol-3,5-bisphosphate 3-phosphatase MTMR3 isoform b

    See identical proteins and their annotated locations for NP_694691.1

    Status: REVIEWED

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

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000022.11 Reference GRCh38.p14 Primary Assembly

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

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

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

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001013676.1: Suppressed sequence

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

Gene LinkOut

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