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

Gene ID: 8897, updated on 15-Jun-2019

Summary

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
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

Genomic context

See MTMR3 in Genome Data Viewer
Location:
22q12.2
Exon count:
21
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 22 NC_000022.11 (29883165..30030868)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (30279149..30426857)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene ubiquinol-cytochrome c reductase, complex III subunit X Neighboring gene activating signal cointegrator 1 complex subunit 2 Neighboring gene RNA, U6 small nuclear 331, pseudogene Neighboring gene RNA, U5F small nuclear 5, pseudogene Neighboring gene HORMAD2 and MTMR3 antisense RNA 1 Neighboring gene microRNA 6818 Neighboring gene calponin 2 pseudogene 1 Neighboring gene HORMA domain containing 2 Neighboring gene ribosomal protein L36 pseudogene 17

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

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

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ32333, KIAA0371

Gene Ontology Provided by GOA

Function Evidence Code Pubs
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity IDA
Inferred from Direct Assay
more info
PubMed 
phosphatidylinositol-3-phosphatase activity IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein phosphatase binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein serine/threonine phosphatase activity IDA
Inferred from Direct Assay
more info
PubMed 
protein tyrosine phosphatase activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
cellular response to glucose starvation IMP
Inferred from Mutant Phenotype
more info
PubMed 
macroautophagy TAS
Traceable Author Statement
more info
 
peptidyl-tyrosine dephosphorylation IEA
Inferred from Electronic Annotation
more info
 
phosphatidylinositol 5-phosphate metabolic process IDA
Inferred from Direct Assay
more info
PubMed 
phosphatidylinositol biosynthetic process TAS
Traceable Author Statement
more info
 
phosphatidylinositol dephosphorylation IDA
Inferred from Direct Assay
more info
PubMed 
protein dephosphorylation IDA
Inferred from Direct Assay
more info
PubMed 
regulation of autophagosome assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of phosphatidylinositol dephosphorylation IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
extrinsic component of membrane IDA
Inferred from Direct Assay
more info
PubMed 
membrane IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
myotubularin-related protein 3
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)

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_021090.4NP_066576.1  myotubularin-related protein 3 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
    Q13615
    Related
    ENSP00000384651.2, ENST00000401950.6
    Conserved Domains (3) summary
    cd13341
    Location:23116
    PH-GRAM_MTMR3; Myotubularian (MTM) related 3 protein (MTMR3) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain
    cd15732
    Location:11151175
    FYVE_MTMR3; FYVE domain found in myotubularin-related protein 3 (MTMR3) and similar proteins
    pfam06602
    Location:127523
    Myotub-related; Myotubularin-like phosphatase domain
  2. NM_153050.2NP_694690.1  myotubularin-related protein 3 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/Swiss-Prot
    Q13615
    Related
    ENSP00000331649.3, ENST00000333027.7
    Conserved Domains (3) summary
    cd13341
    Location:23116
    PH-GRAM_MTMR3; Myotubularian (MTM) related 3 protein (MTMR3) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain
    cd15732
    Location:10781147
    FYVE_MTMR3; FYVE domain found in myotubularin-related protein 3 (MTMR3) and similar proteins
    pfam06602
    Location:127523
    Myotub-related; Myotubularin-like phosphatase domain
  3. NM_153051.3NP_694691.1  myotubularin-related protein 3 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/Swiss-Prot
    Q13615
    UniProtKB/TrEMBL
    A0A024R1I2
    Related
    ENSP00000307271.6, ENST00000351488.7
    Conserved Domains (3) summary
    cd13341
    Location:23116
    PH-GRAM_MTMR3; Myotubularian (MTM) related 3 protein (MTMR3) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain
    cd15732
    Location:10781138
    FYVE_MTMR3; FYVE domain found in myotubularin-related protein 3 (MTMR3) and similar proteins
    pfam06602
    Location:127523
    Myotub-related; Myotubularin-like phosphatase domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000022.11 Reference GRCh38.p13 Primary Assembly

    Range
    29883169..30030868
    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.
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