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

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; 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: mouse all
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Genomic context

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_000022.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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?

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

RH80308 (e-PCR)
- UniSTS:87813

RH11219 (e-PCR)
- UniSTS:83997

SHGC-171878 (e-PCR)
- UniSTS:183593

RH70167 (e-PCR)
- UniSTS:82756

WI-19851 (e-PCR)
- UniSTS:46667

RH80876 (e-PCR)
- UniSTS:86167

RH17431 (e-PCR)
- UniSTS:45230

WI-19805 (e-PCR)
- UniSTS:39612

RH27921 (e-PCR)
- UniSTS:86463

MTMR3__6172 (e-PCR)
- UniSTS:464064

SHGC-37137 (e-PCR)
- UniSTS:64739

RH68755 (e-PCR)
- UniSTS:52453

D22S973E (e-PCR)
- UniSTS:88553

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

EC 3.1.3.95

NP_694690.1

EC 3.1.3.95

NP_694691.1

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_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
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
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