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LAMTOR2 late endosomal/lysosomal adaptor, MAPK and MTOR activator 2 [ Homo sapiens (human) ]

Gene ID: 28956, updated on 3-Nov-2024

Summary

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Official Symbol
LAMTOR2provided by HGNC
Official Full Name
late endosomal/lysosomal adaptor, MAPK and MTOR activator 2provided by HGNC
Primary source
HGNC:HGNC:29796
See related
Ensembl:ENSG00000116586 MIM:610389; AllianceGenome:HGNC:29796
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
p14; ENDAP; ROBLD3; HSPC003; MAPBPIP; MAPKSP1AP; Ragulator2
Summary
The product of this gene is highly conserved with a mouse protein associated with the cytoplasmic face of late endosomes and lysosomes. The mouse protein interacts with MAPK scaffold protein 1, a component of the mitogen-activated protein kinase pathway. In humans, a mutation in this gene has been associated with a primary immunodeficiency syndrome, and suggests a role for this protein in endosomal biogenesis. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2009]
Expression
Ubiquitous expression in kidney (RPKM 22.1), liver (RPKM 22.0) and 25 other tissues See more
Orthologs
mouse all
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Genomic context

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See LAMTOR2 in Genome Data Viewer
Location:
1q22
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (156054782..156058506)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (155193248..155196972)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (156024573..156028297)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene signal sequence receptor subunit 2 Neighboring gene uncharacterized LOC105371729 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1414 Neighboring gene ubiquilin 4 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:156022535-156023256 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1415 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1416 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1417 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1835 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1836 Neighboring gene RAB25, member RAS oncogene family Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr1:156045982-156046889 and GRCh37_chr1:156046890-156047796 Neighboring gene mex-3 RNA binding family member A Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:156051244-156052056 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:156052057-156052870

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 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. A complex immunodeficiency is based on U1 snRNP-mediated poly(A) site suppression. Langemeier J, et al. EMBO J, 2012 Oct 17. PMID 22968171, Free PMC Article
  2. Polymorphisms in the gene regions of the adaptor complex LAMTOR2/LAMTOR3 and their association with breast cancer risk. De Araujo ME, et al. PLoS One, 2013. PMID 23341997, Free PMC Article
  3. Molecular dynamics-solvated interaction energy studies of protein-protein interactions: the MP1-p14 scaffolding complex. Cui Q, et al. J Mol Biol, 2008 Jun 13. PMID 18479705
  4. VSIG2 promotes malignant progression of pancreatic ductal adenocarcinoma by enhancing LAMTOR2-mediated mTOR activation. Xu J, et al. Cell Commun Signal, 2023 Aug 25. PMID 37626304, Free PMC Article
  5. Novel intra-genic large deletions of CTNNB1 gene identified in WT desmoid-type fibromatosis. Colombo C, et al. Genes Chromosomes Cancer, 2018 Oct. PMID 29901254

See all (57) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. VSIG2 promotes malignant progression of pancreatic ductal adenocarcinoma by enhancing LAMTOR2-mediated mTOR activation.
    Title: VSIG2 promotes malignant progression of pancreatic ductal adenocarcinoma by enhancing LAMTOR2-mediated mTOR activation.
  2. In the two wild type (WT) cases, two novel alterations were detected: a complex deletion of APC and a pathogenic mutation of LAMTOR2. Focusing on WT DT subtype, deep sequencing of CTNNB1, APC and LAMTOR2 was conducted on a retrospective series of 11 WT DT using a targeted approach
    Title: Novel intra-genic large deletions of CTNNB1 gene identified in WT desmoid-type fibromatosis.
  3. identified polymorphisms in LAMTOR2 and LAMTOR3 do not seem to play a relevant role in breast cancer
    Title: Polymorphisms in the gene regions of the adaptor complex LAMTOR2/LAMTOR3 and their association with breast cancer risk.
  4. The ROBLD3 C-A, thorn23 mutation creates a 50SS capable of recruiting an inhibitory U1 snRNP complex leading to a failure of proper 30 end formation and rapid degradation of p14 mRNA.
    Title: A complex immunodeficiency is based on U1 snRNP-mediated poly(A) site suppression.
  5. simulations constitute a multi-dimensional exploration of how EGF-dependent EGFR endocytosis and ERK activation are dynamically affected by scaffolds KSR and MP1, co-regulated by Cbl-CIN85 and Endophilin A1
    Title: Simulating EGFR-ERK signaling control by scaffold proteins KSR and MP1 reveals differential ligand-sensitivity co-regulated by Cbl-CIN85 and endophilin.
  6. A complex encoded by the MAPKSP1, ROBLD3, and c11orf59 genes interacts with the Rag GTPases, recruits them to lysosomes, and is essential for mTORC1 activation
    Title: Ragulator-Rag complex targets mTORC1 to the lysosomal surface and is necessary for its activation by amino acids.
Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Primary immunodeficiency syndrome due to p14 deficiency
MedGen: C1835829 OMIM: 610798 GeneReviews: Not available
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Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of late endosomal/lysosomal adaptor, MAPK and MTOR activator 2 (LAMTOR2) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells PubMed

Go to the HIV-1, Human Interaction Database

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

Gene Ontology Provided by GOA

Function Evidence Code Pubs
contributes_to guanyl-nucleotide exchange factor activity IDA
Inferred from Direct Assay
more info
 PubMed 
contributes_to molecular adaptor 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 TORC1 signaling NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in cellular response to amino acid stimulus IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cellular response to amino acid stimulus IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in cellular response to amino acid stimulus IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in fibroblast migration IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of MAPK cascade IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of TOR signaling IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of TOR signaling IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of TORC1 signaling IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein localization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein localization to cell junction IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of cell growth IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within regulation of cell-substrate junction organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
part_of FNIP-folliculin RagC/D GAP IDA
Inferred from Direct Assay
more info
 PubMed 
part_of Ragulator complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of Ragulator complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of Ragulator complex IPI
Inferred from Physical Interaction
more info
 PubMed 
located_in endosome membrane TAS
Traceable Author Statement
more info
  
located_in late endosome ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in late endosome membrane NAS
Non-traceable Author Statement
more info
 PubMed 
located_in lysosomal membrane HDA PubMed 
is_active_in lysosomal membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in lysosomal membrane NAS
Non-traceable Author Statement
more info
 PubMed 
located_in lysosomal membrane TAS
Traceable Author Statement
more info
  
located_in plasma membrane TAS
Traceable Author Statement
more info
  
located_in specific granule membrane TAS
Traceable Author Statement
more info
  
located_in tertiary granule membrane TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
ragulator complex protein LAMTOR2
Names
MAPBP-interacting protein
MAPKSP1 adaptor protein
endosomal adaptor protein p14
late endosomal/lysosomal Mp1-interacting protein
late endosomal/lysosomal adaptor and MAPK and MTOR activator 2
mitogen-activated protein-binding protein-interacting protein (MAPBPIP)
roadblock domain containing 3
roadblock domain-containing protein 3

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

  1. NG_009898.1 RefSeqGene

    Range
    5001..8785
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_81

mRNA and Protein(s)

  1. NM_001145264.2 → NP_001138736.1  ragulator complex protein LAMTOR2 isoform 2

    See identical proteins and their annotated locations for NP_001138736.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the central coding region, compared to variant 1. The resulting isoform (2) lacks an internal segment, compared to isoform 1.
    Source sequence(s)
    AL355388, BU184679
    Consensus CDS
    CCDS44243.1
    UniProtKB/Swiss-Prot
    Q9Y2Q5
    Related
    ENSP00000357287.5, ENST00000368304.9
    Conserved Domains (1) summary
    pfam03259
    Location:5 → 77
    Robl_LC7; Roadblock/LC7 domain

  2. NM_014017.4 → NP_054736.1  ragulator complex protein LAMTOR2 isoform 1

    See identical proteins and their annotated locations for NP_054736.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AL355388, BC024190, CA438137
    Consensus CDS
    CCDS1128.1
    UniProtKB/Swiss-Prot
    Q5VY97, Q5VY98, Q5VY99, Q9Y2Q5
    Related
    ENSP00000357288.4, ENST00000368305.9
    Conserved Domains (1) summary
    pfam03259
    Location:5 → 95
    Robl_LC7; Roadblock/LC7 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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    156054782..156058506
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    155193248..155196972
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9Y2Q5.1 GenPept UniProtKB/Swiss-Prot:Q9Y2Q5

Gene LinkOut

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