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

    Gene ID: 28956, updated on 28-Oct-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. 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
    5. 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

    See all (56) 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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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    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
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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