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    LAMTOR4 late endosomal/lysosomal adaptor, MAPK and MTOR activator 4 [ Homo sapiens (human) ]

    Gene ID: 389541, updated on 3-May-2024

    Summary

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    Official Symbol
    LAMTOR4provided by HGNC
    Official Full Name
    late endosomal/lysosomal adaptor, MAPK and MTOR activator 4provided by HGNC
    Primary source
    HGNC:HGNC:33772
    See related
    Ensembl:ENSG00000188186 MIM:618834; AllianceGenome:HGNC:33772
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    C7orf59
    Summary
    Contributes to guanyl-nucleotide exchange factor activity and molecular adaptor activity. Involved in several processes, including cellular response to amino acid stimulus; positive regulation of TOR signaling; and protein localization to lysosome. Located in lysosome. Part of Ragulator complex. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in skin (RPKM 36.0), spleen (RPKM 29.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See LAMTOR4 in Genome Data Viewer
    Location:
    7q22.1
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (100148918..100154203)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (101379971..101393996)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (99746541..99751826)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene TATA-box binding protein associated factor 6 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26340 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18416 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18417 Neighboring gene metallo-beta-lactamase domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26341 Neighboring gene ribosomal protein L7 pseudogene 60 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:99745544-99746156 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26342 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26343 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:99746769-99747381 Neighboring gene trafficking protein particle complex subunit 14 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:99755453-99755629 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18420 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18421 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:99757927-99758426 Neighboring gene microRNA 4658 Neighboring gene galactose-3-O-sulfotransferase 4

    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. C7orf59/LAMTOR4 phosphorylation and structural flexibility modulate Ragulator assembly. Rasheed N, et al. FEBS Open Bio, 2019 Sep. PMID 31314152, Free PMC Article
    2. Lysosomal TMEM9-LAMTOR4-controlled mTOR signaling integrity is required for mammary tumorigenesis. Zhang S, et al. Cancer Commun (Lond), 2023 Jan. PMID 36336962, Free PMC Article
    3. Structural basis for Ragulator functioning as a scaffold in membrane-anchoring of Rag GTPases and mTORC1. Zhang T, et al. Nat Commun, 2017 Nov 9. PMID 29123114, Free PMC Article
    4. Crystal structure of the human lysosomal mTORC1 scaffold complex and its impact on signaling. de Araujo MEG, et al. Science, 2017 Oct 20. PMID 28935770
    5. An N-terminal SIAH-interacting motif regulates the stability of the ubiquitin specific protease (USP)-19. Velasco K, et al. Biochem Biophys Res Commun, 2013 Apr 19. PMID 23500468

    See all (27) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Lysosomal TMEM9-LAMTOR4-controlled mTOR signaling integrity is required for mammary tumorigenesis.
      Title: Lysosomal TMEM9-LAMTOR4-controlled mTOR signaling integrity is required for mammary tumorigenesis.
    2. The C7orf59 was phosphorylated by protein kinase A (PKA) in vitro and mutation of the conserved Ser67 residue to aspartate prevented phosphorylation and negatively affected the C7orf59 interaction with p18 both in cell culture and in vitro.
      Title: C7orf59/LAMTOR4 phosphorylation and structural flexibility modulate Ragulator assembly.
    3. Study identified HBXIP and C7orf59 as two additional Ragulator components that are required for mTORC1 activation by amino acids.
      Title: Ragulator is a GEF for the rag GTPases that signal amino acid levels to mTORC1.
    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

    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

    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

    • MGC163425, MGC163431

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    contributes_to guanyl-nucleotide exchange factor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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 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 to lysosome IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of cell size 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 intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  
    located_in late endosome membrane NAS
    Non-traceable Author Statement
    more info
    		 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
    		  
    is_active_in lysosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in lysosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    ragulator complex protein LAMTOR4
    Names
    UPF0539 protein C7orf59
    late endosomal/lysosomal adaptor and MAPK and MTOR activator 4

    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_001008395.4 → NP_001008396.1  ragulator complex protein LAMTOR4 isoform 1

      See identical proteins and their annotated locations for NP_001008396.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      BI598677, CU450474
      Consensus CDS
      CCDS34702.1
      UniProtKB/Swiss-Prot
      Q0VGL1
      Related
      ENSP00000343118.5, ENST00000341942.10

    2. NM_001318236.2 → NP_001305165.1  ragulator complex protein LAMTOR4 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site in the 3' coding region, which introduces a frameshift compared to variant 1. The encoded isoform (2) has a shorter and distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AA772120, BG706819, CU450474
      Consensus CDS
      CCDS83210.1
      UniProtKB/TrEMBL
      A0A087WV46
      Related
      ENSP00000479176.1, ENST00000460732.5

    3. NM_001318237.2 → NP_001305166.1  ragulator complex protein LAMTOR4 isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an in-frame exon in the 5' coding region compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
      Source sequence(s)
      BI771662, CU450474
      Consensus CDS
      CCDS83211.1
      UniProtKB/TrEMBL
      A0A087WT92
      Related
      ENSP00000477680.1, ENST00000474141.5

    4. NM_001394587.1 → NP_001381516.1  ragulator complex protein LAMTOR4 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC073842

    5. NM_001394588.1 → NP_001381517.1  ragulator complex protein LAMTOR4 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC073842

    6. NM_001394589.1 → NP_001381518.1  ragulator complex protein LAMTOR4 isoform 6

      Status: VALIDATED

      Source sequence(s)
      AC073842

    RNA

    1. NR_134526.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) uses an alternate splice site in a 5' exon compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
      Source sequence(s)
      AA772120, CU450474, DB539334
      Related
      ENST00000474831.5

    2. NR_134527.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) contains an alternate internal exon compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
      Source sequence(s)
      AA419348, BC063401, BG819624, CU450474

    3. NR_134529.3 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (7) uses an alternate 5'-terminal exon compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
      Source sequence(s)
      AC073842
      Related
      ENST00000468582.5

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      100148918..100154203
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      101379971..101393996
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054358187.1 → XP_054214162.1  ragulator complex protein LAMTOR4 isoform X2

      UniProtKB/TrEMBL
      A0A087WV46

    2. XM_054358186.1 → XP_054214161.1  ragulator complex protein LAMTOR4 isoform X1

      UniProtKB/Swiss-Prot
      Q0VGL1
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q0VGL1.1 GenPept UniProtKB/Swiss-Prot:Q0VGL1

    Gene LinkOut

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

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