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

Gene ID: 389541, updated on 5-Mar-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
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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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