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

Summary

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

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_000001.11 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
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?

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.
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.
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.
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.
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.
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.

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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)

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH45081 (e-PCR)
- UniSTS:781

RH125318 (e-PCR)
- UniSTS:162140

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 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
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

NG_009898.1 RefSeqGene

Range

5001..8785

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_81

mRNA and Protein(s)

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
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