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LAT linker for activation of T cells [ Homo sapiens (human) ]

Gene ID: 27040, updated on 27-Nov-2024

Summary

Official Symbol
LATprovided by HGNC
Official Full Name
linker for activation of T cellsprovided by HGNC
Primary source
HGNC:HGNC:18874
See related
Ensembl:ENSG00000213658 MIM:602354; AllianceGenome:HGNC:18874
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
LAT1; pp36; IMD52
Summary
The protein encoded by this gene is phosphorylated by ZAP-70/Syk protein tyrosine kinases following activation of the T-cell antigen receptor (TCR) signal transduction pathway. This transmembrane protein localizes to lipid rafts and acts as a docking site for SH2 domain-containing proteins. Upon phosphorylation, this protein recruits multiple adaptor proteins and downstream signaling molecules into multimolecular signaling complexes located near the site of TCR engagement. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]
Expression
Broad expression in lymph node (RPKM 29.3), appendix (RPKM 13.0) and 19 other tissues See more
Orthologs
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Genomic context

See LAT in Genome Data Viewer
Location:
16p11.2
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (28984803..28990784)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (29265918..29271899)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (28996124..29002105)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene nuclear factor of activated T cells 2 interacting protein Neighboring gene ReSE screen-validated silencer GRCh37_chr16:28973628-28973836 Neighboring gene microRNA 4517 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10653 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10654 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7321 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7322 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7323 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7324 Neighboring gene SPNS lysolipid transporter 1, lysophospholipid Neighboring gene MPRA-validated peak2553 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:29036345-29036846 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7325 Neighboring gene nuclear pore complex interacting protein family, member B10, pseudogene Neighboring gene phospholipase A2 group XC, pseudogene Neighboring gene MPRA-validated peak2554 silencer Neighboring gene small nucleolar RNA U13

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Severe combined immunodeficiency due to LAT deficiency
MedGen: C4479588 OMIM: 617514 GeneReviews: Not available
Compare labs

EBI GWAS Catalog

Description
Common genetic variants associated with cognitive performance identified using the proxy-phenotype method.
EBI GWAS Catalog
Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.
EBI GWAS Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env Lck is recuited to a virological synapse (VS) interface and is highly colocalized with gp120 when cells interact with gp120+ICAM-1 bilayers, leading to activate ZAP70, LAT, SLP76, and PLCgamma PubMed
Nef nef HIV-1 Nef inhibits expression of the LAT protein and its recruitment to SLP76-containing microclusters (MCs) PubMed
nef HIV-1 Nef induces localization of LAT mainly from the plasma membrane to the intracellular membrane compartment PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Potential readthrough

Included gene: SPIN1

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables molecular condensate scaffold activity IDA
Inferred from Direct Assay
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein kinase binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables protein kinase binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables signaling adaptor activity IDA
Inferred from Direct Assay
more info
PubMed 
enables signaling receptor complex adaptor activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
involved_in Ras protein signal transduction IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in T cell activation TAS
Traceable Author Statement
more info
PubMed 
involved_in T cell receptor signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
involved_in adaptive immune response IEA
Inferred from Electronic Annotation
more info
 
involved_in calcium-mediated signaling IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in gene expression IEA
Inferred from Electronic Annotation
more info
 
involved_in immune response IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in immune response IDA
Inferred from Direct Assay
more info
PubMed 
involved_in inflammatory response IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in integrin-mediated signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
involved_in intracellular signal transduction IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in intracellular signal transduction IDA
Inferred from Direct Assay
more info
PubMed 
involved_in lymphocyte homeostasis IEA
Inferred from Electronic Annotation
more info
 
involved_in mast cell degranulation IEA
Inferred from Electronic Annotation
more info
 
involved_in membrane raft distribution IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of MAPK cascade IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of protein kinase activity IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in regulation of T cell activation IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in regulation of T cell activation IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
part_of COP9 signalosome ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
 
part_of TCR signalosome IDA
Inferred from Direct Assay
more info
PubMed 
located_in cell-cell junction IEA
Inferred from Electronic Annotation
more info
 
is_active_in immunological synapse IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in immunological synapse IDA
Inferred from Direct Assay
more info
PubMed 
located_in membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in membrane raft TAS
Traceable Author Statement
more info
PubMed 
is_active_in plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in plasma membrane IDA
Inferred from Direct Assay
more info
 
located_in plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
linker for activation of T-cells family member 1
Names
36 kDa phospho-tyrosine adapter protein
36 kDa phospho-tyrosine adaptor protein
36 kDa phosphotyrosine adapter protein
linker for activation of T cells, transmembrane adaptor
p36-38

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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_001014987.2NP_001014987.1  linker for activation of T-cells family member 1 isoform b

    See identical proteins and their annotated locations for NP_001014987.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 4. The resulting isoform (b) is shorter at the N-terminus compared to isoform d.
    Source sequence(s)
    AC109460, AJ223280, BC011563, BI769296
    Consensus CDS
    CCDS32425.1
    UniProtKB/TrEMBL
    C7C5T7
    Related
    ENSP00000378841.3, ENST00000395456.7
    Conserved Domains (1) summary
    pfam15234
    Location:1229
    LAT; Linker for activation of T-cells
  2. NM_001014988.2NP_001014988.1  linker for activation of T-cells family member 1 isoform c

    See identical proteins and their annotated locations for NP_001014988.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence and uses an alternate in-frame splice junction at the 5' end of an exon compared to variant 4. The resulting isoform (c) is shorter at the N- terminus and lacks an internal aa compared to isoform d.
    Source sequence(s)
    AC109460, AJ223280, BC011563, BI769296, BI911769
    Consensus CDS
    CCDS45455.1
    UniProtKB/TrEMBL
    C7C5T7
    Related
    ENSP00000398793.2, ENST00000454369.6
    Conserved Domains (1) summary
    pfam15234
    Location:1228
    LAT; Linker for activation of T-cells
  3. NM_001014989.2NP_001014989.2  linker for activation of T-cells family member 1 isoform d

    See identical proteins and their annotated locations for NP_001014989.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) encodes the longest isoform (d).
    Source sequence(s)
    AC109460, BC011563
    Consensus CDS
    CCDS53999.1
    UniProtKB/TrEMBL
    C7C5T7
    Related
    ENSP00000378845.3, ENST00000395461.7
    Conserved Domains (1) summary
    pfam15234
    Location:37269
    LAT; Linker for activation of T-cells
  4. NM_014387.4NP_055202.1  linker for activation of T-cells family member 1 isoform a

    See identical proteins and their annotated locations for NP_055202.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) differs in the 5' UTR and coding sequence and contains an internal in-frame segment compared to variant 4. The resulting isoform (a) is shorter at the N-terminus and contains an internal segment compared to isoform d.
    Source sequence(s)
    AC109460, AF036906, AJ223280, BC011563, BI769296
    Consensus CDS
    CCDS10647.1
    UniProtKB/Swiss-Prot
    B7WPI0, C7C5T6, G5E9K3, O43561, O43919
    UniProtKB/TrEMBL
    C7C5T7
    Related
    ENSP00000354119.5, ENST00000360872.9
    Conserved Domains (1) summary
    pfam15234
    Location:1262
    LAT; Linker for activation of T-cells

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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    28984803..28990784
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    29265918..29271899
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)