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    LCP2 lymphocyte cytosolic protein 2 [ Homo sapiens (human) ]

    Gene ID: 3937, updated on 3-Dec-2024

    Summary

    Official Symbol
    LCP2provided by HGNC
    Official Full Name
    lymphocyte cytosolic protein 2provided by HGNC
    Primary source
    HGNC:HGNC:6529
    See related
    Ensembl:ENSG00000043462 MIM:601603; AllianceGenome:HGNC:6529
    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
    IMD81; SLP76; SLP-76
    Summary
    This gene encodes an adapter protein that acts as a substrate of the T cell antigen receptor (TCR)-activated protein tyrosine kinase pathway. The encoded protein associates with growth factor receptor bound protein 2, and is thought to play a role TCR-mediated intracellular signal transduction. A similar protein in mouse plays a role in normal T-cell development and activation. Mice lacking this gene show subcutaneous and intraperitoneal fetal hemorrhaging, dysfunctional platelets and impaired viability. [provided by RefSeq, Nov 2016]
    Expression
    Broad expression in bone marrow (RPKM 53.7), appendix (RPKM 44.7) and 19 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See LCP2 in Genome Data Viewer
    Location:
    5q35.1
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (170246233..170297777, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (170785090..170836631, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (169673237..169724781, complement)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene keratin 18 pseudogene 41 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:169581531-169582061 Neighboring gene long intergenic non-protein coding RNA 1187 Neighboring gene Sharpr-MPRA regulatory region 15284 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:169646378-169647577 Neighboring gene chromosome 5 open reading frame 58 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16604 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23604 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16605 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23605 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:169730050-169731249 Neighboring gene uncharacterized LOC100128059 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23606 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23607 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:169757700-169758899 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:169759699-169760548 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:169760549-169761396 Neighboring gene long intergenic non-protein coding RNA 1366

    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
    Immunodeficiency 81
    MedGen: C5543540 OMIM: 619374 GeneReviews: Not available
    Compare labs

    EBI GWAS Catalog

    Description
    Genome-wide association study identifies three novel susceptibility loci for severe Acne vulgaris.
    EBI GWAS Catalog

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    Knockdown of lymphocyte cytosolic protein 2 (SH2 domain containing leukocyte protein of 76kDa) (LCP2; SLP76) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed
    Knockdown of SLP76 by siRNA inhibits HIV-1 infection in MT4 cells and PBMCs PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env HIV-1 gp120 upregulates the expression of lymphocyte cytosolic protein 2 (LCP2, SLP76) in human B cells PubMed
    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 The association of HIV-1 Nef with Vav1, Pak2, and Nck1 is greatly reduced in SLP76-deficient T cells. SLP-76 associates with Nef and modulates actin cytoskeletal reorganization PubMed
    nef HIV-1 Nef inhibits colocalization of activated ZAP70 with SLP76 in microclusters (MCs) PubMed
    nef HIV-1 Nef potently inhibits formation of SLP76-containing microclusters (MCs) and causes disruption of the SLP76-containing MCs proliferation and translocation 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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in T cell receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in cell surface receptor protein tyrosine kinase signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in immune response TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in intracellular signal transduction IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in mast cell activation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of protein kinase activity IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    Component Evidence Code Pubs
    part_of TCR signalosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cell-cell junction IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in plasma membrane raft IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    lymphocyte cytosolic protein 2
    Names
    76 kDa tyrosine phosphoprotein
    SH2 domain-containing leukocyte protein of 76 kDa
    SLP-76 tyrosine phosphoprotein

    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_005565.5NP_005556.1  lymphocyte cytosolic protein 2

      See identical proteins and their annotated locations for NP_005556.1

      Status: REVIEWED

      Source sequence(s)
      AC034199, AW291566, BC016618, BY995095, DB116470, U20158
      Consensus CDS
      CCDS47339.1
      UniProtKB/Swiss-Prot
      A8KA25, Q13094, Q53XV4
      UniProtKB/TrEMBL
      B4DT07
      Related
      ENSP00000046794.5, ENST00000046794.10
      Conserved Domains (3) summary
      cd09522
      Location:1078
      SAM_SLP76; SAM domain of SLP76 subfamily
      cd09929
      Location:411531
      SH2_BLNK_SLP-76; Src homology 2 (SH2) domain found in B-cell linker (BLNK) protein and SH2 domain-containing leukocyte protein of 76 kDa (SLP-76)
      cl26464
      Location:130421
      Atrophin-1; Atrophin-1 family

    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_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      170246233..170297777 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047417171.1XP_047273127.1  lymphocyte cytosolic protein 2 isoform X1

      UniProtKB/TrEMBL
      B4DT07

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      170785090..170836631 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054352575.1XP_054208550.1  lymphocyte cytosolic protein 2 isoform X1

      UniProtKB/TrEMBL
      B4DT07