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    CLTB clathrin light chain B [ Homo sapiens (human) ]

    Gene ID: 1212, updated on 7-Mar-2021

    Summary

    Official Symbol
    CLTBprovided by HGNC
    Official Full Name
    clathrin light chain Bprovided by HGNC
    Primary source
    HGNC:HGNC:2091
    See related
    Ensembl:ENSG00000175416 MIM:118970
    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
    LCB
    Summary
    Clathrin is a large, soluble protein composed of heavy and light chains. It functions as the main structural component of the lattice-type cytoplasmic face of coated pits and vesicles which entrap specific macromolecules during receptor-mediated endocytosis. This gene encodes one of two clathrin light chain proteins which are believed to function as regulatory elements. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in esophagus (RPKM 44.6), skin (RPKM 37.3) and 25 other tissues See more
    Orthologs
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    Genomic context

    See CLTB in Genome Data Viewer
    Location:
    5q35.2
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    109.20210226 current GRCh38.p13 (GCF_000001405.39) 5 NC_000005.10 (176392455..176416569, complement)
    105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (175819456..175843570, complement)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene ADP ribosylation factor like GTPase 10 Neighboring gene NOP16 nucleolar protein Neighboring gene HIG1 hypoxia inducible domain family member 2A Neighboring gene Fas associated factor family member 2 Neighboring gene ring finger protein 44 Neighboring gene cadherin related family member 2

    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
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    GeneReviews: Not available

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env HIV-1 matrix and gp120 co-localize with clathrin in primary T lymphocytes PubMed
    Gag-Pol gag-pol HIV-1 particles incorporate the clathrin heavy chain together with associated light chains through HIV-1 Gag-Pol in an IN-dependent manner PubMed
    Nef nef HIV-1 Nef induces the formation of clathrin-coated pits in the presence of CD4 in human lymphocytes by interacting with components of the clathrin-coated surface domain PubMed
    nef The leucine-based motif of Nef is required for targeting into clathrin-associated AP complexes and the Nef-mediated alterations of trafficking of CD4 receptor PubMed
    nef Knocking down either AP-1 gamma, AP-1 mu1, or clathrin strongly inhibits Nef-induced downregulation of HLA-A2 PubMed
    Pol gag-pol Clathrin stabilizes HIV-1 Pol proteins in HIV-1 infected cells PubMed
    Vpr vpr HIV-1 Vpr C-terminus (residues 52-96) entry into cells is mediated through clathrin- and caveolae/raft-dependent endocytosis PubMed
    integrase gag-pol Deletion of the HIV-1 IN C-terminal domain and the IN N184L/F185K mutation abolish clathrin incorporation into virions PubMed
    gag-pol HIV-1 particles incorporate the clathrin heavy chain together with associated light chains through HIV-1 Gag-Pol in an IN-dependent manner PubMed
    matrix gag HIV-1 matrix and gp120 co-localize with clathrin in primary T lymphocytes PubMed
    reverse transcriptase gag-pol Mutations in HIV-1 RT, including L234A, that inhibit RT dimerization abolish clathrin incorporation into virions 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

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    clathrin heavy chain binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    peptide binding IEA
    Inferred from Electronic Annotation
    more info
     
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    structural molecule activity IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    clathrin coat assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    clathrin-dependent endocytosis IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    intracellular protein transport IEA
    Inferred from Electronic Annotation
    more info
     
    membrane organization TAS
    Traceable Author Statement
    more info
     
    Component Evidence Code Pubs
    ciliary membrane IEA
    Inferred from Electronic Annotation
    more info
     
    clathrin coat ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    clathrin coat NAS
    Non-traceable Author Statement
    more info
    PubMed 
    clathrin coat of coated pit IEA
    Inferred from Electronic Annotation
    more info
     
    clathrin coat of trans-Golgi network vesicle IEA
    Inferred from Electronic Annotation
    more info
     
    clathrin vesicle coat IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    clathrin-coated endocytic vesicle NAS
    Non-traceable Author Statement
    more info
    PubMed 
    cytosol IDA
    Inferred from Direct Assay
    more info
     
    cytosol TAS
    Traceable Author Statement
    more info
     
    intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
     
    plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    plasma membrane IDA
    Inferred from Direct Assay
    more info
     
    postsynaptic endocytic zone cytoplasmic component IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    presynaptic endocytic zone membrane IEA
    Inferred from Electronic Annotation
    more info
     
    synaptic vesicle membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    trans-Golgi network IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    clathrin light chain B
    Names
    clathrin, light chain (Lcb)
    clathrin, light polypeptide (Lcb)

    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_001364126.3NP_001351055.1  clathrin light chain B isoform c

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and coding sequence and lacks an alternate in-frame exon compared to variant 2. The resulting isoform (c) is shorter at the N-terminus and lacks an alternate internal segment compared to isoform b.
      Source sequence(s)
      AC138956
      Conserved Domains (1) summary
      pfam01086
      Location:14141
      Clathrin_lg_ch; Clathrin light chain
    2. NM_001364127.2NP_001351056.1  clathrin light chain B isoform d

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 3' UTR and coding sequence compared to variant 2. The resulting isoform (d) has a shorter and distinct C-terminus compared to isoform b.
      Source sequence(s)
      AC138956
      Consensus CDS
      CCDS87350.1
      Related
      ENSP00000422978.1, ENST00000510734.5
      Conserved Domains (1) summary
      pfam01086
      Location:163
      Clathrin_lg_ch; Clathrin light chain
    3. NM_001834.5NP_001825.1  clathrin light chain B isoform a

      See identical proteins and their annotated locations for NP_001825.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) lacks an alternate in-frame exon compared to variant 2, resulting in a shorter isoform (a) compared to isoform b.
      Source sequence(s)
      AC138956
      Consensus CDS
      CCDS4402.1
      UniProtKB/Swiss-Prot
      P09497
      UniProtKB/TrEMBL
      A0A024R7S3
      Related
      ENSP00000310812.4, ENST00000345807.7
      Conserved Domains (1) summary
      pfam01086
      Location:1208
      Clathrin_lg_ch; Clathrin light chain
    4. NM_007097.5NP_009028.1  clathrin light chain B isoform b

      See identical proteins and their annotated locations for NP_009028.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) encodes the longest isoform (b).
      Source sequence(s)
      AC138956
      Consensus CDS
      CCDS4403.1
      UniProtKB/Swiss-Prot
      P09497
      Related
      ENSP00000309415.4, ENST00000310418.8
      Conserved Domains (1) summary
      pfam01086
      Location:1226
      Clathrin_lg_ch; Clathrin light chain

    RNA

    1. NR_045724.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) has an additional exon in the center region, which results in an early translation termination and a nonsense-mediated mRNA decay candidate, compared to variant 2. The transcript does not encode a functinal protein.
      Source sequence(s)
      AC138956
    2. NR_157088.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC138956

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210226

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p13 Primary Assembly

      Range
      176392455..176416569 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    RNA

    1. XR_001741996.2 RNA Sequence

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