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    CLTC clathrin heavy chain [ Homo sapiens (human) ]

    Gene ID: 1213, updated on 4-Jan-2025

    Summary

    Official Symbol
    CLTCprovided by HGNC
    Official Full Name
    clathrin heavy chainprovided by HGNC
    Primary source
    HGNC:HGNC:2092
    See related
    Ensembl:ENSG00000141367 MIM:118955; AllianceGenome:HGNC:2092
    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
    Hc; CHC; CHC17; MRD56; CLH-17; CLTCL2
    Summary
    Clathrin is a major protein component of the cytoplasmic face of intracellular organelles, called coated vesicles and coated pits. These specialized organelles are involved in the intracellular trafficking of receptors and endocytosis of a variety of macromolecules. The basic subunit of the clathrin coat is composed of three heavy chains and three light chains. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in brain (RPKM 67.0), thyroid (RPKM 49.4) and 25 other tissues See more
    Orthologs
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    Genomic context

    See CLTC in Genome Data Viewer
    Location:
    17q23.1
    Exon count:
    32
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (59619895..59696956)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (60488657..60565708)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (57697256..57774317)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105371847 Neighboring gene RNA, U4 small nuclear 13, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:57642652-57643194 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8781 Neighboring gene DEAH-box helicase 40 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:57695690-57696502 Neighboring gene Sharpr-MPRA regulatory region 22 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8782 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:57760547-57761746 Neighboring gene Sharpr-MPRA regulatory region 12460 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12513 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:57780642-57781146 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:57781147-57781650 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:57784605-57785260 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:57794547-57795046 Neighboring gene peptidyl-tRNA hydrolase 2 Neighboring gene vacuole membrane protein 1 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr17:57831571-57832770 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:57845677-57846178 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:57860713-57861526 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12515 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12516 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:57911971-57912470 Neighboring gene VISTA enhancer hs1656 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr17:57917673-57918402 Neighboring gene microRNA 21

    Genomic regions, transcripts, and products

    Expression

    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    BioGRID CRISPR Screen Phenotypes (694 hits/1293 screens)

    Associated conditions

    Description Tests
    Intellectual disability, autosomal dominant 56
    MedGen: C4693389 OMIM: 617854 GeneReviews: Not available
    Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2022-09-27)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2022-09-27)

    ClinGen Genome Curation PagePubMed

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env Tandem affinity purification and mass spectrometry analysis identify heavy chain of clathrin (CLTC), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into Staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    env HIV-1 matrix and gp120 co-localize with clathrin in primary T lymphocytes PubMed
    Gag-Pol gag-pol Tandem affinity purification and mass spectrometry analysis identify heavy chain of clathrin (CLTC), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into Staufen1 RNP complexes isolated from HIV-1-expressing cells 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
    Nef nef Tandem affinity purification and mass spectrometry analysis identify heavy chain of clathrin (CLTC), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into Staufen1 RNP complexes isolated from HIV-1-expressing cells 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
    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
    Pol gag-pol Clathrin stabilizes HIV-1 Pol proteins in HIV-1 infected cells PubMed
    Pr55(Gag) gag Tandem affinity purification and mass spectrometry analysis identify heavy chain of clathrin (CLTC), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into Staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Vpr vpr A stable-isotope labeling by amino acids in cell culture coupled with mass spectrometry-based proteomics identifies upregulation of clathrin, heavy chain (CLTC) expression by HIV-1 Vpr in Vpr transduced macrophages PubMed
    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

    General gene information

    Clone Names

    • KIAA0034

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in amyloid-beta clearance by transcytosis PubMed 
    involved_in autophagy  
    involved_in cell division  
    involved_in clathrin coat assembly  
    involved_in clathrin coat assembly PubMed 
    involved_in clathrin coat disassembly  
    involved_in clathrin-dependent endocytosis PubMed 
    involved_in intracellular protein transport PubMed 
    involved_in mitotic cell cycle  
    involved_in mitotic cell cycle PubMed 
    involved_in negative regulation of hyaluronan biosynthetic process PubMed 
    involved_in negative regulation of hyaluronan biosynthetic process PubMed 
    involved_in negative regulation of protein localization to plasma membrane PubMed 
    involved_in osteoblast differentiation PubMed 
    involved_in receptor internalization PubMed 
    involved_in receptor-mediated endocytosis  
    involved_in receptor-mediated endocytosis PubMed 
    involved_in regulation of mitotic spindle organization PubMed 
    involved_in retrograde transport, endosome to Golgi PubMed 
    involved_in transferrin transport PubMed 
    Items 1 - 20 of 26
    Component Evidence Code Pubs
    part_of clathrin coat PubMed 
    part_of clathrin coat PubMed 
    part_of clathrin coat of coated pit  
    part_of clathrin coat of trans-Golgi network vesicle  
    part_of clathrin complex  
    part_of clathrin complex PubMed 
    is_active_in clathrin-coated endocytic vesicle  
    located_in clathrin-coated endocytic vesicle PubMed 
    located_in clathrin-coated endocytic vesicle membrane  
    located_in clathrin-coated vesicle PubMed 
    located_in cytosol  
    located_in endolysosome membrane  
    located_in endosome  
    located_in extracellular exosome PubMed 
    located_in extracellular vesicle PubMed 
    located_in focal adhesion PubMed 
    located_in lysosome  
    located_in melanosome  
    located_in membrane PubMed 
    located_in mitotic spindle  
    located_in mitotic spindle microtubule PubMed 
    located_in plasma membrane  
    part_of protein-containing complex PubMed 
    is_active_in spindle  
    located_in spindle PubMed 
    located_in trans-Golgi network membrane  
    Items 1 - 20 of 26

    General protein information

    Preferred Names
    clathrin heavy chain 1
    Names
    clathrin heavy chain on chromosome 17
    clathrin, heavy polypeptide (Hc)
    clathrin, heavy polypeptide-like 2

    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.

    Genomic

    1. NG_047043.1 RefSeqGene

      Range
      5207..82268
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001288653.2 → NP_001275582.1  clathrin heavy chain 1 isoform 2

      See identical proteins and their annotated locations for NP_001275582.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region compared to variant 1. The resulting protein (isoform 2) is longer compared to isoform 1.
      Source sequence(s)
      AC091271, AK127134
      Consensus CDS
      CCDS74115.1
      UniProtKB/TrEMBL
      A0A087WVQ6, A0A8V8TQ14, J3KSQ2
      Related
      ENSP00000462592.2, ENST00000580081.2
      Conserved Domains (6) summary
      smart00299
      Location:1278 → 1420
      CLH; Clathrin heavy chain repeat homology
      sd00006
      Location:1109 → 1135
      TPR; TPR repeat [structural motif]
      pfam01394
      Location:202 → 238
      Clathrin_propel; Clathrin propeller repeat
      pfam00637
      Location:1431 → 1565
      Clathrin; Region in Clathrin and VPS
      pfam09268
      Location:335 → 358
      Clathrin-link; Clathrin, heavy-chain linker
      pfam13838
      Location:360 → 425
      Clathrin_H_link; Clathrin-H-link
    2. NM_004859.4 → NP_004850.1  clathrin heavy chain 1 isoform 1

      See identical proteins and their annotated locations for NP_004850.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the shorter transcript and encodes the shorter protein (isoform 1).
      Source sequence(s)
      AC091271, BC054489
      Consensus CDS
      CCDS32696.1
      UniProtKB/Swiss-Prot
      D3DU00, Q00610, Q6N0A0, Q86TF2
      UniProtKB/TrEMBL
      A0A8V8TR47
      Related
      ENSP00000269122.3, ENST00000269122.8
      Conserved Domains (6) summary
      smart00299
      Location:1274 → 1416
      CLH; Clathrin heavy chain repeat homology
      sd00006
      Location:1105 → 1131
      TPR; TPR repeat [structural motif]
      pfam00637
      Location:979 → 1119
      Clathrin; Region in Clathrin and VPS
      pfam01394
      Location:198 → 234
      Clathrin_propel; Clathrin propeller repeat
      pfam09268
      Location:331 → 354
      Clathrin-link; Clathrin, heavy-chain linker
      pfam13838
      Location:356 → 421
      Clathrin_H_link; Clathrin-H-link

    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_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      59619895..59696956
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      60488657..60565708
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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