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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

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)

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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

  1. NG_047043.1 RefSeqGene

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

mRNA and Protein(s)

  1. NM_001288653.2NP_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:12781420
    CLH; Clathrin heavy chain repeat homology
    sd00006
    Location:11091135
    TPR; TPR repeat [structural motif]
    pfam01394
    Location:202238
    Clathrin_propel; Clathrin propeller repeat
    pfam00637
    Location:14311565
    Clathrin; Region in Clathrin and VPS
    pfam09268
    Location:335358
    Clathrin-link; Clathrin, heavy-chain linker
    pfam13838
    Location:360425
    Clathrin_H_link; Clathrin-H-link
  2. NM_004859.4NP_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:12741416
    CLH; Clathrin heavy chain repeat homology
    sd00006
    Location:11051131
    TPR; TPR repeat [structural motif]
    pfam00637
    Location:9791119
    Clathrin; Region in Clathrin and VPS
    pfam01394
    Location:198234
    Clathrin_propel; Clathrin propeller repeat
    pfam09268
    Location:331354
    Clathrin-link; Clathrin, heavy-chain linker
    pfam13838
    Location:356421
    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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