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CLTCL1 clathrin heavy chain like 1 [ Homo sapiens (human) ]

Gene ID: 8218, updated on 13-Mar-2020

Summary

Official Symbol
CLTCL1provided by HGNC
Official Full Name
clathrin heavy chain like 1provided by HGNC
Primary source
HGNC:HGNC:2093
See related
Ensembl:ENSG00000070371 MIM:601273
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
CLTD; CHC22; CLH22; CLTCL
Summary
This gene is a member of the clathrin heavy chain family and encodes a major protein of the polyhedral coat of coated pits and vesicles. Chromosomal aberrations involving this gene are associated with meningioma, DiGeorge syndrome, and velo-cardio-facial syndrome. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2009]
Expression
Biased expression in testis (RPKM 21.0), bone marrow (RPKM 6.6) and 8 other tissues See more
Orthologs

Genomic context

See CLTCL1 in Genome Data Viewer
Location:
22q11.21
Exon count:
34
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 22 NC_000022.11 (19179473..19291719, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (19166986..19279247, complement)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1311 Neighboring gene solute carrier family 25 member 1 Neighboring gene uncharacterized LOC112268289 Neighboring gene ribosomal protein L34 pseudogene 35 Neighboring gene keratin 18 pseudogene 62 Neighboring gene dishevelled segment polarity protein 1 pseudogene 1 Neighboring gene uncharacterized LOC105372859 Neighboring gene histone cell cycle regulator Neighboring gene RNA, 7SL, cytoplasmic 168, pseudogene

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

NHGRI GWAS Catalog

Description
Novel Loci for metabolic networks and multi-tissue expression studies reveal genes for atherosclerosis.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Nef nef Genome-wide shRNA screening identifies CLTCL1, which is required for HIV-1 Nef-induced downregulation of CD4 in HeLa CD4+ cells PubMed

Go to the HIV-1, Human Interaction Database

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ36032

Gene Ontology Provided by GOA

Function Evidence Code Pubs
clathrin light chain binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
structural molecule activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
anatomical structure morphogenesis TAS
Traceable Author Statement
more info
PubMed 
intracellular protein transport IEA
Inferred from Electronic Annotation
more info
 
membrane organization TAS
Traceable Author Statement
more info
 
mitotic cell cycle IDA
Inferred from Direct Assay
more info
PubMed 
NOT mitotic cell cycle IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of glucose import IMP
Inferred from Mutant Phenotype
more info
PubMed 
receptor-mediated endocytosis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
receptor-mediated endocytosis IDA
Inferred from Direct Assay
more info
PubMed 
retrograde transport, endosome to Golgi IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
clathrin coat of trans-Golgi network vesicle IEA
Inferred from Electronic Annotation
more info
 
clathrin complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
clathrin-coated endocytic vesicle IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
clathrin-coated endocytic vesicle NAS
Non-traceable Author Statement
more info
PubMed 
clathrin-coated pit IDA
Inferred from Direct Assay
more info
PubMed 
clathrin-coated vesicle IDA
Inferred from Direct Assay
more info
PubMed 
coated vesicle IDA
Inferred from Direct Assay
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
NOT early endosome IDA
Inferred from Direct Assay
more info
PubMed 
extracellular exosome HDA PubMed 
late endosome IDA
Inferred from Direct Assay
more info
PubMed 
membrane HDA PubMed 
NOT plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
NOT recycling endosome IDA
Inferred from Direct Assay
more info
PubMed 
sorting endosome IDA
Inferred from Direct Assay
more info
PubMed 
spindle IDA
Inferred from Direct Assay
more info
PubMed 
trans-Golgi network IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
clathrin heavy chain 2
Names
CLH-22
Clathrin, heavy polypeptide D
clathrin heavy chain on chromosome 22
clathrin, heavy polypeptide-like 1

NCBI Reference Sequences (RefSeq)

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_033805.1 RefSeqGene

    Range
    4998..117244
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001835.4NP_001826.3  clathrin heavy chain 2 isoform 2

    See identical proteins and their annotated locations for NP_001826.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 3' coding region, compared to variant 1. The resulting isoform (2) lacks an internal segment near the C-terminus, compared to isoform 1.
    Source sequence(s)
    AC000085, AK302506, BP281338, U41763
    Consensus CDS
    CCDS54497.2
    UniProtKB/Swiss-Prot
    P53675
    Related
    ENSP00000485020.1, ENST00000621271.4
    Conserved Domains (5) summary
    smart00299
    Location:9791119
    CLH; Clathrin heavy chain repeat homology
    pfam00637
    Location:9831119
    Clathrin; Region in Clathrin and VPS
    pfam01394
    Location:198234
    Clathrin_propel; Clathrin propeller repeat
    pfam09268
    Location:331353
    Clathrin-link; Clathrin, heavy-chain linker
    pfam13838
    Location:364421
    Clathrin_H_link; Clathrin-H-link
  2. NM_007098.4NP_009029.3  clathrin heavy chain 2 isoform 1

    See identical proteins and their annotated locations for NP_009029.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC000085, AK302506, BP281338, U41763, X95486
    Consensus CDS
    CCDS46662.2
    UniProtKB/Swiss-Prot
    P53675
    Related
    ENSP00000441158.1, ENST00000427926.6
    Conserved Domains (5) summary
    smart00299
    Location:9791119
    CLH; Clathrin heavy chain repeat homology
    pfam00637
    Location:14271564
    Clathrin; Region in Clathrin and VPS
    pfam01394
    Location:198234
    Clathrin_propel; Clathrin propeller repeat
    pfam09268
    Location:331353
    Clathrin-link; Clathrin, heavy-chain linker
    pfam13838
    Location:364421
    Clathrin_H_link; Clathrin-H-link

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000022.11 Reference GRCh38.p13 Primary Assembly

    Range
    19179473..19291719 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017028954.2XP_016884443.1  clathrin heavy chain 2 isoform X2

  2. XM_017028956.2XP_016884445.1  clathrin heavy chain 2 isoform X4

  3. XM_017028953.2XP_016884442.1  clathrin heavy chain 2 isoform X1

  4. XM_017028955.2XP_016884444.1  clathrin heavy chain 2 isoform X3

  5. XM_011530401.2XP_011528703.1  clathrin heavy chain 2 isoform X6

    Conserved Domains (2) summary
    smart00299
    Location:376516
    CLH; Clathrin heavy chain repeat homology
    pfam00637
    Location:824961
    Clathrin; Region in Clathrin and VPS
  6. XM_017028957.2XP_016884446.1  clathrin heavy chain 2 isoform X5

RNA

  1. XR_001755314.2 RNA Sequence

  2. XR_001755313.2 RNA Sequence

  3. XR_001755312.2 RNA Sequence

  4. XR_001755311.2 RNA Sequence

  5. XR_001755309.2 RNA Sequence

  6. XR_937923.3 RNA Sequence

  7. XR_001755310.2 RNA Sequence

    Related
    ENST00000617103.4
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