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

    Gene ID: 8218, updated on 28-Oct-2024

    Summary

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    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; AllianceGenome:HGNC:2093
    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
    all
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    Genomic context

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    See CLTCL1 in Genome Data Viewer
    Location:
    22q11.21
    Exon count:
    35
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (19179473..19291719, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (19555423..19668426, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (19166986..19279242, complement)

    Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:19159167-19160103 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19162549-19163296 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:19165547-19166294 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13457 Neighboring gene long intergenic non-protein coding RNA 1311 Neighboring gene solute carrier family 25 member 1 Neighboring gene uncharacterized LOC112268289 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:19205227-19205964 Neighboring gene NANOG hESC enhancer GRCh37_chr22:19210904-19211455 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr22:19220751-19221950 Neighboring gene small nucleolar RNA SNORA15 Neighboring gene ribosomal protein L34 pseudogene 35 Neighboring gene keratin 18 pseudogene 62 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19262319-19262820 Neighboring gene dishevelled segment polarity protein 1 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19262821-19263320 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19278431-19278944 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:19279055-19279239 Neighboring gene uncharacterized LOC105372859 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19284079-19284580 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19284581-19285080 Neighboring gene histone cell cycle regulator Neighboring gene RNA, 7SL, cytoplasmic 168, pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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

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    Related articles in PubMed

    1. Isolation of a new clathrin heavy chain gene with muscle-specific expression from the region commonly deleted in velo-cardio-facial syndrome. Sirotkin H, et al. Hum Mol Genet, 1996 May. PMID 8733128
    2. A novel disorder reveals clathrin heavy chain-22 is essential for human pain and touch development. Nahorski MS, et al. Brain, 2015 Aug. PMID 26068709, Free PMC Article
    3. Clathrin heavy chain 22 contributes to the control of neuropeptide degradation and secretion during neuronal development. Nahorski MS, et al. Sci Rep, 2018 Feb 5. PMID 29402896, Free PMC Article
    4. Cloning and characterization of a novel human clathrin heavy chain gene (CLTCL). Long KR, et al. Genomics, 1996 Aug 1. PMID 8844170
    5. Genetic diversity of CHC22 clathrin impacts its function in glucose metabolism. Fumagalli M, et al. Elife, 2019 Jun 4. PMID 31159924, Free PMC Article

    See all (78) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Building GLUT4 Vesicles: CHC22 Clathrin's Human Touch.
      Title: Building GLUT4 Vesicles: CHC22 Clathrin's Human Touch.
    2. These analyses suggest that ancestral human dietary change influenced selection of allotypes that affect CHC22's role in metabolism and have potential to differentially influence the human insulin response.
      Title: Genetic diversity of CHC22 clathrin impacts its function in glucose metabolism.
    3. Provide biochemical evidence for separate regulation and distinct functional niches for CHC17 and CHC22 in HeLa cells. Furthermore, the greater stability of the CHC22 coat relative to the CHC17 coat may be relevant to its excessive accumulation with GLUT4 during insulin resistance.
      Title: CHC22 and CHC17 clathrins have distinct biochemical properties and display differential regulation and function.
    4. Clathrin heavy chain 22 contributes to the control of neuropeptide degradation and secretion during neuronal development. Study suggests This suggests that a reduction in CHC22 expression in sensory neural precursors may license a step in neuron precursor neurodevelopment; and that this step is mediated through control of a novel neuropeptide processing pathway.
      Title: Clathrin heavy chain 22 contributes to the control of neuropeptide degradation and secretion during neuronal development.
    5. CLTCL1 is significantly upregulated in the developing human brain
      Title: A novel disorder reveals clathrin heavy chain-22 is essential for human pain and touch development.
    6. Depletion of clathrin heavy chain (CHC)17, but not the CHC22 clathrin isoform, by ribonucleic acid interference (RNAi) induces centrosome amplification and multipolar spindles.
      Title: Clathrin promotes centrosome integrity in early mitosis through stabilization of centrosomal ch-TOG.
    7. A protein encoded by this locus was found to be differentially expressed in postmortem brains from patients with atypical frontotemporal lobar degeneration.
      Title: Proteomic analysis identifies dysfunction in cellular transport, energy, and protein metabolism in different brain regions of atypical frontotemporal lobar degeneration.
    8. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    9. CHC22 was required for retrograde trafficking of certain cargo molecules from endosomes to the trans-Golgi network.
      Title: The clathrin heavy chain isoform CHC22 functions in a novel endosomal sorting step.
    10. role for CHC22 in formation of insulin-responsive GLUT4 compartments in muscle & adipocytes; CHC22 associated with expanded GLUT4 compartments in muscle in type 2 diabetes
      Title: A role for the CHC22 clathrin heavy-chain isoform in human glucose metabolism.
    Submit: New GeneRIF Correction See all GeneRIFs (11)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    HIV-1 interactions

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    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

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ36032

    Gene Ontology Provided by GOA

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

    General protein information

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    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)

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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_033805.1 RefSeqGene

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

    mRNA and Protein(s)

    1. NM_001835.4 → NP_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:979 → 1119
      CLH; Clathrin heavy chain repeat homology
      pfam00637
      Location:983 → 1119
      Clathrin; Region in Clathrin and VPS
      pfam01394
      Location:198 → 234
      Clathrin_propel; Clathrin propeller repeat
      pfam09268
      Location:331 → 353
      Clathrin-link; Clathrin, heavy-chain linker
      pfam13838
      Location:364 → 421
      Clathrin_H_link; Clathrin-H-link

    2. NM_007098.4 → NP_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
      B7Z7U5, P53675, Q14017, Q15808, Q15809
      Related
      ENSP00000441158.1, ENST00000427926.6
      Conserved Domains (5) summary
      smart00299
      Location:979 → 1119
      CLH; Clathrin heavy chain repeat homology
      pfam00637
      Location:1427 → 1564
      Clathrin; Region in Clathrin and VPS
      pfam01394
      Location:198 → 234
      Clathrin_propel; Clathrin propeller repeat
      pfam09268
      Location:331 → 353
      Clathrin-link; Clathrin, heavy-chain linker
      pfam13838
      Location:364 → 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_000022.11 Reference GRCh38.p14 Primary Assembly

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

    mRNA and Protein(s)

    1. XM_047441517.1 → XP_047297473.1  clathrin heavy chain 2 isoform X11

    2. XM_047441515.1 → XP_047297471.1  clathrin heavy chain 2 isoform X9

    3. XM_017028954.3 → XP_016884443.1  clathrin heavy chain 2 isoform X2

    4. XM_047441518.1 → XP_047297474.1  clathrin heavy chain 2 isoform X12

    5. XM_047441516.1 → XP_047297472.1  clathrin heavy chain 2 isoform X10

    6. XM_047441513.1 → XP_047297469.1  clathrin heavy chain 2 isoform X5

    7. XM_047441511.1 → XP_047297467.1  clathrin heavy chain 2 isoform X3

    8. XM_017028956.3 → XP_016884445.1  clathrin heavy chain 2 isoform X7

    9. XM_047441512.1 → XP_047297468.1  clathrin heavy chain 2 isoform X4

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

    11. XM_017028955.3 → XP_016884444.1  clathrin heavy chain 2 isoform X6

    12. XM_047441514.1 → XP_047297470.1  clathrin heavy chain 2 isoform X8

    13. XM_011530401.2 → XP_011528703.1  clathrin heavy chain 2 isoform X18

      Conserved Domains (2) summary
      smart00299
      Location:376 → 516
      CLH; Clathrin heavy chain repeat homology
      pfam00637
      Location:824 → 961
      Clathrin; Region in Clathrin and VPS

    14. XM_047441520.1 → XP_047297476.1  clathrin heavy chain 2 isoform X14

    15. XM_047441519.1 → XP_047297475.1  clathrin heavy chain 2 isoform X13

    16. XM_047441521.1 → XP_047297477.1  clathrin heavy chain 2 isoform X15

      UniProtKB/TrEMBL
      A0A087WX41
      Related
      ENSP00000480709.1, ENST00000617103.4

    17. XM_047441522.1 → XP_047297478.1  clathrin heavy chain 2 isoform X16

    18. XM_017028957.3 → XP_016884446.1  clathrin heavy chain 2 isoform X17

    19. XM_047441523.1 → XP_047297479.1  clathrin heavy chain 2 isoform X17

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060946.1 Alternate T2T-CHM13v2.0

      Range
      19555423..19668426 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054325964.1 → XP_054181939.1  clathrin heavy chain 2 isoform X11

    2. XM_054325962.1 → XP_054181937.1  clathrin heavy chain 2 isoform X9

    3. XM_054325955.1 → XP_054181930.1  clathrin heavy chain 2 isoform X2

    4. XM_054325965.1 → XP_054181940.1  clathrin heavy chain 2 isoform X12

    5. XM_054325963.1 → XP_054181938.1  clathrin heavy chain 2 isoform X10

    6. XM_054325958.1 → XP_054181933.1  clathrin heavy chain 2 isoform X5

    7. XM_054325956.1 → XP_054181931.1  clathrin heavy chain 2 isoform X3

    8. XM_054325960.1 → XP_054181935.1  clathrin heavy chain 2 isoform X7

    9. XM_054325957.1 → XP_054181932.1  clathrin heavy chain 2 isoform X4

    10. XM_054325954.1 → XP_054181929.1  clathrin heavy chain 2 isoform X1

    11. XM_054325959.1 → XP_054181934.1  clathrin heavy chain 2 isoform X6

    12. XM_054325961.1 → XP_054181936.1  clathrin heavy chain 2 isoform X8

    13. XM_054325972.1 → XP_054181947.1  clathrin heavy chain 2 isoform X18

    14. XM_054325967.1 → XP_054181942.1  clathrin heavy chain 2 isoform X14

    15. XM_054325966.1 → XP_054181941.1  clathrin heavy chain 2 isoform X13

    16. XM_054325968.1 → XP_054181943.1  clathrin heavy chain 2 isoform X15

      UniProtKB/TrEMBL
      A0A087WX41

    17. XM_054325969.1 → XP_054181944.1  clathrin heavy chain 2 isoform X16

    18. XM_054325971.1 → XP_054181946.1  clathrin heavy chain 2 isoform X17

    19. XM_054325970.1 → XP_054181945.1  clathrin heavy chain 2 isoform X17

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P53675.2 GenPept UniProtKB/Swiss-Prot:P53675

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