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CLTC (clathrin heavy polypeptide)

Written2001-08Jean-Loup Huret
Genetics, Dept Medical Information, University of Poitiers, CHU Poitiers Hospital, F-86021 Poitiers, France
Updated2003-08Jean-Loup Huret, Sylvie Senon
Genetics, Dept Medical Information, University of Poitiers, CHU Poitiers Hospital, F-86021 Poitiers, France
Updated2005-04Pedram Argani, Marc Ladanyi
The Johns Hopkins Hospital/ Surgical Pathology Weinberg Building, Room 2242, 4O1 N. Broadway, Baltimore, MD 21231-2410, USA

(Note : for Links provided by Atlas : click)

Identity

Other namesclathrin heavy chain
KIAAOO34
CLH-17
HGNC (Hugo) CLTC
LocusID (NCBI) 1213
Atlas_Id 360
Location 17q23.1  [Link to chromosome band 17q23]
Location_base_pair Starts at 57697050 and ends at 57774317 bp from pter ( according to hg19-Feb_2009)  [Mapping CLTC.png]
Fusion genes
(updated 2016)
ALK (2p23.2) / CLTC (17q23.1)CLTC (17q23.1) / ALK (2p23.2)CLTC (17q23.1) / CLTC (17q23.1)
CLTC (17q23.1) / COPS8 (2q37.3)CLTC (17q23.1) / FAM129C (19p13.11)CLTC (17q23.1) / FCHO2 (5q13.2)
CLTC (17q23.1) / OTOP3 (17q25.1)CLTC (17q23.1) / PTRH2 (17q23.1)CLTC (17q23.1) / ROS1 (6q22.1)
CLTC (17q23.1) / RPS6KB1 (17q23.1)CLTC (17q23.1) / SLTM (15q22.1)CLTC (17q23.1) / TFE3 (Xp11.23)
CLTC (17q23.1) / TFEB (6p21.1)CLTC (17q23.1) / VMP1 (17q23.1)KMT2A (11q23.3) / CLTC (17q23.1)
MYO1D (17q11.2) / CLTC (17q23.1)NF1 (17q11.2) / CLTC (17q23.1)PPP1R9B (17q21.33) / CLTC (17q23.1)
PTK2 (8q24.3) / CLTC (17q23.1)SERPINA1 (14q32.13) / CLTC (17q23.1)SLTM (15q22.1) / CLTC (17q23.1)
TFE3 (Xp11.23) / CLTC (17q23.1)USP32 (17q23.1) / CLTC (17q23.1)VMP1 (17q23.1) / CLTC (17q23.1)
Note must not be confused with CLTCL1 (clathrin heavy polypeptide-like 1).

DNA/RNA

Transcription 32 exons, 6111 bp mRNA

Protein

Description Clathrin is the major protein constituent of the coat that surrounds organelles (cytoplasmic vesicles) to mediate selective protein transport. Clathrin coats are involved in receptor-mediated endocytosis and intracellular trafficking and recycling of receptors, which accounts for its characteristic punctate cytoplasmic and perinuclear cellular distribution. Structurally, clathrin is a triskelion (three-legged) shaped protein complex that is composed of a trimer of heavy chains (CLTC) each bound to a single light chain. CLTC is a 1675 amino acid residue protein encoded by a gene consisting of 32 exons. Its known domains include a N-terminal globular domain (residues 1-494) that interacts with adaptor proteins (AP-1, AP-2, b-arrestin), a light chain-binding region (residues 1074-1552), and a trimerization domain (residues 1550-1600) near the C-terminus.
Localisation Cytoplasmic vesicles
Function mediate endocytosis of transmembrane receptors.

Implicated in

Note
Entity Anaplasic large cell lymphoma (ALCL) with t(2;17)(p23;q23) --> ALK - CLTC
Disease ALCL are high grade non Hodgkin lymphomas; ALK+ ALCL are ALCL where ALK is involved in a fusion gene; ALK+ ALCL represent 50 to 60 % of ALCL cases (they are CD30+, ALK+;); belong to the "cytoplasmic ALK+" subset.
Prognosis Although presenting as a high grade tumour, a 80% five yr survival is associated with this anomaly
Hybrid/Mutated Gene 5' CLTC - 3' ALK
Abnormal Protein NH2 CLTC - COOH ALK
  
Entity Inflammatory myofibroblastic tumors with t(2;17)(p23;q23)
Note In these tumors, the fusion point in CLTC is identical, being at amino acid 1634 (corresponding to the 3' end of exon 31 of CLTC), such that almost all of CLTC is included in the fusion protein, including its trimerization domain . As a fusion partner, CLTC has been postulated to provide CLTC-ALK with deregulated expression driven by its constitutively activated promoter and constitutive oligomerization of the chimeric protein via the CLTC multimerization domains normally used for clathrin coat assembly. Since ALK is a tyrosine kinase that is activated by cross-phosphorylation following ligand binding, CLTC-ALK-induced oligomerization may result in a constitutively activated ALK tyrosine kinase domain. In this sense, CLTC is likely to function in CLTC-ALK as other prototypical "dimerizing translocation partners" in fusions involving tyrosine kinase genes.
Disease rare soft tissue tumour found in children and young adults
Prognosis good prognosis
Hybrid/Mutated Gene 5' CLTC - 3' ALK
  
Entity Xp11 renal translocation carcinoma with t(X;17)(p11;q23)
Note In the CLTC-TFE3 fusion, the fusion point on CLTC is at amino acid 932 (corresponding to the end of exon 17), thereby excluding the CLTC trimerization domain from the predicted fusion protein. As in other TFE3 gene fusions, the nuclear localization and DNA binding domains of TFE3 are retained in CLTC-TFE3. Based on these features and existing data on other TFE3 fusion proteins, CLTC-TFE3 may act as an aberrant transcription factor, with the CLTC promoter driving constitutive expression.
Disease rare renal carcinoma (single case report)
Prognosis Unknown prognosis
Hybrid/Mutated Gene 5' CLTC 3'TFE3
  

Breakpoints

 

Bibliography

A novel CLTC-TFE3 gene fusion in pediatric renal adenocarcinoma with t(X;17)(p11.2;q23).
Argani P, Lui MY, Couturier J, Bouvier R, Fournet JC, Ladanyi M
Oncogene. 2003 ; 22 (34) : 5374-5378.
PMID 12917640
 
Fusion of the ALK gene to the clathrin heavy chain gene, CLTC, in inflammatory myofibroblastic tumor.
Bridge JA, Kanamori M, Ma Z, Pickering D, Hill DA, Lydiatt W, Lui MY, Colleoni GW, Antonescu CR, Ladanyi M, Morris SW
The American journal of pathology. 2001 ; 159 (2) : 411-415.
PMID 11485898
 
Identification of novel fusion partners of ALK, the anaplastic lymphoma kinase, in anaplastic large-cell lymphoma and inflammatory myofibroblastic tumor.
Cools J, Wlodarska I, Somers R, Mentens N, Pedeutour F, Maes B, De Wolf-Peeters C, Pauwels P, Hagemeijer A, Marynen P
Genes, chromosomes & cancer. 2002 ; 34 (4) : 354-362.
PMID 12112524
 
Human clathrin heavy chain (CLTC): partial molecular cloning, expression, and mapping of the gene to human chromosome 17q11-qter.
Dodge GR, Kovalszky I, McBride OW, Yi HF, Chu ML, Saitta B, Stokes DG, Iozzo RV
Genomics. 1991 ; 11 (1) : 174-178.
PMID 1765375
 
Clathrin.
Kirchhausen T
Annual review of biochemistry. 2000 ; 69 : 699-727.
PMID 10966473
 
Clathrin-coated vesicle formation and protein sorting: an integrated process.
Schmid SL
Annual review of biochemistry. 1997 ; 66 : 511-548.
PMID 9242916
 
Clathrin self-assembly is mediated by a tandemly repeated superhelix.
Ybe JA, Brodsky FM, Hofmann K, Lin K, Liu SH, Chen L, Earnest TN, Fletterick RJ, Hwang PK
Nature. 1999 ; 399 (6734) : 371-375.
PMID 10360576
 

Citation

This paper should be referenced as such :
Argani, P ; Ladanyi, M
CLTC (clathrin heavy polypeptide)
Atlas Genet Cytogenet Oncol Haematol. 2005;9(3):211-213.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/CLTCID360.html
History of this paper:
Huret, JL. CLTC (clathrin heavy polypeptide). Atlas Genet Cytogenet Oncol Haematol. 2001;5(4):256-256.
http://documents.irevues.inist.fr/bitstream/handle/2042/37778/08-2001-CLTCID360.pdf
Huret, JL ; Senon, S. CLTC (clathrin heavy polypeptide). Atlas Genet Cytogenet Oncol Haematol. 2003;7(4):222-223.
http://documents.irevues.inist.fr/bitstream/handle/2042/38007/08-2003-CLTCID360.pdf


Other Leukemias implicated (Data extracted from papers in the Atlas) [ 3 ]
  ALK -positive diffuse large B-cell lymphoma
Anaplastic large cell lymphoma (ALCL)
t(2;17)(p23;q23) CLTC/ALK

Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 3 ]
  Soft Tissues: Inflammatory myofibroblastic tumor
Kidney: Renal cell carcinoma with t(X;17)(p11;q23) CLTC/TFE3
Soft tissue tumors: an overview
Soft Tissues: Inflammatory myofibroblastic tumor with t(2;17)(p23;q23) CLTC/ALK

External links

Nomenclature
HGNC (Hugo)CLTC   2092
Cards
AtlasCLTCID360
Entrez_Gene (NCBI)CLTC  1213  clathrin heavy chain
AliasesCHC; CHC17; CLH-17; CLTCL2; 
Hc
GeneCards (Weizmann)CLTC
Ensembl hg19 (Hinxton)ENSG00000141367 [Gene_View]  chr17:57697050-57774317 [Contig_View]  CLTC [Vega]
Ensembl hg38 (Hinxton)ENSG00000141367 [Gene_View]  chr17:57697050-57774317 [Contig_View]  CLTC [Vega]
ICGC DataPortalENSG00000141367
TCGA cBioPortalCLTC
AceView (NCBI)CLTC
Genatlas (Paris)CLTC
WikiGenes1213
SOURCE (Princeton)CLTC
Genomic and cartography
GoldenPath hg19 (UCSC)CLTC  -     chr17:57697050-57774317 +  17q23.1   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)CLTC  -     17q23.1   [Description]    (hg38-Dec_2013)
EnsemblCLTC - 17q23.1 [CytoView hg19]  CLTC - 17q23.1 [CytoView hg38]
Mapping of homologs : NCBICLTC [Mapview hg19]  CLTC [Mapview hg38]
OMIM118955   
Gene and transcription
Genbank (Entrez)AB073891 AK127134 BC015854 BC036430 BC051800
RefSeq transcript (Entrez)NM_001288653 NM_004859
RefSeq genomic (Entrez)NC_000017 NC_018928 NT_010783 NW_004929407
Consensus coding sequences : CCDS (NCBI)CLTC
Cluster EST : UnigeneHs.491351 [ NCBI ]
CGAP (NCI)Hs.491351
Alternative Splicing GalleryENSG00000141367
Gene ExpressionCLTC [ NCBI-GEO ]   CLTC [ EBI - ARRAY_EXPRESS ]   CLTC [ SEEK ]   CLTC [ MEM ]
Gene Expression Viewer (FireBrowse)CLTC [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)1213
GTEX Portal (Tissue expression)CLTC
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ00610 (Uniprot)
NextProtQ00610  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ00610
Splice isoforms : SwissVarQ00610 (Swissvar)
PhosPhoSitePlusQ00610
Domaine pattern : Prosite (Expaxy)CHCR (PS50236)   
Domains : Interpro (EBI)ARM-type_fold    Clathrin_H-chain/VPS_repeat    Clathrin_H-chain_link/propller    Clathrin_H-chain_linker_core    Clathrin_H-chain_propeller_N    Clathrin_H-chain_propeller_rpt    Clathrin_heavy_chain    TPR-like_helical_dom   
Domain families : Pfam (Sanger)Clathrin (PF00637)    Clathrin-link (PF09268)    Clathrin_propel (PF01394)   
Domain families : Pfam (NCBI)pfam00637    pfam09268    pfam01394   
Domain families : Smart (EMBL)CLH (SM00299)  
DMDM Disease mutations1213
Blocks (Seattle)CLTC
PDB (SRS)2XZG    4G55   
PDB (PDBSum)2XZG    4G55   
PDB (IMB)2XZG    4G55   
PDB (RSDB)2XZG    4G55   
Structural Biology KnowledgeBase2XZG    4G55   
SCOP (Structural Classification of Proteins)2XZG    4G55   
CATH (Classification of proteins structures)2XZG    4G55   
SuperfamilyQ00610
Human Protein AtlasENSG00000141367
Peptide AtlasQ00610
HPRD00350
IPIIPI00024067   IPI00455383   
Protein Interaction databases
DIP (DOE-UCLA)Q00610
IntAct (EBI)Q00610
FunCoupENSG00000141367
BioGRIDCLTC
STRING (EMBL)CLTC
ZODIACCLTC
Ontologies - Pathways
QuickGOQ00610
Ontology : AmiGOosteoblast differentiation  double-stranded RNA binding  structural molecule activity  protein binding  spindle  cytosol  plasma membrane  focal adhesion  intracellular protein transport  receptor-mediated endocytosis  mitotic nuclear division  membrane  antigen processing and presentation of exogenous peptide antigen via MHC class II  protein kinase binding  clathrin coat  clathrin coat of trans-Golgi network vesicle  clathrin coat of coated pit  clathrin-coated vesicle  clathrin-coated endocytic vesicle membrane  receptor internalization  clathrin light chain binding  trans-Golgi network membrane  transferrin transport  endolysosome membrane  retrograde transport, endosome to Golgi  melanosome  intracellular membrane-bounded organelle  protein complex  poly(A) RNA binding  Wnt signaling pathway, planar cell polarity pathway  extracellular exosome  clathrin complex  negative regulation of hyaluronan biosynthetic process  negative regulation of hyaluronan biosynthetic process  negative regulation of protein localization to plasma membrane  extracellular vesicle  
Ontology : EGO-EBIosteoblast differentiation  double-stranded RNA binding  structural molecule activity  protein binding  spindle  cytosol  plasma membrane  focal adhesion  intracellular protein transport  receptor-mediated endocytosis  mitotic nuclear division  membrane  antigen processing and presentation of exogenous peptide antigen via MHC class II  protein kinase binding  clathrin coat  clathrin coat of trans-Golgi network vesicle  clathrin coat of coated pit  clathrin-coated vesicle  clathrin-coated endocytic vesicle membrane  receptor internalization  clathrin light chain binding  trans-Golgi network membrane  transferrin transport  endolysosome membrane  retrograde transport, endosome to Golgi  melanosome  intracellular membrane-bounded organelle  protein complex  poly(A) RNA binding  Wnt signaling pathway, planar cell polarity pathway  extracellular exosome  clathrin complex  negative regulation of hyaluronan biosynthetic process  negative regulation of hyaluronan biosynthetic process  negative regulation of protein localization to plasma membrane  extracellular vesicle  
Pathways : KEGGLysosome    Endocytosis    Synaptic vesicle cycle    Endocrine and other factor-regulated calcium reabsorption    Huntington's disease    Bacterial invasion of epithelial cells   
REACTOMEQ00610 [protein]
REACTOME PathwaysR-HSA-196025 Formation of annular gap junctions [pathway]
REACTOME PathwaysR-HSA-3928665 EPH-ephrin mediated repulsion of cells [pathway]
REACTOME PathwaysR-HSA-190873 Gap junction degradation [pathway]
REACTOME PathwaysR-HSA-5099900 WNT5A-dependent internalization of FZD4 [pathway]
REACTOME PathwaysR-HSA-432720 Lysosome Vesicle Biogenesis [pathway]
NDEx Network
Atlas of Cancer Signalling NetworkCLTC
Wikipedia pathwaysCLTC
Orthology - Evolution
OrthoDB1213
GeneTree (enSembl)ENSG00000141367
Phylogenetic Trees/Animal Genes : TreeFamCLTC
Homologs : HomoloGeneCLTC
Homology/Alignments : Family Browser (UCSC)CLTC
Gene fusions - Rearrangements
Fusion : MitelmanCLTC/ALK [17q23.1/2p23.2]  
Fusion : MitelmanCLTC/FAM129C [17q23.1/19p13.11]  [t(17;19)(q23;p13)]  
Fusion : MitelmanCLTC/OTOP3 [17q23.1/17q25.1]  [t(17;17)(q23;q25)]  
Fusion : MitelmanCLTC/PTRH2 [17q23.1/17q23.1]  [t(17;17)(q23;q23)]  
Fusion : MitelmanCLTC/ROS1 [17q23.1/6q22.1]  [t(6;17)(q22;q23)]  
Fusion : MitelmanCLTC/TFE3 [17q23.1/Xp11.23]  [t(X;17)(p11;q23)]  
Fusion : MitelmanCLTC/TFEB [17q23.1/6p21.1]  [t(6;17)(p21;q23)]  
Fusion : MitelmanCLTC/VMP1 [17q23.1/17q23.1]  [t(17;17)(q23;q23)]  
Fusion : MitelmanNF1/CLTC [17q11.2/17q23.1]  [t(17;17)(q11;q23)]  
Fusion : MitelmanUSP32/CLTC [17q23.1/17q23.1]  [t(17;17)(q23;q23)]  
Fusion : MitelmanVMP1/CLTC [17q23.1/17q23.1]  [t(17;17)(q23;q23)]  
Fusion : COSMICCLTC [17q23.1]  -  TFE3 [Xp11.23]  [fusion_799]  [fusion_800]  
Fusion: TCGACLTC 17q23.1 FAM129C 19p13.11 BRCA
Fusion: TCGACLTC 17q23.1 OTOP3 17q25.1 BRCA
Fusion: TCGACLTC 17q23.1 PTRH2 17q23.1 LUAD
Fusion: TCGACLTC 17q23.1 ROS1 6q22.1 LUAD
Fusion: TCGANF1 17q11.2 CLTC 17q23.1 BRCA
Fusion: TCGAUSP32 17q23.1 CLTC 17q23.1 BRCA
Fusion: TCGAVMP1 17q23.1 CLTC 17q23.1 BRCA
Fusion : TICdbCLTC [17q23.1]  -  ALK [2p23.2]
Fusion : TICdbCLTC [17q23.1]  -  TFE3 [Xp11.23]
Fusion Cancer (Beijing)CLTC [17q23.1]  -  VMP1 [17q23.1]  [FUSC003429]
Fusion Cancer (Beijing)SERPINA1 [14q32.13]  -  CLTC [17q23.1]  [FUSC002196]
Polymorphisms : SNP, variants
NCBI Variation ViewerCLTC [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)CLTC
dbVarCLTC
ClinVarCLTC
1000_GenomesCLTC 
Exome Variant ServerCLTC
ExAC (Exome Aggregation Consortium)CLTC (select the gene name)
Genetic variants : HAPMAP1213
Genomic Variants (DGV)CLTC [DGVbeta]
Mutations
ICGC Data PortalCLTC 
TCGA Data PortalCLTC 
Broad Tumor PortalCLTC
OASIS PortalCLTC [ Somatic mutations - Copy number]
Cancer Gene: CensusCLTC 
Somatic Mutations in Cancer : COSMICCLTC 
intOGen PortalCLTC
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch CLTC
DgiDB (Drug Gene Interaction Database)CLTC
DoCM (Curated mutations)CLTC (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)CLTC (select a term)
intoGenCLTC
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)17:57697050-57774317  ENSG00000141367
CONAN: Copy Number AnalysisCLTC 
Mutations and Diseases : HGMDCLTC
OMIM118955   
MedgenCLTC
Genetic Testing Registry CLTC
NextProtQ00610 [Medical]
TSGene1213
GENETestsCLTC
Huge Navigator CLTC [HugePedia]
snp3D : Map Gene to Disease1213
BioCentury BCIQCLTC
ClinGenCLTC
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD1213
Chemical/Pharm GKB GenePA26618
Clinical trialCLTC
Miscellaneous
canSAR (ICR)CLTC (select the gene name)
Probes
Litterature
PubMed240 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineCLTC
EVEXCLTC
GoPubMedCLTC
iHOPCLTC
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Wed Aug 10 19:00:50 CEST 2016

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