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 20... See more...

Aliases for CLTCL1 Gene

Aliases for CLTCL1 Gene

  • Clathrin Heavy Chain Like 1 2 3 5
  • Clathrin Heavy Chain On Chromosome 22 3 4
  • Clathrin, Heavy Polypeptide-Like 1 2 3
  • Clathrin Heavy Chain 2 3 4
  • CLH-22 3 4
  • CLTCL 3 4
  • CLH22 3 4
  • CLTD 3 4
  • Clathrin, Heavy Polypeptide D 3
  • Clathrin, Heavy Chain-Like 1 2
  • CHC22 3

External Ids for CLTCL1 Gene

Previous HGNC Symbols for CLTCL1 Gene

  • CLTCL

Previous GeneCards Identifiers for CLTCL1 Gene

  • GC22M016107
  • GC22M017541
  • GC22M002788

Summaries for CLTCL1 Gene

Entrez Gene Summary for CLTCL1 Gene

  • 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]

GeneCards Summary for CLTCL1 Gene

CLTCL1 (Clathrin Heavy Chain Like 1) is a Protein Coding gene. Diseases associated with CLTCL1 include Congenital Insensitivity To Pain With Severe Intellectual Disability and Chromosome 22Q11.2 Duplication Syndrome. Among its related pathways are Notch Signaling Pathway (WikiPathways) and Synaptic vesicle cycle. Gene Ontology (GO) annotations related to this gene include binding and structural molecule activity. An important paralog of this gene is CLTC.

UniProtKB/Swiss-Prot Summary for CLTCL1 Gene

  • Clathrin is the major protein of the polyhedral coat of coated pits and vesicles. Two different adapter protein complexes link the clathrin lattice either to the plasma membrane or to the trans-Golgi network (By similarity).

Additional gene information for CLTCL1 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CLTCL1 Gene

Genomics for CLTCL1 Gene

GeneHancer (GH) Regulatory Elements for CLTCL1 Gene

Promoters and enhancers for CLTCL1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CLTCL1 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CLTCL1

Top Transcription factor binding sites by QIAGEN in the CLTCL1 gene promoter:
  • NRSF form 1
  • NRSF form 2

Genomic Locations for CLTCL1 Gene

Genomic Locations for CLTCL1 Gene
chr22:19,179,473-19,291,725
(GRCh38/hg38)
Size:
112,253 bases
Orientation:
Minus strand
chr22:19,166,986-19,279,239
(GRCh37/hg19)
Size:
112,254 bases
Orientation:
Minus strand

Genomic View for CLTCL1 Gene

Genes around CLTCL1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CLTCL1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CLTCL1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLTCL1 Gene

Proteins for CLTCL1 Gene

  • Protein details for CLTCL1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P53675-CLH2_HUMAN
    Recommended name:
    Clathrin heavy chain 2
    Protein Accession:
    P53675
    Secondary Accessions:
    • B7Z7U5
    • Q14017
    • Q15808
    • Q15809

    Protein attributes for CLTCL1 Gene

    Size:
    1640 amino acids
    Molecular mass:
    187030 Da
    Quaternary structure:
    • Clathrin triskelions, composed of 3 heavy chains and 3 light chains, are the basic subunits of the clathrin coat. In the presence of light chains, hub assembly is influenced by both the pH and the concentration of calcium (By similarity). May interact with OCRL (By similarity).

    Alternative splice isoforms for CLTCL1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CLTCL1 Gene

Post-translational modifications for CLTCL1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for CLTCL1 Gene

Domains & Families for CLTCL1 Gene

Gene Families for CLTCL1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for CLTCL1 Gene

Suggested Antigen Peptide Sequences for CLTCL1 Gene

GenScript: Design optimal peptide antigens:
  • CLTCL1 protein (A4FU99_HUMAN)
  • Clathrin heavy chain on chromosome 22 (CLH2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P53675

UniProtKB/Swiss-Prot:

CLH2_HUMAN :
  • The C-terminal third of the heavy chains forms the hub of the triskelion. This region contains the trimerization domain and the light-chain binding domain involved in the assembly of the clathrin lattice.
  • Belongs to the clathrin heavy chain family.
Domain:
  • The C-terminal third of the heavy chains forms the hub of the triskelion. This region contains the trimerization domain and the light-chain binding domain involved in the assembly of the clathrin lattice.
  • The N-terminal seven-bladed beta-propeller is formed by WD40-like repeats, and projects inward from the polyhedral outer clathrin coat. It constitutes a major protein-protein interaction node (By similarity).
Family:
  • Belongs to the clathrin heavy chain family.
genes like me logo Genes that share domains with CLTCL1: view

Function for CLTCL1 Gene

Molecular function for CLTCL1 Gene

UniProtKB/Swiss-Prot Function:
Clathrin is the major protein of the polyhedral coat of coated pits and vesicles. Two different adapter protein complexes link the clathrin lattice either to the plasma membrane or to the trans-Golgi network (By similarity).
GENATLAS Biochemistry:
clathrin heavy chain-like sequence in the DiGeorge critical region (DGCR)

Phenotypes From GWAS Catalog for CLTCL1 Gene

Gene Ontology (GO) - Molecular Function for CLTCL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005198 structural molecule activity IEA --
GO:0005515 protein binding IPI,IEA 19478182
GO:0032051 clathrin light chain binding IEA,IBA 21873635
genes like me logo Genes that share ontologies with CLTCL1: view
genes like me logo Genes that share phenotypes with CLTCL1: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CLTCL1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for CLTCL1 Gene

Localization for CLTCL1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLTCL1 Gene

Cytoplasmic vesicle membrane; Peripheral membrane protein; Cytoplasmic side. Membrane, coated pit; Peripheral membrane protein; Cytoplasmic side. Note=Cytoplasmic face of coated pits and vesicles. {ECO:0000250}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CLTCL1 gene
Compartment Confidence
cytoskeleton 5
endosome 5
golgi apparatus 5
cytosol 4
nucleus 2
plasma membrane 1
extracellular 1
mitochondrion 1
endoplasmic reticulum 1
lysosome 1
peroxisome 0

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for CLTCL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005623 cell IEA --
GO:0005769 NOT early endosome IDA 20065094
GO:0005770 late endosome IDA 20065094
GO:0005802 trans-Golgi network IDA 19509056
GO:0005819 spindle IDA 19509056
genes like me logo Genes that share ontologies with CLTCL1: view

Pathways & Interactions for CLTCL1 Gene

genes like me logo Genes that share pathways with CLTCL1: view

SIGNOR curated interactions for CLTCL1 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for CLTCL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000278 NOT mitotic cell cycle IDA 20065094
GO:0006886 intracellular protein transport IEA --
GO:0006898 receptor-mediated endocytosis TAS,IDA 19509056
GO:0009653 anatomical structure morphogenesis TAS 8733128
GO:0016192 vesicle-mediated transport IEA --
genes like me logo Genes that share ontologies with CLTCL1: view

Drugs & Compounds for CLTCL1 Gene

(3) Drugs for CLTCL1 Gene - From: ClinicalTrials and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Calcium Approved Nutra 7884
Calamus Pharma 750
Pharmaceutical Solutions Pharma 11396
genes like me logo Genes that share compounds with CLTCL1: view

Transcripts for CLTCL1 Gene

mRNA/cDNA for CLTCL1 Gene

2 REFSEQ mRNAs :
16 NCBI additional mRNA sequence :
12 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CLTCL1

Alternative Splicing Database (ASD) splice patterns (SP) for CLTCL1 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11a · 11b ^ 12a · 12b ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^ 23 ^
SP1: - -
SP2: - -
SP3:
SP4:
SP5:
SP6:
SP7:

ExUns: 24 ^ 25 ^ 26 ^ 27a · 27b ^ 28 ^ 29a · 29b ^ 30 ^ 31a · 31b ^ 32a · 32b ^ 33 ^ 34a · 34b
SP1: - - -
SP2: - - - -
SP3: -
SP4:
SP5:
SP6:
SP7:

Relevant External Links for CLTCL1 Gene

GeneLoc Exon Structure for
CLTCL1

Expression for CLTCL1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CLTCL1 Gene

mRNA differential expression in normal tissues according to GTEx for CLTCL1 Gene

This gene is overexpressed in Muscle - Skeletal (x22.2).

Protein differential expression in normal tissues from HIPED for CLTCL1 Gene

This gene is overexpressed in Brain (44.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CLTCL1 Gene



Protein tissue co-expression partners for CLTCL1 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CLTCL1

SOURCE GeneReport for Unigene cluster for CLTCL1 Gene:

Hs.368266

mRNA Expression by UniProt/SwissProt for CLTCL1 Gene:

P53675-CLH2_HUMAN
Tissue specificity: Maximal levels in skeletal muscle. High levels in heart and testis. Low expression detected in all other tissues.

Evidence on tissue expression from TISSUES for CLTCL1 Gene

  • Muscle(4.5)
  • Nervous system(4.2)
genes like me logo Genes that share expression patterns with CLTCL1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and Phenotype-based relationships between genes and organs from Gene ORGANizer for CLTCL1 Gene

Orthologs for CLTCL1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for CLTCL1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CLTCL1 31 30
  • 99.67 (n)
OneToOne
dog
(Canis familiaris)
Mammalia CLTCL1 31 30
  • 90.13 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia CLTCL1 31
  • 86 (a)
OneToOne
chicken
(Gallus gallus)
Aves CLTCL1 31 30
  • 79.13 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia CLTCL1 31
  • 89 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100492311 30
  • 77.19 (n)
zebrafish
(Danio rerio)
Actinopterygii CLTCL1 (2 of 2) 31
  • 82 (a)
OneToMany
CLTCL1 (1 of 2) 31
  • 66 (a)
OneToMany
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.619 30
fruit fly
(Drosophila melanogaster)
Insecta Chc 31 32
  • 75 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea chc-1 31
  • 67 (a)
OneToMany
T20G5.1 32
  • 66 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes CHC1 31
  • 48 (a)
OneToMany
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.5152 30
corn
(Zea mays)
Liliopsida Zm.12119 30
sea squirt
(Ciona savignyi)
Ascidiacea CSA.1583 31
  • 62 (a)
OneToMany
Species where no ortholog for CLTCL1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • cow (Bos Taurus)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • mouse (Mus musculus)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for CLTCL1 Gene

ENSEMBL:
Gene Tree for CLTCL1 (if available)
TreeFam:
Gene Tree for CLTCL1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CLTCL1: view image

Paralogs for CLTCL1 Gene

Paralogs for CLTCL1 Gene

(1) SIMAP similar genes for CLTCL1 Gene using alignment to 6 proteins:

  • CLH2_HUMAN
  • A4FU99_HUMAN
  • F5H5N6_HUMAN
  • H0Y529_HUMAN
  • H0YGJ9_HUMAN
  • J3KR87_HUMAN
genes like me logo Genes that share paralogs with CLTCL1: view

Variants for CLTCL1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CLTCL1 Gene

SNP ID Clinical significance and condition Chr 22 pos Variation AA Info Type
708745 Likely Benign: not provided 19,234,536(-) G/A SYNONYMOUS_VARIANT
716364 Benign: not provided 19,183,443(-) C/G MISSENSE_VARIANT
716365 Benign: not provided 19,232,468(-) A/G INTRON_VARIANT
716366 Benign: not provided 19,232,542(-) C/T SYNONYMOUS_VARIANT
718483 Likely Benign: not provided 19,183,561(-) C/CT FRAMESHIFT_VARIANT

Additional dbSNP identifiers (rs#s) for CLTCL1 Gene

Structural Variations from Database of Genomic Variants (DGV) for CLTCL1 Gene

Variant ID Type Subtype PubMed ID
esv1007063 CNV deletion 20482838
esv2532331 CNV insertion 19546169
esv2664681 CNV deletion 23128226
esv2672843 CNV deletion 23128226
esv2676900 CNV deletion 23128226
esv3307775 CNV mobile element insertion 20981092
esv3308015 CNV mobile element insertion 20981092
esv3308782 CNV mobile element insertion 20981092
esv3387591 CNV insertion 20981092
esv3575418 CNV gain 25503493
esv3647265 CNV loss 21293372
esv3647268 CNV loss 21293372
esv3647269 CNV loss 21293372
nsv1116942 CNV deletion 24896259
nsv1125751 CNV tandem duplication 24896259
nsv1143025 CNV tandem duplication 24896259
nsv459398 CNV loss 19166990
nsv513584 CNV insertion 21212237
nsv588213 CNV gain 21841781
nsv588216 CNV gain 21841781
nsv588217 CNV loss 21841781
nsv828933 CNV loss 20364138
nsv834122 CNV loss 17160897
nsv834123 CNV loss 17160897
nsv834124 CNV loss 17160897
nsv834125 CNV loss 17160897
nsv979633 CNV duplication 23825009

Variation tolerance for CLTCL1 Gene

Residual Variation Intolerance Score: 99.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 17.78; 98.33% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CLTCL1 Gene

Human Gene Mutation Database (HGMD)
CLTCL1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CLTCL1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CLTCL1 Gene

Disorders for CLTCL1 Gene

MalaCards: The human disease database

(6) MalaCards diseases for CLTCL1 Gene - From: Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
congenital insensitivity to pain with severe intellectual disability
  • congenital absence of pain with severe intellectual disability
chromosome 22q11.2 duplication syndrome
  • chromosome 22q11.2 microduplication syndrome
digeorge syndrome
  • cayler cardiofacial syndrome
ichthyosis, congenital, autosomal recessive 9
  • arci9
chromosomal duplication syndrome
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for CLTCL1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with CLTCL1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CLTCL1 Gene

Publications for CLTCL1 Gene

  1. Isolation of a new clathrin heavy chain gene with muscle-specific expression from the region commonly deleted in velo-cardio-facial syndrome. (PMID: 8733128) Sirotkin H … Kucherlapati R (Human molecular genetics 1996) 3 4 23 54
  2. Cloning and characterization of a novel human clathrin heavy chain gene (CLTCL). (PMID: 8844170) Long KR … Buckler AJ (Genomics 1996) 2 3 4 54
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 41 54
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 54
  5. Clathrin isoform CHC22, a component of neuromuscular and myotendinous junctions, binds sorting nexin 5 and has increased expression during myogenesis and muscle regeneration. (PMID: 15133132) Towler MC … Brodsky FM (Molecular biology of the cell 2004) 2 3 54

Products for CLTCL1 Gene

Sources for CLTCL1 Gene