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Aliases for CLTB Gene

Aliases for CLTB Gene

  • Clathrin Light Chain B 2 3 3 5
  • Clathrin, Light Polypeptide (Lcb) 2 3
  • Clathrin, Light Chain (Lcb) 3
  • Clathrin, Light Chain B 2
  • LCB 3
  • Lcb 4

External Ids for CLTB Gene

Previous GeneCards Identifiers for CLTB Gene

  • GC05M176168
  • GC05M176638
  • GC05M175754
  • GC05M175800
  • GC05M175752
  • GC05M175819
  • GC05M170744

Summaries for CLTB Gene

Entrez Gene Summary for CLTB Gene

  • Clathrin is a large, soluble protein composed of heavy and light chains. It functions as the main structural component of the lattice-type cytoplasmic face of coated pits and vesicles which entrap specific macromolecules during receptor-mediated endocytosis. This gene encodes one of two clathrin light chain proteins which are believed to function as regulatory elements. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2008]

GeneCards Summary for CLTB Gene

CLTB (Clathrin Light Chain B) is a Protein Coding gene. Diseases associated with CLTB include Leber Congenital Amaurosis 6 and Leber Congenital Amaurosis. Among its related pathways are wtCFTR and delta508-CFTR traffic / Generic schema (norm and CF) and Signaling by Wnt. Gene Ontology (GO) annotations related to this gene include structural molecule activity and peptide binding. An important paralog of this gene is CLTA.

UniProtKB/Swiss-Prot for CLTB Gene

  • Clathrin is the major protein of the polyhedral coat of coated pits and vesicles.

Additional gene information for CLTB Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLTB Gene

Genomics for CLTB Gene

GeneHancer (GH) Regulatory Elements for CLTB Gene

Promoters and enhancers for CLTB Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH05J176410 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 658.3 +1.7 1653 8.8 PKNOX1 ARNT ARID4B NEUROD1 SIN3A DMAP1 ZNF2 YY1 ZNF207 ZNF143 CLTB ENSG00000251414 FAF2 HIGD2A ARL10 NOP16 UIMC1 ENSG00000250909 MIR1271 KIAA1191
GH05J176386 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 9.9 +28.1 28147 4.1 CLOCK FEZF1 DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 ZNF263 SP3 HIGD2A NOP16 FAF2 ENSG00000251414 ENSG00000250909 NSD1 UIMC1 RPL21P60 MXD3 ZNF346-IT1
GH05J176529 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 5.6 -117.7 -117730 10.3 MLX DMAP1 YY1 ZNF213 E2F8 ZNF143 SP3 NFYC ZC3H11A ZNF610 RNF44 GC05P176534 ENSG00000250909 NSD1 ENSG00000251414 FAF2 RPL21P60 ZNF346-IT1 UIMC1 CDHR2
GH05J176539 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 5 -129.2 -129216 11.8 HDGF FOXA2 MLX ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 IRF4 CDHR2 RN7SL684P FAF2 NSD1 ENSG00000250909 ENSG00000251414 ZNF346-IT1 ZNF346 RNF44 UIMC1
GH05J176481 Enhancer 0.7 ENCODE 17.1 -65.4 -65362 0.8 HDAC1 KLF1 SAP130 BACH1 ZNF316 NFE2 PRDM10 MAFK NFE2L2 ZNF639 CLTB FAF2 NOP16 HIGD2A CDHR2 RN7SL684P MIR1271 ARL10 KIAA1191 PIR40188
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CLTB on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CLTB gene promoter:
  • Hand1
  • E47
  • Arnt
  • NF-E2 p45
  • NF-E2
  • CUTL1
  • C/EBPbeta
  • C/EBPalpha
  • CREB
  • deltaCREB

Genomic Locations for CLTB Gene

Genomic Locations for CLTB Gene
24,115 bases
Minus strand
24,115 bases
Minus strand

Genomic View for CLTB Gene

Genes around CLTB on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for CLTB Gene

Proteins for CLTB Gene

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

    Protein Symbol:
    Recommended name:
    Clathrin light chain B
    Protein Accession:
    Secondary Accessions:
    • Q53Y37
    • Q6FHW1

    Protein attributes for CLTB Gene

    229 amino acids
    Molecular mass:
    25190 Da
    Quaternary structure:
    • Clathrin coats are formed from molecules containing 3 heavy chains and 3 light chains. Interacts (via N-terminus) with HIP1. Interacts with HIP1R.

    Alternative splice isoforms for CLTB Gene


neXtProt entry for CLTB Gene

Post-translational modifications for CLTB Gene

  • Ubiquitination at posLast=223223
  • Modification sites at PhosphoSitePlus

Other Protein References for CLTB Gene

No data available for DME Specific Peptides for CLTB Gene

Domains & Families for CLTB Gene

Gene Families for CLTB Gene

Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for CLTB Gene


Suggested Antigen Peptide Sequences for CLTB Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the clathrin light chain family.
  • Belongs to the clathrin light chain family.
genes like me logo Genes that share domains with CLTB: view

Function for CLTB Gene

Molecular function for CLTB Gene

UniProtKB/Swiss-Prot Function:
Clathrin is the major protein of the polyhedral coat of coated pits and vesicles.
GENATLAS Biochemistry:
clathrin,light chain B (Lcb),component of coated vesicles and coated pits,translocated to plasma membrane through AP2 binding,also expressed in synaptic vesicles

Phenotypes From GWAS Catalog for CLTB Gene

Gene Ontology (GO) - Molecular Function for CLTB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005198 structural molecule activity IBA --
GO:0005515 protein binding IPI 11889126
GO:0032050 clathrin heavy chain binding IBA --
GO:0042277 peptide binding IEA --
genes like me logo Genes that share ontologies with CLTB: view
genes like me logo Genes that share phenotypes with CLTB: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

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

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

Localization for CLTB Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLTB 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.

Subcellular locations from

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 CLTB gene
Compartment Confidence
plasma membrane 5
cytosol 5
nucleus 2
golgi apparatus 2
extracellular 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Vesicles (3)
  • Cytosol (2)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CLTB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005802 trans-Golgi network IEA --
GO:0005829 cytosol TAS,IDA --
GO:0005886 plasma membrane IDA --
GO:0005905 clathrin-coated pit IEA --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with CLTB: view

Pathways & Interactions for CLTB Gene

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

SIGNOR curated interactions for CLTB Gene

Other effect:

Gene Ontology (GO) - Biological Process for CLTB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006886 intracellular protein transport IEA --
GO:0016192 vesicle-mediated transport IEA --
GO:0048268 clathrin coat assembly IBA --
GO:0061024 membrane organization TAS --
GO:0072583 clathrin-dependent endocytosis IBA --
genes like me logo Genes that share ontologies with CLTB: view

Drugs & Compounds for CLTB Gene

No Compound Related Data Available

Transcripts for CLTB Gene

mRNA/cDNA for CLTB Gene

Unigene Clusters for CLTB Gene

Clathrin, light chain B:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

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

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

ExUns: 1a · 1b · 1c · 1d · 1e ^ 2 ^ 3 ^ 4a · 4b ^ 5a · 5b ^ 6 ^ 7a · 7b · 7c · 7d · 7e · 7f
SP1: -
SP2: - -
SP3: - - - - -
SP4: - - - - - -
SP6: - - - - - - -

Relevant External Links for CLTB Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CLTB Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for CLTB Gene

This gene is overexpressed in Brain (20.5).

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

Protein tissue co-expression partners for CLTB Gene

NURSA nuclear receptor signaling pathways regulating expression of CLTB Gene:


SOURCE GeneReport for Unigene cluster for CLTB Gene:


Evidence on tissue expression from TISSUES for CLTB Gene

  • Liver(4.5)
  • Lung(4.3)
  • Eye(4.2)
  • Nervous system(3.2)
  • Muscle(2.8)
  • Skin(2.4)
genes like me logo Genes that share expression patterns with CLTB: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for CLTB Gene

Orthologs for CLTB Gene

This gene was present in the common ancestor of animals.

Orthologs for CLTB Gene

Organism Taxonomy Gene Similarity Type Details
(Canis familiaris)
Mammalia CLTB 34 33
  • 93.52 (n)
(Bos Taurus)
Mammalia CLTB 34 33
  • 92.06 (n)
(Pan troglodytes)
Mammalia CLTB 33
  • 91.25 (n)
(Rattus norvegicus)
Mammalia Cltb 33
  • 90.84 (n)
(Mus musculus)
Mammalia Cltb 16 34 33
  • 89.73 (n)
(Monodelphis domestica)
Mammalia CLTB 34
  • 84 (a)
(Ornithorhynchus anatinus)
Mammalia CLTB 34
  • 82 (a)
(Gallus gallus)
Aves CLTB 34 33
  • 79.39 (n)
(Anolis carolinensis)
Reptilia CLTB 34
  • 72 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia cltb 33
  • 69.77 (n)
Str.3405 33
African clawed frog
(Xenopus laevis)
Amphibia MGC68704 33
(Danio rerio)
Actinopterygii LOC100329879 33
  • 68.91 (n)
FP102272.1 34
  • 63 (a)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.226 33
fruit fly
(Drosophila melanogaster)
Insecta Clc 34
  • 35 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.79 34
  • 40 (a)
-- 34
  • 29 (a)
Species where no ortholog for CLTB was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • 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)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for CLTB Gene

Gene Tree for CLTB (if available)
Gene Tree for CLTB (if available)
Evolutionary constrained regions (ECRs) for CLTB: view image

Paralogs for CLTB Gene

Paralogs for CLTB Gene

(1) SIMAP similar genes for CLTB Gene using alignment to 4 proteins:

  • H0Y9Q6_HUMAN
genes like me logo Genes that share paralogs with CLTB: view

Variants for CLTB Gene

Sequence variations from dbSNP and Humsavar for CLTB Gene

SNP ID Clin Chr 05 pos Variation AA Info Type
rs1000027940 -- 176,400,004(-) C/T genic_downstream_transcript_variant, intron_variant
rs1000162708 -- 176,405,779(-) C/T 3_prime_UTR_variant, intron_variant, non_coding_transcript_variant
rs1000214507 -- 176,405,976(-) C/G 3_prime_UTR_variant, intron_variant
rs1000563581 -- 176,417,819(-) T/C upstream_transcript_variant
rs1000576641 -- 176,418,144(-) G/A upstream_transcript_variant

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

Variant ID Type Subtype PubMed ID
esv3607670 CNV loss 21293372
nsv1023853 CNV gain 25217958

Variation tolerance for CLTB Gene

Residual Variation Intolerance Score: 31.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.25; 5.69% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CLTB Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

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

Disorders for CLTB Gene

MalaCards: The human disease database

(2) MalaCards diseases for CLTB Gene - From: DISEASES

Disorder Aliases PubMed IDs
leber congenital amaurosis 6
  • lca6
leber congenital amaurosis
  • lca
- elite association - COSMIC cancer census association via MalaCards
Search CLTB in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CLTB

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

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

Publications for CLTB Gene

  1. Chromosomal location and some structural features of human clathrin light-chain genes (CLTA and CLTB). (PMID: 7713494) Ponnambalam S … Parham P (Genomics 1994) 2 3 22 58
  2. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 44 58
  3. Huntingtin-interacting protein 1 (Hip1) and Hip1-related protein (Hip1R) bind the conserved sequence of clathrin light chains and thereby influence clathrin assembly in vitro and actin distribution in vivo. (PMID: 15533940) Chen CY … Brodsky FM (The Journal of biological chemistry 2005) 3 4 58
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  5. HIP1 and HIP12 display differential binding to F-actin, AP2, and clathrin. Identification of a novel interaction with clathrin light chain. (PMID: 11889126) Legendre-Guillemin V … McPherson PS (The Journal of biological chemistry 2002) 3 4 58

Products for CLTB Gene

Sources for CLTB Gene

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