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Aliases for CLDN6 Gene

Aliases for CLDN6 Gene

  • Claudin 6 2 3 5
  • Skullin 3 4

External Ids for CLDN6 Gene

Previous GeneCards Identifiers for CLDN6 Gene

  • GC16M003085
  • GC16M003064
  • GC16M003004
  • GC16M003036
  • GC16M003056

Summaries for CLDN6 Gene

Entrez Gene Summary for CLDN6 Gene

  • Tight junctions represent one mode of cell-to-cell adhesion in epithelial or endothelial cell sheets, forming continuous seals around cells and serving as a physical barrier to prevent solutes and water from passing freely through the paracellular space. These junctions are comprised of sets of continuous networking strands in the outwardly facing cytoplasmic leaflet, with complementary grooves in the inwardly facing extracytoplasmic leaflet. This gene encodes a component of tight junction strands, which is a member of the claudin family. The protein is an integral membrane protein and is one of the entry cofactors for hepatitis C virus. The gene methylation may be involved in esophageal tumorigenesis. This gene is adjacent to another family member CLDN9 on chromosome 16.[provided by RefSeq, Aug 2010]

GeneCards Summary for CLDN6 Gene

CLDN6 (Claudin 6) is a Protein Coding gene. Diseases associated with CLDN6 include Monosomy 22 and Hepatitis C Virus. Among its related pathways are Cell junction organization and Tight junction. GO annotations related to this gene include identical protein binding and structural molecule activity. An important paralog of this gene is CLDN9.

UniProtKB/Swiss-Prot for CLDN6 Gene

  • Plays a major role in tight junction-specific obliteration of the intercellular space (By similarity). May act as a coreceptor for HCV entry into hepatic cells.

Gene Wiki entry for CLDN6 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLDN6 Gene

Genomics for CLDN6 Gene

Regulatory Elements for CLDN6 Gene

Enhancers for CLDN6 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around CLDN6 on UCSC Golden Path with GeneCards custom track

Genomic Location for CLDN6 Gene

3,014,712 bp from pter
3,020,071 bp from pter
5,360 bases
Minus strand

Genomic View for CLDN6 Gene

Genes around CLDN6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CLDN6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CLDN6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLDN6 Gene

Proteins for CLDN6 Gene

  • Protein details for CLDN6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • B3KQP9
    • D3DUA5

    Protein attributes for CLDN6 Gene

    220 amino acids
    Molecular mass:
    23292 Da
    Quaternary structure:
    • Directly interacts with TJP1/ZO-1, TJP2/ZO-2 and TJP3/ZO-3.

neXtProt entry for CLDN6 Gene

Proteomics data for CLDN6 Gene at MOPED

Post-translational modifications for CLDN6 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for CLDN6 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for CLDN6 Gene

Domains & Families for CLDN6 Gene

Gene Families for CLDN6 Gene

Protein Domains for CLDN6 Gene

Suggested Antigen Peptide Sequences for CLDN6 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the claudin family.
  • Belongs to the claudin family.
genes like me logo Genes that share domains with CLDN6: view

Function for CLDN6 Gene

Molecular function for CLDN6 Gene

GENATLAS Biochemistry:
claudin 6,clostridium perfringens enterotoxin receptor,integral membrane protein,claudin family of major structural components of tight junction (TJ) strands,not detected in adult tissues
UniProtKB/Swiss-Prot Function:
Plays a major role in tight junction-specific obliteration of the intercellular space (By similarity). May act as a coreceptor for HCV entry into hepatic cells.

Gene Ontology (GO) - Molecular Function for CLDN6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005198 structural molecule activity IEA --
genes like me logo Genes that share ontologies with CLDN6: view
genes like me logo Genes that share phenotypes with CLDN6: view

Animal Model Products

  • Taconic Biosciences Mouse Models for CLDN6

miRNA for CLDN6 Gene

miRTarBase miRNAs that target CLDN6

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CLDN6 Gene

Localization for CLDN6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLDN6 Gene

Cell junction, tight junction. Cell membrane; Multi-pass membrane protein.

Subcellular locations from

Jensen Localization Image for CLDN6 Gene COMPARTMENTS Subcellular localization image for CLDN6 gene
Compartment Confidence
plasma membrane 4
nucleus 1

Gene Ontology (GO) - Cellular Components for CLDN6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
genes like me logo Genes that share ontologies with CLDN6: view

Pathways & Interactions for CLDN6 Gene

genes like me logo Genes that share pathways with CLDN6: view

Gene Ontology (GO) - Biological Process for CLDN6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016032 viral process IEA --
genes like me logo Genes that share ontologies with CLDN6: view

No data available for SIGNOR curated interactions for CLDN6 Gene

Drugs & Compounds for CLDN6 Gene

No Compound Related Data Available

Transcripts for CLDN6 Gene

mRNA/cDNA for CLDN6 Gene

Unigene Clusters for CLDN6 Gene

Claudin 6:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for CLDN6 Gene

No ASD Table

Relevant External Links for CLDN6 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CLDN6 Gene

mRNA expression in normal human tissues for CLDN6 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CLDN6 Gene

This gene is overexpressed in Brain - Putamen (basal ganglia) (x7.0), Brain - Caudate (basal ganglia) (x4.9), Pancreas (x4.8), Brain - Cerebellum (x4.6), and Brain - Cerebellar Hemisphere (x4.3).

Protein differential expression in normal tissues from HIPED for CLDN6 Gene

This gene is overexpressed in Fetal heart (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for CLDN6 Gene

SOURCE GeneReport for Unigene cluster for CLDN6 Gene Hs.533779

mRNA Expression by UniProt/SwissProt for CLDN6 Gene

Tissue specificity: Expressed in the liver, in peripheral blood mononuclear cells and hepatocarcinoma cell lines.
genes like me logo Genes that share expression patterns with CLDN6: view

Protein tissue co-expression partners for CLDN6 Gene

- Elite partner

Primer Products

Orthologs for CLDN6 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CLDN6 Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia CLDN6 35
  • 88.03 (n)
  • 91.36 (a)
CLDN6 36
  • 91 (a)
(Canis familiaris)
Mammalia CLDN6 35
  • 87.27 (n)
  • 89.09 (a)
CLDN6 36
  • 89 (a)
(Mus musculus)
Mammalia Cldn6 35
  • 84.47 (n)
  • 88.13 (a)
Cldn6 16
Cldn6 36
  • 88 (a)
(Pan troglodytes)
Mammalia CLDN6 35
  • 99.24 (n)
  • 99.55 (a)
CLDN6 36
  • 100 (a)
(Rattus norvegicus)
Mammalia Cldn6 35
  • 83.11 (n)
  • 86.76 (a)
(Monodelphis domestica)
Mammalia CLDN6 36
  • 76 (a)
(Anolis carolinensis)
Reptilia -- 36
  • 60 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100493413 35
  • 69.65 (n)
  • 69.81 (a)
MGC75756 35
(Danio rerio)
Actinopterygii cldnd 35
  • 65.84 (n)
  • 63.37 (a)
Species with no ortholog for CLDN6:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • chicken (Gallus gallus)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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 CLDN6 Gene

Gene Tree for CLDN6 (if available)
Gene Tree for CLDN6 (if available)

Paralogs for CLDN6 Gene

(18) SIMAP similar genes for CLDN6 Gene using alignment to 2 proteins: Pseudogenes for CLDN6 Gene

genes like me logo Genes that share paralogs with CLDN6: view

Variants for CLDN6 Gene

Sequence variations from dbSNP and Humsavar for CLDN6 Gene

SNP ID Clin Chr 16 pos Sequence Context AA Info Type
rs2257295 - 3,015,595(-) ATGCC(A/G)TCATC reference, missense
rs61747759 -- 3,015,755(+) GCCAC(A/G)AGGAG reference, synonymous-codon
rs5026503 -- 3,016,741(+) ctccc(C/G)ggttc intron-variant
rs5815142 -- 3,016,648(+) GCTAA(-/T)TTTTT intron-variant
rs62635591 -- 3,015,484(+) CAGCA(A/G)CCCCC reference, synonymous-codon

Structural Variations from Database of Genomic Variants (DGV) for CLDN6 Gene

Variant ID Type Subtype PubMed ID
nsv905162 CNV Gain 21882294
nsv905170 CNV Loss 21882294
dgv2575n71 CNV Loss 21882294
dgv2576n71 CNV Loss 21882294
nsv509588 CNV Insertion 20534489
nsv510673 CNV Loss 20534489
nsv905185 CNV Loss 21882294
dgv2577n71 CNV Loss 21882294
dgv2578n71 CNV Loss 21882294
nsv905193 CNV Loss 21882294
dgv2579n71 CNV Loss 21882294
nsv905197 CNV Loss 21882294
nsv833125 CNV Loss 17160897

Variation tolerance for CLDN6 Gene

Residual Variation Intolerance Score: 66.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.93; 83.88% of all genes are more intolerant (likely to be disease-causing)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Relevant External Links for CLDN6 Gene

Disorders for CLDN6 Gene

MalaCards: The human disease database

(2) MalaCards diseases for CLDN6 Gene - From: GeneCards

Disorder Aliases PubMed IDs
monosomy 22
  • del(22)
hepatitis c virus
  • hepatitic c virus
- elite association - COSMIC cancer census association via MalaCards
Search CLDN6 in MalaCards View complete list of genes associated with diseases

Relevant External Links for CLDN6

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with CLDN6: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CLDN6 Gene

Publications for CLDN6 Gene

  1. Association between genetic variants in VEGF, ERCC3 and occupational benzene haematotoxicity. (PMID: 19773279) Hosgood H.D. … Lan Q. (Occup Environ Med 2009) 3 48 67
  2. Claudin 6 is a positive marker for atypical teratoid/rhabdoid tumors. (PMID: 19220299) Birks D.K. … Handler M.H. (Brain Pathol. 2010) 3 23
  3. Distribution and expression pattern of claudins 6, 7, and 9 in diffuse- and intestinal-type gastric adenocarcinomas. (PMID: 19960275) RendA^n-Huerta E. … MontaA+o L.F. (J Gastrointest Cancer 2010) 3 23
  4. Epithelioid versus rhabdoid glioblastomas are distinguished by monosomy 22 and immunohistochemical expression of INI-1 but not claudin 6. (PMID: 20118769) Kleinschmidt-DeMasters B.K. … Lillehei K.O. (Am. J. Surg. Pathol. 2010) 3 23
  5. Tight junction protein, claudin-6, downregulates the malignant phenotype of breast carcinoma. (PMID: 20215972) Wu Q. … Quan C. (Eur. J. Cancer Prev. 2010) 3 23

Products for CLDN6 Gene

Sources for CLDN6 Gene