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Aliases for CLDN6 Gene

Aliases for CLDN6 Gene

  • Claudin 6 2 3 5
  • Skullin 3 4
  • Claudin-6 3

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 Blood-Brain Barrier and Immune Cell Transmigration: VCAM-1/CD106 Signaling Pathways and Sertoli-Sertoli Cell Junction Dynamics. Gene Ontology (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.

  • (Microbial infection) Acts as a receptor for hepatitis C virus (HCV) entry into hepatic cells.

Gene Wiki entry for CLDN6 Gene

Additional gene information for CLDN6 Gene

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

Genomics for CLDN6 Gene

GeneHancer (GH) Regulatory Elements for CLDN6 Gene

Promoters and enhancers for CLDN6 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
GH16J003017 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE 650.7 +2.2 2156 1.8 ATF1 SIN3A RAD21 ETS1 ZNF143 ATF7 CREM THAP11 SP5 REST CLDN6 TNFRSF12A PKMYT1 BICDL2 ENSG00000272079 CLDN9
GH16J003020 Enhancer 0.9 ENCODE dbSUPER 650.7 +0.4 436 0.2 SMARCE1 ZBTB21 GTF2E2 ZNF140 ZNF266 ZC3H11A ZBTB8A ZNF514 ZNF518A ZNF560 CLDN6 TNFRSF12A ENSG00000261938 ZNF263 E4F1 TSC2 ERVK13-1 SRRM2 SNORD60 CREBBP
GH16J003097 Promoter/Enhancer 2.1 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 11.1 -80.0 -80029 6.2 ARID4B SIN3A IRF4 YY1 ETS1 ARID2 ZNF143 RUNX3 SP3 RXRA ZSCAN10 ZNF205 ZNF213-AS1 CLDN6 TNFRSF12A ZNF205-AS1 ZNF213 ZNF263 OR1F1 ZNF597
GH16J003069 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 11.7 -54.3 -54309 9.8 HDGF PKNOX1 YBX1 IRF4 ZNF207 ZNF143 ZFP91 ATF7 RUNX3 PAF1 GC16P003606 ZNF205 LOC105371058 MMP25 ZNF597 IL32 FLYWCH2 ZNF200 ZNF174 ZSCAN32
GH16J003128 Promoter/Enhancer 1.6 Ensembl ENCODE dbSUPER 11.5 -109.5 -109495 1.8 PKNOX1 ATF1 ARID4B SIN3A ZNF2 YY1 E2F8 ARID2 ZNF143 ATF7 PIR58259 ZNF213 GC16M003129 IL32 RNU1-125P MMP25 BICDL2 LOC100128770 THOC6 HCFC1R1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CLDN6 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CLDN6 gene promoter:
  • AP-1
  • c-Jun
  • ATF-2
  • HNF-4alpha2
  • HNF-4alpha1
  • COUP-TF1
  • COUP

Genomic Locations for CLDN6 Gene

Genomic Locations for CLDN6 Gene
5,360 bases
Minus strand
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 (By similarity). Interacts with CLDN1, CD81 and OCLN (PubMed:20375010).

neXtProt entry for CLDN6 Gene

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

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

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

UniProtKB/Swiss-Prot Function:
Plays a major role in tight junction-specific obliteration of the intercellular space.
UniProtKB/Swiss-Prot Function:
(Microbial infection) Acts as a receptor for hepatitis C virus (HCV) entry into hepatic cells.
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

Phenotypes From GWAS Catalog for CLDN6 Gene

Gene Ontology (GO) - Molecular Function for CLDN6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001618 virus receptor activity IMP 20375010
GO:0005198 structural molecule activity IEA --
GO:0005515 protein binding IPI 20375010
GO:0042802 identical protein binding ISS --
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

CRISPR Products

miRNA for CLDN6 Gene

miRTarBase miRNAs that target CLDN6

Inhibitory RNA Products

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

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 CLDN6 gene
Compartment Confidence
plasma membrane 5

Gene Ontology (GO) - Cellular Components for CLDN6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IDA,IEA 20375010
GO:0005923 bicellular tight junction ISS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0016327 apicolateral plasma membrane IEA --
genes like me logo Genes that share ontologies with CLDN6: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CLDN6 Gene

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 --
GO:0016338 calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules ISS --
GO:0045216 cell-cell junction organization IEA --
GO:0046718 viral entry into host cell 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

(1) REFSEQ mRNAs :
(5) Additional mRNA sequences :
(51) Selected AceView cDNA sequences:
(3) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for CLDN6 Gene

Claudin 6:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CLDN6

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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, MaxQB, and MOPED for CLDN6 Gene

Protein tissue co-expression partners for CLDN6 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of CLDN6 Gene:


SOURCE GeneReport for Unigene cluster for CLDN6 Gene:


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

No data available for Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for CLDN6 Gene

Orthologs for CLDN6 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CLDN6 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CLDN6 34 33
  • 99.24 (n)
(Bos Taurus)
Mammalia CLDN6 34 33
  • 88.03 (n)
(Canis familiaris)
Mammalia CLDN6 34 33
  • 87.27 (n)
(Mus musculus)
Mammalia Cldn6 16 34 33
  • 84.47 (n)
(Rattus norvegicus)
Mammalia Cldn6 33
  • 83.11 (n)
(Monodelphis domestica)
Mammalia CLDN6 34
  • 76 (a)
(Anolis carolinensis)
Reptilia -- 34
  • 60 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100493413 33
  • 69.65 (n)
MGC75756 33
(Danio rerio)
Actinopterygii cldnd 33
  • 65.84 (n)
Species where no ortholog for CLDN6 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)
  • 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)
Evolutionary constrained regions (ECRs) for CLDN6: view image

Paralogs for CLDN6 Gene

Paralogs for CLDN6 Gene

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

  • I3L1E7_HUMAN 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 Variation AA Info Type
rs1000512408 -- 3,019,366(-) TTTTTTTT/TTTT/TTTTTTT upstream_transcript_variant
rs1000881626 -- 3,018,111(-) A/T intron_variant
rs1001172979 -- 3,019,173(-) G/A upstream_transcript_variant
rs1001562802 -- 3,017,900(-) G/T intron_variant
rs1001614680 -- 3,017,151(-) C/A intron_variant

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

Variant ID Type Subtype PubMed ID
nsv509588 CNV insertion 20534489
nsv510673 CNV deletion 20534489
nsv833125 CNV loss 17160897
nsv952906 CNV deletion 24416366

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)

Additional Variant Information for CLDN6 Gene

Human Gene Mutation Database (HGMD)
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 CLDN6 Gene

Disorders for CLDN6 Gene

MalaCards: The human disease database

(4) MalaCards diseases for CLDN6 Gene - From: HGMD and GeneCards

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

Additional Disease Information for CLDN6

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 CLDN6: view

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

Publications for CLDN6 Gene

  1. Claudin association with CD81 defines hepatitis C virus entry. (PMID: 20375010) Harris HJ … McKeating JA (The Journal of biological chemistry 2010) 3 4 58
  2. [Effects of 17β-estradiol on proliferation and migration of MCF-7 cell by regulating expression of claudin-6]. (PMID: 20388399) Liu YF … Li YL (Zhonghua bing li xue za zhi = Chinese journal of pathology 2010) 3 22 58
  3. [Effects of stable up-regulation of tight junction protein claudin-6 upon biological phenotypes of breast cancer cell MCF-7]. (PMID: 20367941) Wu Q … Quan CS (Zhonghua yi xue za zhi 2010) 3 22 58
  4. Tight junction protein, claudin-6, downregulates the malignant phenotype of breast carcinoma. (PMID: 20215972) Wu Q … Quan C (European journal of cancer prevention : the official journal of the European Cancer Prevention Organisation (ECP) 2010) 3 22 58
  5. Epithelioid versus rhabdoid glioblastomas are distinguished by monosomy 22 and immunohistochemical expression of INI-1 but not claudin 6. (PMID: 20118769) Kleinschmidt-DeMasters BK … Lillehei KO (The American journal of surgical pathology 2010) 3 22 58

Products for CLDN6 Gene

Sources for CLDN6 Gene

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