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Aliases for CLDN1 Gene

Aliases for CLDN1 Gene

  • Claudin 1 2 3 5
  • Senescence-Associated Epithelial Membrane Protein 1 2 3
  • SEMP1 3 4
  • CLD1 3 4
  • Senescence-Associated Epithelial Membrane Protein 4
  • Claudin-1 3
  • ILVASC 3

External Ids for CLDN1 Gene

Previous GeneCards Identifiers for CLDN1 Gene

  • GC03M187025
  • GC03M191284
  • GC03M191425
  • GC03M191344
  • GC03M191506
  • GC03M190023
  • GC03M187423

Summaries for CLDN1 Gene

Entrez Gene Summary for CLDN1 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. The protein encoded by this gene, a member of the claudin family, is an integral membrane protein and a component of tight junction strands. Loss of function mutations result in neonatal ichthyosis-sclerosing cholangitis syndrome. [provided by RefSeq, Jul 2008]

GeneCards Summary for CLDN1 Gene

CLDN1 (Claudin 1) is a Protein Coding gene. Diseases associated with CLDN1 include Ichthyosis, Leukocyte Vacuoles, Alopecia, And Sclerosing Cholangitis and Sclerosing Cholangitis. Among its related pathways are Blood-Brain Barrier and Immune Cell Transmigration: VCAM-1/CD106 Signaling Pathways and Cytoskeleton remodeling Regulation of actin cytoskeleton by Rho GTPases. GO annotations related to this gene include identical protein binding and structural molecule activity. An important paralog of this gene is CLDN7.

UniProtKB/Swiss-Prot for CLDN1 Gene

  • Claudins function as major constituents of the tight junction complexes that regulate the permeability of epithelia. While some claudin family members play essential roles in the formation of impermeable barriers, others mediate the permeability to ions and small molecules. Often, several claudin family members are coexpressed and interact with each other, and this determines the overall permeability. CLDN1 is required to prevent the paracellular diffusion of small molecules through tight junctions in the epidermis and is required for the normal barrier function of the skin. Required for normal water homeostasis and to prevent excessive water loss through the skin, probably via an indirect effect on the expression levels of other proteins, since CLDN1 itself seems to be dispensable for water barrier formation in keratinocyte tight junctions (PubMed:23407391).

  • (Microbial infection) Acts as a receptor for hepatitis C virus in hepatocytes (PubMed:17325668). Acts as a receptor for dengue virus (PubMed:24074594).

Gene Wiki entry for CLDN1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLDN1 Gene

Genomics for CLDN1 Gene

Regulatory Elements for CLDN1 Gene

Enhancers for CLDN1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH03G190343 1.8 FANTOM5 Ensembl ENCODE dbSUPER 29.3 -23.2 -23242 3.7 FOXA2 ATF1 ARID4B SIN3A YY1 GATA2 FOS SP5 PPARG TBX21 CLDN16 CLDN1 P3H2 TMEM207
GH03G190229 1.2 Ensembl ENCODE 19.3 +91.3 91336 3.8 FOXA2 INSM2 BRCA1 RAD21 RFX5 YY1 GATA2 RCOR1 RELB FOS CLDN1 CLDN16 NMNAT1P3
GH03G190325 0.9 ENCODE dbSUPER 21.2 -3.9 -3892 1.6 CTCF JUNB FEZF1 RAD21 ZNF335 JUND ZNF692 EED HNF4A PRDM10 CLDN16 CLDN1 TMEM207
GH03G190205 1.1 Ensembl ENCODE 15.8 +116.4 116445 1.0 FOS RELB ETV6 IKZF2 CREM CEBPB JUNB TBX21 IKZF1 NBN CLDN1 P3H2 CLDN16 NMNAT1P3
GH03G190264 0.9 Ensembl ENCODE 17.1 +56.7 56658 2.2 JUN MAFG USF2 CEBPB ATF2 NR2F2 JUND ZNF316 MAFF POU5F1 CLDN1 CLDN16 NMNAT1P3
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around CLDN1 on UCSC Golden Path with GeneCards custom track

Promoters for CLDN1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000163768 75 801 HDGF ARID4B SIN3A DMAP1 ZNF2 ZNF48 YY1 ZNF121 GLIS2 ZNF143

Genomic Location for CLDN1 Gene

Chromosome:
3
Start:
190,305,701 bp from pter
End:
190,322,475 bp from pter
Size:
16,775 bases
Orientation:
Minus strand

Genomic View for CLDN1 Gene

Genes around CLDN1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CLDN1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CLDN1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLDN1 Gene

Proteins for CLDN1 Gene

  • Protein details for CLDN1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O95832-CLD1_HUMAN
    Recommended name:
    Claudin-1
    Protein Accession:
    O95832

    Protein attributes for CLDN1 Gene

    Size:
    211 amino acids
    Molecular mass:
    22744 Da
    Quaternary structure:
    • Homopolymers interact with CLDN3, but not CLDN2, homopolymers. Directly interacts with TJP1/ZO-1, TJP2/ZO-2 and TJP3/ZO-3. Interacts with MPDZ and PATJ (By similarity). Can form homo- and heteropolymers with other claudin family members.
    • (Microbial infection) Interacts with hepatitis c virus E1 and E2 proteins.
    • (Microbial infection) Interacts with dengue virus small envelope protein M.

neXtProt entry for CLDN1 Gene

Post-translational modifications for CLDN1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for CLDN1 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for CLDN1 (Claudin-1)

No data available for DME Specific Peptides for CLDN1 Gene

Domains & Families for CLDN1 Gene

Gene Families for CLDN1 Gene

Graphical View of Domain Structure for InterPro Entry

O95832

UniProtKB/Swiss-Prot:

CLD1_HUMAN :
  • Belongs to the claudin family.
Family:
  • Belongs to the claudin family.
genes like me logo Genes that share domains with CLDN1: view

Function for CLDN1 Gene

Molecular function for CLDN1 Gene

GENATLAS Biochemistry:
claudin 1,clostridium perfringens enterotoxin receptor 1,claudin family of major structural components of tight junction (TJ) strands,expressed in thyroid,placenta,pancreas,lung and kidney
UniProtKB/Swiss-Prot Function:
Claudins function as major constituents of the tight junction complexes that regulate the permeability of epithelia. While some claudin family members play essential roles in the formation of impermeable barriers, others mediate the permeability to ions and small molecules. Often, several claudin family members are coexpressed and interact with each other, and this determines the overall permeability. CLDN1 is required to prevent the paracellular diffusion of small molecules through tight junctions in the epidermis and is required for the normal barrier function of the skin. Required for normal water homeostasis and to prevent excessive water loss through the skin, probably via an indirect effect on the expression levels of other proteins, since CLDN1 itself seems to be dispensable for water barrier formation in keratinocyte tight junctions (PubMed:23407391).
UniProtKB/Swiss-Prot Function:
(Microbial infection) Acts as a receptor for hepatitis C virus in hepatocytes (PubMed:17325668). Acts as a receptor for dengue virus (PubMed:24074594).

Gene Ontology (GO) - Molecular Function for CLDN1 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 CLDN1: view
genes like me logo Genes that share phenotypes with CLDN1: view

Human Phenotype Ontology for CLDN1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for CLDN1 Gene

MGI Knock Outs for CLDN1:

Animal Model Products

  • Taconic Biosciences Mouse Models for CLDN1

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for CLDN1

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for CLDN1 Gene

Localization for CLDN1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLDN1 Gene

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

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 CLDN1 gene
Compartment Confidence
plasma membrane 5
extracellular 1
cytoskeleton 1

Gene Ontology (GO) - Cellular Components for CLDN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005886 plasma membrane IEA --
GO:0005887 integral component of plasma membrane IMP 23407391
GO:0005923 bicellular tight junction TAS,ISS --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with CLDN1: view

Pathways & Interactions for CLDN1 Gene

genes like me logo Genes that share pathways with CLDN1: view

Gene Ontology (GO) - Biological Process for CLDN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007568 aging IEA --
GO:0008065 establishment of blood-nerve barrier IEA --
GO:0009636 response to toxic substance IEA --
GO:0016032 viral process IEA --
GO:0016338 calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules ISS --
genes like me logo Genes that share ontologies with CLDN1: view

No data available for SIGNOR curated interactions for CLDN1 Gene

Drugs & Compounds for CLDN1 Gene

(1) Drugs for CLDN1 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Nutra 0
genes like me logo Genes that share compounds with CLDN1: view

Transcripts for CLDN1 Gene

mRNA/cDNA for CLDN1 Gene

Unigene Clusters for CLDN1 Gene

Claudin 1:
Representative Sequences:

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for CLDN1

Alternative Splicing Database (ASD) splice patterns (SP) for CLDN1 Gene

No ASD Table

Relevant External Links for CLDN1 Gene

GeneLoc Exon Structure for
CLDN1
ECgene alternative splicing isoforms for
CLDN1

Expression for CLDN1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CLDN1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CLDN1 Gene

This gene is overexpressed in Skin - Sun Exposed (Lower leg) (x12.4), Skin - Not Sun Exposed (Suprapubic) (x11.7), and Liver (x5.1).

Protein differential expression in normal tissues from HIPED for CLDN1 Gene

This gene is overexpressed in Nasal epithelium (39.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for CLDN1 Gene



NURSA nuclear receptor signaling pathways regulating expression of CLDN1 Gene:

CLDN1

SOURCE GeneReport for Unigene cluster for CLDN1 Gene:

Hs.439060

mRNA Expression by UniProt/SwissProt for CLDN1 Gene:

O95832-CLD1_HUMAN
Tissue specificity: Strongly expressed in liver and kidney. Expressed in heart, brain, spleen, lung and testis.

Evidence on tissue expression from TISSUES for CLDN1 Gene

  • Liver(3.4)
  • Skin(3)
  • Intestine(2.5)
  • Lung(2.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for CLDN1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • immune
  • integumentary
  • lymphatic
  • nervous
  • skeleton
Organs:
Head and neck:
  • brain
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • skull
  • tooth
Thorax:
  • thymus
Abdomen:
  • abdominal wall
  • biliary tract
  • gallbladder
  • liver
  • pancreas
  • spleen
Limb:
  • nail
General:
  • blood
  • bone marrow
  • coagulation system
  • hair
  • red blood cell
  • skin
  • white blood cell
genes like me logo Genes that share expression patterns with CLDN1: view

Primer Products

No data available for Protein tissue co-expression partners for CLDN1 Gene

Orthologs for CLDN1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CLDN1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CLDN1 34 35
  • 99.53 (n)
dog
(Canis familiaris)
Mammalia CLDN1 34 35
  • 91.79 (n)
cow
(Bos Taurus)
Mammalia CLDN1 34 35
  • 91.31 (n)
oppossum
(Monodelphis domestica)
Mammalia CLDN1 35
  • 89 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Cldn1 34 16 35
  • 88.15 (n)
rat
(Rattus norvegicus)
Mammalia Cldn1 34
  • 87.2 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia CLDN1 35
  • 80 (a)
OneToOne
chicken
(Gallus gallus)
Aves CLDN1 34 35
  • 72.99 (n)
lizard
(Anolis carolinensis)
Reptilia CLDN1 35
  • 78 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia cldn1 34
  • 65.56 (n)
zebrafish
(Danio rerio)
Actinopterygii cldn1 34
  • 61.6 (n)
-- 34
Species where no ortholog for CLDN1 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)
  • 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)
  • 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 CLDN1 Gene

ENSEMBL:
Gene Tree for CLDN1 (if available)
TreeFam:
Gene Tree for CLDN1 (if available)

Paralogs for CLDN1 Gene

(19) SIMAP similar genes for CLDN1 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with CLDN1: view

Variants for CLDN1 Gene

Sequence variations from dbSNP and Humsavar for CLDN1 Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type
rs864309516 Pathogenic 190,322,006(-) AGTCT(-/TT)GACTC reference, frameshift-variant
rs864309517 Pathogenic 190,312,902(-) TGGCT(-/G)TCATT intron-variant, reference, frameshift-variant
rs141961866 Uncertain significance 190,322,166(+) GGAAG(A/G/T)CGAGA reference, missense
rs142778400 Uncertain significance 190,310,163(+) AATAG(C/T)GTTAC intron-variant
rs145197251 Uncertain significance 190,322,012(+) AAGAC(C/G/T)TTGCA reference, synonymous-codon

Structural Variations from Database of Genomic Variants (DGV) for CLDN1 Gene

Variant ID Type Subtype PubMed ID
esv3893843 CNV gain 25118596
nsv1014822 CNV gain 25217958

Variation tolerance for CLDN1 Gene

Residual Variation Intolerance Score: 46.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.56; 72.21% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CLDN1 Gene

Human Gene Mutation Database (HGMD)
CLDN1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CLDN1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CLDN1 Gene

Disorders for CLDN1 Gene

MalaCards: The human disease database

(9) MalaCards diseases for CLDN1 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
ichthyosis, leukocyte vacuoles, alopecia, and sclerosing cholangitis
  • ichthyosis-sclerosing cholangitis syndrome
sclerosing cholangitis
  • primary sclerosing cholangitis
cholangitis
prostate transitional cell carcinoma
  • transitional cell carcinoma of prostate
hepatitis c
  • chronic hepatitis c
- elite association - COSMIC cancer census association via MalaCards
Search CLDN1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

CLD1_HUMAN
  • Ichthyosis-sclerosing cholangitis neonatal syndrome (NISCH) [MIM:607626]: A rare autosomal recessive complex ichthyosis syndrome characterized by scalp hypotrichosis, scarring alopecia, mild diffuse ichthyosis, sclerosing cholangitis and leukocyte vacuolization. {ECO:0000269 PubMed:15521008, ECO:0000269 PubMed:16619213}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for CLDN1

Genetic Association Database (GAD)
CLDN1
Human Genome Epidemiology (HuGE) Navigator
CLDN1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
CLDN1
genes like me logo Genes that share disorders with CLDN1: view

No data available for Genatlas for CLDN1 Gene

Publications for CLDN1 Gene

  1. Assignment of claudin-1 (CLDN1) to human chromosome 3q28-->q29 with somatic cell hybrids. (PMID: 10828592) Halford S. … Adamson P. (Cytogenet. Cell Genet. 2000) 2 3 4 22 64
  2. Claudin-1 is a hepatitis C virus co-receptor required for a late step in entry. (PMID: 17325668) Evans M.J. … Rice C.M. (Nature 2007) 3 4 22 64
  3. Genomic organization of claudin-1 and its assessment in hereditary and sporadic breast cancer. (PMID: 11071387) Kraemer F. … Weber B.H.F. (Hum. Genet. 2000) 3 4 22 64
  4. SEMP1, a senescence-associated cDNA isolated from human mammary epithelial cells, is a member of an epithelial membrane protein superfamily. (PMID: 9931503) Swisshelm K.L. … Hosier S. (Gene 1999) 3 4 22 64
  5. Contribution of tight junction proteins to ion, macromolecule, and water barrier in keratinocytes. (PMID: 23407391) Kirschner N. … Brandner J.M. (J. Invest. Dermatol. 2013) 3 4 64

Products for CLDN1 Gene

  • Addgene plasmids for CLDN1

Sources for CLDN1 Gene

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