CLDN1 claudin 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: CLDN1provided by HGNC
Official Full Name: claudin 1provided by HGNC
Primary source: HGNC:HGNC:2032
See related: Ensembl:ENSG00000163347 MIM:603718; AllianceGenome:HGNC:2032
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: CLD1; SEMP1; ILVASC
Summary: 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]
Expression: Biased expression in skin (RPKM 138.8), liver (RPKM 107.2) and 6 other tissues See more
Orthologs: mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 3q28

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (190305707..190322446, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (193121997..193138734, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (190023496..190040235, complement)

Chromosome 3 - NC_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

CLDN1 knock out keratinocytes as a model to investigate multiple skin disorders.
Title: CLDN1 knock out keratinocytes as a model to investigate multiple skin disorders.
Claudin-1 as a novel target gene induced in obesity and associated to inflammation, fibrosis, and cell differentiation.
Title: Claudin-1 as a novel target gene induced in obesity and associated to inflammation, fibrosis, and cell differentiation.
Immunohistochemical Expression of Claudin-1 and Claudin-4 in Urothelial Carcinoma of the Urinary Bladder.
Title: Immunohistochemical Expression of Claudin-1 and Claudin-4 in Urothelial Carcinoma of the Urinary Bladder.
Upregulation of SEMP1 Contributes to Improving the Biological Functions of Trophoblast via the PI3K/AKT Pathway in Preeclampsia.
Title: Upregulation of SEMP1 Contributes to Improving the Biological Functions of Trophoblast via the PI3K/AKT Pathway in Preeclampsia.
USP40 promotes hepatocellular carcinoma cell proliferation, migration and stemness by deubiquitinating and stabilizing Claudin1.
Title: USP40 promotes hepatocellular carcinoma cell proliferation, migration and stemness by deubiquitinating and stabilizing Claudin1.
Roles of epidermal growth factor receptor, claudin-1 and occludin in multi-step entry of hepatitis C virus into polarized hepatoma spheroids.
Title: Roles of epidermal growth factor receptor, claudin-1 and occludin in multi-step entry of hepatitis C virus into polarized hepatoma spheroids.
CLDN1 Arg81His founder variant causes ichthyosis, leukocyte vacuoles, alopecia, and sclerosing cholangitis (ILVASC) syndrome in Moroccan Jews.
Title: CLDN1 Arg81His founder variant causes ichthyosis, leukocyte vacuoles, alopecia, and sclerosing cholangitis (ILVASC) syndrome in Moroccan Jews.
Claudin-1 interacts with EPHA2 to promote cancer stemness and chemoresistance in colorectal cancer.
Title: Claudin-1 interacts with EPHA2 to promote cancer stemness and chemoresistance in colorectal cancer.
LncRNA-WAKMAR2 regulates expression of CLDN1 to affect skin barrier through recruiting c-Fos.
Title: LncRNA-WAKMAR2 regulates expression of CLDN1 to affect skin barrier through recruiting c-Fos.
Identification and characterization of a first-generation inhibitor of claudin-1 in colon cancer progression and metastasis.
Title: Identification and characterization of a first-generation inhibitor of claudin-1 in colon cancer progression and metastasis.

Submit: New GeneRIF Correction See all GeneRIFs (236)

Phenotypes

Go to the top of the page Help

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Neonatal ichthyosis-sclerosing cholangitis syndrome MedGen: C1843355 OMIM: 607626 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
Genome-wide pharmacogenomic study of neurocognition as an indicator of antipsychotic treatment response in schizophrenia. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

Go to the top of the page Help

Protein interactions

Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp120	env	The exposure to HIV-1 or HIV-1 gp120 results in a significant downregulation of tight junction proteins ZO-1, Occludin, Claudin-1, Claudin-2, Claudin-3, Claudin-4, and Claudin-5 in human retinal pigment epithelial cells	PubMed
Tat	tat	HIV-1 Tat disrupts and downregulates the tight-junction proteins claudin-1, claudin-3, and claudin-4 in retinal pigment epithelial cells, whereas claudin-2 is upregulated	PubMed
	tat	Exposure of brain micro vascular endothelial cells to HIV-1 Tat results in a decrease of claudin-1, claudin-5, and zonula occludens-2 expression and cellular redistribution of claudin-5, suggesting potential disturbance of the blood-brain barrier by Tat	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

WI-19957 (e-PCR)
- UniSTS:78391

G19705 (e-PCR)
- UniSTS:58725

A001W08 (e-PCR)
- UniSTS:58726

CLDN1_530 (e-PCR)
- UniSTS:277102

G30141 (e-PCR)
- UniSTS:44945

D3S1601 (e-PCR), detects polymorphism
- UniSTS:20392

G49585 (e-PCR)
- UniSTS:109254

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables identical protein binding	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables structural molecule activity	IEA Inferred from Electronic Annotation more info
enables virus receptor activity	IMP Inferred from Mutant Phenotype more info	PubMed

Process	Evidence Code	Pubs
involved_in bicellular tight junction assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in bicellular tight junction assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules	ISS Inferred from Sequence or Structural Similarity more info
involved_in cell adhesion	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell junction maintenance	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within cell-cell junction organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cellular response to butyrate	IEA Inferred from Electronic Annotation more info
involved_in cellular response to lead ion	IEA Inferred from Electronic Annotation more info
involved_in cellular response to transforming growth factor beta stimulus	IEA Inferred from Electronic Annotation more info
involved_in cellular response to tumor necrosis factor	IEA Inferred from Electronic Annotation more info
involved_in cellular response to type II interferon	IEA Inferred from Electronic Annotation more info
involved_in establishment of blood-nerve barrier	IEA Inferred from Electronic Annotation more info
involved_in establishment of endothelial intestinal barrier	IEA Inferred from Electronic Annotation more info
involved_in establishment of skin barrier	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in liver regeneration	IEA Inferred from Electronic Annotation more info
involved_in maintenance of blood-brain barrier	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of bicellular tight junction assembly	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of cell migration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of epithelial cell proliferation involved in wound healing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of wound healing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein complex oligomerization	IDA Inferred from Direct Assay more info	PubMed
involved_in response to dexamethasone	IEA Inferred from Electronic Annotation more info
involved_in response to ethanol	IEA Inferred from Electronic Annotation more info
involved_in response to interleukin-18	IEA Inferred from Electronic Annotation more info
involved_in response to lipopolysaccharide	IEA Inferred from Electronic Annotation more info
involved_in response to toxic substance	IEA Inferred from Electronic Annotation more info
involved_in symbiont entry into host cell	IEA Inferred from Electronic Annotation more info
involved_in xenobiotic transport across blood-nerve barrier	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in apical plasma membrane	IEA Inferred from Electronic Annotation more info
located_in basolateral plasma membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in bicellular tight junction	IBA Inferred from Biological aspect of Ancestor more info
located_in bicellular tight junction	IDA Inferred from Direct Assay more info	PubMed
located_in bicellular tight junction	ISS Inferred from Sequence or Structural Similarity more info
located_in lateral plasma membrane	IEA Inferred from Electronic Annotation more info
located_in membrane	TAS Traceable Author Statement more info	PubMed
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	IMP Inferred from Mutant Phenotype more info	PubMed
part_of protein-containing complex	IDA Inferred from Direct Assay more info	PubMed
located_in tight junction	IDA Inferred from Direct Assay more info	PubMed

General protein information

Go to the top of the page Help

Preferred Names: claudin-1

Names: senescence-associated epithelial membrane protein 1

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.