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Aliases for CLDN16 Gene

Aliases for CLDN16 Gene

  • Claudin 16 2 3 5
  • Paracellin-1 2 3 4
  • Hypomagnesemia 3, With Hypercalciuria And Nephrocalcinosis 2 3
  • PCLN-1 3 4
  • PCLN1 3 4
  • Claudin-16 3
  • HOMG3 3

External Ids for CLDN16 Gene

Previous GeneCards Identifiers for CLDN16 Gene

  • GC03P187107
  • GC03P191367
  • GC03P191507
  • GC03P191426
  • GC03P191588
  • GC03P190040
  • GC03P187505

Summaries for CLDN16 Gene

Entrez Gene Summary for CLDN16 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. It is found primarily in the kidneys, specifically in the thick ascending limb of Henle, where it acts as either an intercellular pore or ion concentration sensor to regulate the paracellular resorption of magnesium ions. Defects in this gene are a cause of primary hypomagnesemia, which is characterized by massive renal magnesium wasting with hypomagnesemia and hypercalciuria, resulting in nephrocalcinosis and renal failure. This gene and the CLDN1 gene are clustered on chromosome 3q28. [provided by RefSeq, Jun 2010]

GeneCards Summary for CLDN16 Gene

CLDN16 (Claudin 16) is a Protein Coding gene. Diseases associated with CLDN16 include Hypomagnesemia 3, Renal and Primary Hypomagnesemia. Among its related pathways are Tight junction and Cytoskeleton remodeling Regulation of actin cytoskeleton by Rho GTPases. GO annotations related to this gene include identical protein binding and magnesium ion transmembrane transporter activity.

UniProtKB/Swiss-Prot for CLDN16 Gene

  • Plays a major role in tight junction-specific obliteration of the intercellular space, through calcium-independent cell-adhesion activity. Involved in paracellular magnesium reabsorption. Required for a selective paracellular conductance. May form, alone or in partnership with other constituents, an intercellular pore permitting paracellular passage of magnesium and calcium ions down their electrochemical gradients. Alternatively, it could be a sensor of magnesium concentration that could alter paracellular permeability mediated by other factors.

Gene Wiki entry for CLDN16 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLDN16 Gene

Genomics for CLDN16 Gene

Regulatory Elements for CLDN16 Gene

Enhancers for CLDN16 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
GH03F190343 1.6 FANTOM5 Ensembl ENCODE 32.6 +23.2 23176 3.7 ELF3 TBP ATF1 INSM2 ARID4B SIN3A THRB ZSCAN9 DNMT3B RFX5 CLDN16 CLDN1 P3H2 TMEM207
GH03F190318 1.3 Ensembl ENCODE 24.6 -1.4 -1420 5.4 HDGF PKNOX1 ARID4B SIN3A FEZF1 GLI4 DMAP1 ZNF48 ZNF2 YY1 CLDN16 RN7SKP296 CLDN1 NMNAT1P3
GH03F190325 0.9 Ensembl ENCODE 24.8 +3.8 3826 1.6 JUNB FEZF1 RAD21 ZNF335 ZNF692 EED PRDM10 WT1 ZBTB17 CLDN16 CLDN1 TMEM207
GH03F190229 1.2 Ensembl ENCODE 18.6 -91.4 -91402 3.8 INSM2 BRCA1 RAD21 RFX5 YY1 RCOR1 ETV6 FOS CREM ZNF362 CLDN1 CLDN16 NMNAT1P3
GH03F190368 1.1 Ensembl ENCODE 17.5 +49.4 49362 7.3 SOX13 PKNOX1 MAX BRCA1 POLR2A EED RCOR1 ETV6 FOS CREM CLDN16 CLDN1 TMEM207
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around CLDN16 on UCSC Golden Path with GeneCards custom track

Promoters for CLDN16 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001856275 759 201 HDGF SCRT2 IKZF1 EED ETV6 FEZF1 TCF7L2

Genomic Location for CLDN16 Gene

Chromosome:
3
Start:
190,322,541 bp from pter
End:
190,412,143 bp from pter
Size:
89,603 bases
Orientation:
Plus strand

Genomic View for CLDN16 Gene

Genes around CLDN16 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CLDN16 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CLDN16 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLDN16 Gene

Proteins for CLDN16 Gene

  • Protein details for CLDN16 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y5I7-CLD16_HUMAN
    Recommended name:
    Claudin-16
    Protein Accession:
    Q9Y5I7

    Protein attributes for CLDN16 Gene

    Size:
    305 amino acids
    Molecular mass:
    33836 Da
    Quaternary structure:
    No Data Available

neXtProt entry for CLDN16 Gene

Post-translational modifications for CLDN16 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for CLDN16 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Santa Cruz Biotechnology (SCBT) Antibodies for CLDN16

No data available for DME Specific Peptides for CLDN16 Gene

Domains & Families for CLDN16 Gene

Gene Families for CLDN16 Gene

Suggested Antigen Peptide Sequences for CLDN16 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9Y5I7

UniProtKB/Swiss-Prot:

CLD16_HUMAN :
  • Belongs to the claudin family.
Family:
  • Belongs to the claudin family.
genes like me logo Genes that share domains with CLDN16: view

Function for CLDN16 Gene

Molecular function for CLDN16 Gene

UniProtKB/Swiss-Prot Function:
Plays a major role in tight junction-specific obliteration of the intercellular space, through calcium-independent cell-adhesion activity. Involved in paracellular magnesium reabsorption. Required for a selective paracellular conductance. May form, alone or in partnership with other constituents, an intercellular pore permitting paracellular passage of magnesium and calcium ions down their electrochemical gradients. Alternatively, it could be a sensor of magnesium concentration that could alter paracellular permeability mediated by other factors.

Gene Ontology (GO) - Molecular Function for CLDN16 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005198 structural molecule activity IEA --
GO:0005515 protein binding IPI 22373575
GO:0015095 magnesium ion transmembrane transporter activity TAS 10390358
GO:0042802 identical protein binding ISS --
genes like me logo Genes that share ontologies with CLDN16: view
genes like me logo Genes that share phenotypes with CLDN16: view

Human Phenotype Ontology for CLDN16 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for CLDN16 Gene

MGI Knock Outs for CLDN16:

Animal Model Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for CLDN16 Gene

Localization for CLDN16 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLDN16 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 CLDN16 gene
Compartment Confidence
plasma membrane 5
lysosome 1

Gene Ontology (GO) - Cellular Components for CLDN16 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
GO:0005923 bicellular tight junction IEA,ISS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0030054 cell junction IEA --
genes like me logo Genes that share ontologies with CLDN16: view

Pathways & Interactions for CLDN16 Gene

genes like me logo Genes that share pathways with CLDN16: view

Gene Ontology (GO) - Biological Process for CLDN16 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport IEA --
GO:0006811 ion transport IEA --
GO:0006875 cellular metal ion homeostasis TAS 10390358
GO:0007588 excretion TAS 10390358
GO:0016338 calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules ISS --
genes like me logo Genes that share ontologies with CLDN16: view

No data available for SIGNOR curated interactions for CLDN16 Gene

Drugs & Compounds for CLDN16 Gene

(3) Drugs for CLDN16 Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Nutra 0
Magnesium Nutra 0
genes like me logo Genes that share compounds with CLDN16: view

Transcripts for CLDN16 Gene

mRNA/cDNA for CLDN16 Gene

Unigene Clusters for CLDN16 Gene

Claudin 16:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for CLDN16 Gene

No ASD Table

Relevant External Links for CLDN16 Gene

GeneLoc Exon Structure for
CLDN16
ECgene alternative splicing isoforms for
CLDN16

Expression for CLDN16 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CLDN16 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CLDN16 Gene

This gene is overexpressed in Kidney - Cortex (x19.7).

NURSA nuclear receptor signaling pathways regulating expression of CLDN16 Gene:

CLDN16

SOURCE GeneReport for Unigene cluster for CLDN16 Gene:

Hs.251391

mRNA Expression by UniProt/SwissProt for CLDN16 Gene:

Q9Y5I7-CLD16_HUMAN
Tissue specificity: Kidney-specific, including the thick ascending limb of Henle (TAL).
genes like me logo Genes that share expression patterns with CLDN16: view

Primer Products

No data available for Protein differential expression in normal tissues , Protein expression and Protein tissue co-expression partners for CLDN16 Gene

Orthologs for CLDN16 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CLDN16 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CLDN16 34 35
  • 99.34 (n)
cow
(Bos Taurus)
Mammalia CLDN16 34 35
  • 88.71 (n)
oppossum
(Monodelphis domestica)
Mammalia CLDN16 35
  • 86 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Cldn16 34 16 35
  • 85.96 (n)
dog
(Canis familiaris)
Mammalia CLDN16 34 35
  • 85.57 (n)
rat
(Rattus norvegicus)
Mammalia Cldn16 34
  • 85.53 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia CLDN16 35
  • 85 (a)
OneToOne
chicken
(Gallus gallus)
Aves CLDN16 34 35
  • 74.4 (n)
lizard
(Anolis carolinensis)
Reptilia CLDN16 35
  • 69 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia cldn16 34
  • 71.23 (n)
Species where no ortholog for CLDN16 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)
  • zebrafish (Danio rerio)

Evolution for CLDN16 Gene

ENSEMBL:
Gene Tree for CLDN16 (if available)
TreeFam:
Gene Tree for CLDN16 (if available)

Paralogs for CLDN16 Gene

No data available for Paralogs for CLDN16 Gene

Variants for CLDN16 Gene

Sequence variations from dbSNP and Humsavar for CLDN16 Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type
rs104893721 Hypomagnesemia 3 (HOMG3) [MIM:248250], Pathogenic 190,408,436(+) GGCTC(A/G)GAATG reference, missense
rs104893722 Hypomagnesemia 3 (HOMG3) [MIM:248250], Pathogenic 190,404,905(+) TTGCT(A/G)GAGCC reference, missense
rs104893723 Hypomagnesemia 3 (HOMG3) [MIM:248250], Pathogenic 190,408,314(+) TTCAG(A/G)TACCC reference, missense
rs104893724 Hypomagnesemia 3 (HOMG3) [MIM:248250], Pathogenic 190,388,331(+) CACAA(G/T)GAGGG reference, missense
rs104893725 Hypomagnesemia 3 (HOMG3) [MIM:248250], Pathogenic 190,404,834(+) CCTGC(C/T)CCTTG reference, missense

Structural Variations from Database of Genomic Variants (DGV) for CLDN16 Gene

Variant ID Type Subtype PubMed ID
esv2726381 CNV deletion 23290073
esv2762372 CNV loss 21179565
esv3045230 CNV deletion 24192839
esv3563078 CNV deletion 23714750
esv3563079 CNV deletion 23714750
esv3599075 CNV loss 21293372
esv3893843 CNV gain 25118596
esv991712 CNV deletion 20482838
nsv1014822 CNV gain 25217958
nsv516391 CNV loss 19592680
nsv829820 CNV gain 17160897
esv2726380 CNV deletion 23290073
esv2726379 CNV deletion 23290073
esv2726378 CNV deletion 23290073
esv2000222 CNV deletion 18987734
dgv902e199 CNV deletion 23128226
dgv2660n106 CNV deletion 24896259

Variation tolerance for CLDN16 Gene

Residual Variation Intolerance Score: 60.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.13; 75.63% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CLDN16 Gene

Human Gene Mutation Database (HGMD)
CLDN16
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CLDN16

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CLDN16 Gene

Disorders for CLDN16 Gene

MalaCards: The human disease database

(10) MalaCards diseases for CLDN16 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
hypomagnesemia 3, renal
  • fhhnc
primary hypomagnesemia
  • familial hypomagnesemia with hypercalciuria and nephrocalcinosis
nephrocalcinosis
  • hypercalcemic nephropathy
hypomagnesemia 2, renal
  • renal hypomagnesemia 2
hypercalciuria, absorptive
  • hypercalciuria, absorptive 2
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

CLD16_HUMAN
  • Hypomagnesemia 3 (HOMG3) [MIM:248250]: A progressive renal disease characterized by primary renal magnesium wasting with hypomagnesemia, hypercalciuria and nephrocalcinosis. Recurrent urinary tract infections and kidney stones are often observed. In spite of hypercalciuria, patients do not show hypocalcemia. {ECO:0000269 PubMed:10390358, ECO:0000269 PubMed:10878661, ECO:0000269 PubMed:11518780}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for CLDN16

Genetic Association Database (GAD)
CLDN16
Human Genome Epidemiology (HuGE) Navigator
CLDN16
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
CLDN16
genes like me logo Genes that share disorders with CLDN16: view

No data available for Genatlas for CLDN16 Gene

Publications for CLDN16 Gene

  1. Paracellin-1, a renal tight junction protein required for paracellular Mg2+ resorption. (PMID: 10390358) Simon D.B. … Lifton R.P. (Science 1999) 2 3 4 22 64
  2. Novel paracellin-1 mutations in 25 families with familial hypomagnesemia with hypercalciuria and nephrocalcinosis. (PMID: 11518780) Weber S. … Konrad M. (J. Am. Soc. Nephrol. 2001) 3 4 22 64
  3. Familial hypomagnesaemia with hypercalciuria and nephrocalcinosis maps to chromosome 3q27 and is associated with mutations in the PCLN-1 gene. (PMID: 10878661) Weber S. … Konrad M. (Eur. J. Hum. Genet. 2000) 3 4 22 64
  4. Transcriptional regulation of the claudin-16 gene by Mg2+ availability. (PMID: 20511716) Efrati E. … Zelikovic I. (Cell. Physiol. Biochem. 2010) 3 22 64
  5. Familial hypomagnesemia with hypercalciuria and nephrocalcinosis: unusual clinical associations and novel claudin16 mutation in an Egyptian family. (PMID: 19165416) Al-Haggar M. … Abdel-Hady D. (Clin. Exp. Nephrol. 2009) 3 22 64

Products for CLDN16 Gene

Sources for CLDN16 Gene

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