Skip to content
Use your HSA or FSA funds

Gene

CLDN16

claudin 16

Summary

Cytogenetic location
3q28
Coordinates
Chromosome 3: 190,388,163–190,412,138 (GRCh38)
Exons
5 exons across 24 kb
Protein
235 amino acids
Also known as
PCLN1, HOMG3
MANE Select transcript
ENST00000264734.3NM_006580.4
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

Curated report relevant to this gene

  • Familial Hypomagnesemia

    • Familial Primary Hypomagnesemia

      A group of inherited magnesium-wasting disorders caused by variants in genes such as CLDN16, CLDN19, TRPM6, CNNM2 and FXYD2; the CLDN16 and CLDN19 forms can progress to chronic kidney disease.

      • ClinGen rates the link definitive
      • 2 GenCC submitters rate it definitive or strong
      What knowing changes

      Magnesium supplementation can control symptoms, and some forms need kidney function and eye monitoring.

How CLDN16 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 3, with a bracket where CLDN16 sits. CLDN16 and 5 genes near it on chromosome 3, from 189,900,151 to 190,900,150.Chromosome 33q28p26.3p26.2p26.1p25.3p25.2p25.1p24.3p24.2p24.1p23p22.3p22.2p22.1p21.33p21.32p21.31p21.2p21.1p14.3p14.2p14.1p13p12.3p12.2p12.1p11.2p11.1q11.1q11.2q12.1q12.2q12.3q13.11q13.12q13.13q13.2q13.31q13.32q13.33q21.1q21.2q21.3q22.1q22.2q22.3q23q24q25.1q25.2q25.31q25.32q25.33q26.1q26.2q26.31q26.32q26.33q27.1q27.2q27.3q28q29190 Mb190.2 Mb190.4 Mb190.6 Mb190.8 MbP3H2: 189,956,728–190,122,437, reverse strandP3H2CLDN1: 190,305,706–190,322,977, reverse strandCLDN1CLDN16: 190,388,163–190,412,138, forward strandCLDN16TMEM207: 190,428,655–190,449,901, reverse strandTMEM207IL1RAP: 190,487,420–190,659,750, forward strandIL1RAPGMNC: 190,851,806–190,892,429, reverse strandGMNCDiagram of CLDN16: 5 exons on the forward strand of chromosome 3Exon 1: 4 known disease-causing sitesExon 2: 8 known disease-causing sitesExon 3: 7 known disease-causing sitesExon 4: 7 known disease-causing sitesExon 5: 1 known disease-causing siteExon 1: 190,388,163–190,388,443, 281 basesExon 2: 190,402,337–190,402,439, 103 basesExon 3: 190,404,762–190,404,926, 165 basesExon 4: 190,408,314–190,408,505, 192 basesExon 5: 190,409,903–190,412,138, 2,236 bases123455′3′

Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

Nearby genes from Ensembl release 116, on GRCh38.

Exons make up 3 kb of the gene's 24 kb; 708 of those bases code for the protein.

How a genome test reads CLDN16

32

positions in CLDN16 where ClinVar classes a change as pathogenic or likely pathogenic

None of them falls in a region short reads find hard.

A whole genome covers all 24 kb of CLDN16, introns included, not only the 3 kb of exons.

Where this comes from

  • HGNC: the gene's symbol, name, other symbols and location.
  • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
  • GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
  • The ACMG secondary findings list, SF v3.2.
  • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
  • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
  • Data release 2026.10.16-c6eea6bf.

Cite this page

APA

Dante Labs. (n.d.). CLDN16 gene: claudin 16. Retrieved 16 October 2026, from https://dantelabs.com/genes/cldn16

Vancouver

Dante Labs. CLDN16 gene: claudin 16 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/cldn16

One test. A lifetime of answers.

From $449Free shipping · Results in 6–8 weeks

Get my Genome Test