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Gene

CLDN19

claudin 19

Summary

Cytogenetic location
1p34.2
Coordinates
Chromosome 1: 42,733,093–42,740,236 (GRCh38)
Exons
5 exons across 7.1 kb
Protein
224 amino acids
MANE Select transcript
ENST00000296387.6NM_148960.3
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.

      • 3 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 CLDN19 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
Chromosome 1, with a bracket where CLDN19 sits. CLDN19 and 18 genes near it on chromosome 1, from 42,236,665 to 43,236,664.Chromosome 11p34.2p36.33p36.32p36.31p36.23p36.22p36.21p36.13p36.12p36.11p35.3p35.2p35.1p34.3p34.2p34.1p33p32.3p32.2p32.1p31.3p31.2p31.1p22.3p22.2p22.1p21.3p21.2p21.1p13.3p13.2p13.1p12p11.2p11.1q11q12q21.1q21.2q21.3q22q23.1q23.2q23.3q24.1q24.2q24.3q25.1q25.2q25.3q31.1q31.2q31.3q32.1q32.2q32.3q41q42.11q42.12q42.13q42.2q42.3q43q4442.4 Mb42.6 Mb42.8 Mb43 Mb43.2 MbFOXJ3: 42,176,535–42,335,913, reverse strandFOXJ3RIMKLA: 42,380,772–42,424,232, forward strandRIMKLAZMYND12: 42,430,315–42,456,253, reverse strandZMYND12PPCS: 42,456,117–42,473,417, forward strandPPCSCCDC30: 42,463,221–42,657,190, forward strandCCDC30PPIH: 42,658,185–42,676,758, forward strandPPIHYBX1: 42,682,144–42,703,805, forward strandYBX1CLDN19: 42,733,093–42,740,236, reverse strandCLDN19P3H1: 42,746,335–42,767,084, reverse strandP3H1C1orf50: 42,767,245–42,781,980, forward strandC1orf50: 42,767,292–42,794,493, forward strandTMEM269: 42,784,991–42,816,619, forward strandSVBP: 42,788,324–42,824,810, reverse strandSVBPERMAP: 42,817,078–42,845,920, forward strandERMAPZNF691: 42,846,573–42,854,023, forward strandZNF691SLC2A1: 42,925,353–42,958,904, reverse strandSLC2A1CFAP144: 43,145,153–43,156,396, forward strandCFAP144EBNA1BP2: 43,162,085–43,270,936, reverse strandEBNA1BP2CFAP57: 43,172,326–43,254,358, forward strandCFAP57Diagram of CLDN19: 5 exons on the reverse strand of chromosome 1Exon 4: 3 known disease-causing sitesExon 3: 2 known disease-causing sitesExon 2: 4 known disease-causing sitesExon 1: 7 known disease-causing sitesExon 5: 42,733,093–42,735,134, 2,042 basesExon 4: 42,735,878–42,736,030, 153 basesExon 3: 42,738,229–42,738,313, 85 basesExon 2: 42,738,421–42,738,585, 165 basesExon 1: 42,739,841–42,740,236, 396 bases543215′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 2.8 kb of the gene's 7.1 kb; 675 of those bases code for the protein.

How a genome test reads CLDN19

18

positions in CLDN19 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 7.1 kb of CLDN19, introns included, not only the 2.8 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.). CLDN19 gene: claudin 19. Retrieved 17 October 2026, from https://dantelabs.com/genes/cldn19

Vancouver

Dante Labs. CLDN19 gene: claudin 19 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/cldn19

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