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Gene

JAG1

jagged canonical Notch ligand 1

Summary

Cytogenetic location
20p12.2
Coordinates
Chromosome 20: 10,637,684–10,673,999 (GRCh38)
Exons
26 exons across 36.3 kb
Protein
1,218 amino acids
Inheritance
Autosomal dominant
Also known as
AHD, AWS, HJ1, CD339
Previous symbols
AGS, JAGL1
MANE Select transcript
ENST00000254958.10NM_000214.3
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 reports relevant to this gene

  • Alagille Syndrome

    • Autosomal dominant

      Alagille (AGS) syndrome is variably characterized by chronic cholestasis due to paucity of intrahepatic bile ducts, peripheral pulmonary artery stenosis, vertebrae segmentation anomalies, characteristic facies, posterior embryotoxon/anterior segment abnormalities, pigmentary retinopathy, and dysplastic kidneys.

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

      Maralixibat (Livmarli, FDA 2021) for cholestatic pruritus; ursodeoxycholic acid; fat-soluble vitamin supplementation; liver transplantation for progressive liver failure; cardiac surgery for complex heart defects

Broader groupings

  • Charcot-Marie-Tooth Disease

    • One of 62 genes linked to it

      A group of inherited peripheral neuropathies causing progressive weakness and wasting of the distal muscles and loss of sensation, mainly in the feet and hands.

      • 2 GenCC submitters rate it definitive or strong
      What knowing changes

      Genetic counseling, subtype-specific monitoring, physical therapy, orthotics, neurotoxic drug avoidance, gene-specific clinical trials, surveillance for associated features

Inheritance

Autosomal dominant
One changed copy, from either parent, is enough. A parent who has one passes it on to each child with a one-in-two chance.

How JAG1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
Chromosome 20, with a bracket where JAG1 sits. JAG1 and 5 genes near it on chromosome 20, from 10,155,842 to 11,155,841.Chromosome 2020p12.2p13p12.3p12.2p12.1p11.23p11.22p11.21p11.1q11.1q11.21q11.22q11.23q12q13.11q13.12q13.13q13.2q13.31q13.32q13.3310.2 Mb10.4 Mb10.6 Mb10.8 Mb11 MbSNAP25: 10,172,395–10,308,258, forward strandSNAP25MKKS: 10,401,009–10,434,236, reverse strandMKKS: 10,411,653–10,434,236, reverse strand: 10,411,653–10,434,236, reverse strandSLX4IP: 10,434,668–10,638,912, forward strandSLX4IPJAG1: 10,637,684–10,673,999, reverse strandJAG1Diagram of JAG1: 26 exons on the reverse strand of chromosome 20Exon 26: 5 known disease-causing sitesExon 25: 7 known disease-causing sitesExon 24: 20 known disease-causing sitesExon 23: 20 known disease-causing sitesExon 22: 10 known disease-causing sitesExon 21: 8 known disease-causing sitesExon 20: 5 known disease-causing sitesExon 18: 11 known disease-causing sitesExon 17: 8 known disease-causing sitesExon 16: 8 known disease-causing sitesExon 15: 6 known disease-causing sitesExon 14: 15 known disease-causing sitesExon 13: 12 known disease-causing sitesExon 12: 11 known disease-causing sitesExon 11: 6 known disease-causing sitesExon 10: 8 known disease-causing sitesExon 9: 9 known disease-causing sitesExon 8: 7 known disease-causing sitesExon 7: 8 known disease-causing sitesExon 6: 12 known disease-causing sitesExon 5: 6 known disease-causing sitesExon 4: 20 known disease-causing sitesExon 3: 6 known disease-causing sitesExon 2: 23 known disease-causing sitesExon 1: 11 known disease-causing sitesExon 26: 10,637,684–10,639,955, 2,272 basesExon 25: 10,640,783–10,640,933, 151 basesExon 24: 10,641,113–10,641,244, 132 basesExon 23: 10,641,460–10,641,693, 234 basesExon 22: 10,641,783–10,641,892, 110 basesExon 21: 10,642,488–10,642,601, 114 basesExon 20: 10,643,778–10,643,863, 86 basesExon 19: 10,644,357–10,644,384, 28 basesExon 18: 10,644,863–10,644,979, 117 basesExon 17: 10,645,143–10,645,256, 114 basesExon 16: 10,645,356–10,645,469, 114 basesExon 15: 10,645,971–10,646,084, 114 basesExon 14: 10,646,939–10,647,103, 165 basesExon 13: 10,647,960–10,648,110, 151 basesExon 12: 10,648,549–10,648,722, 174 basesExon 11: 10,649,061–10,649,107, 47 basesExon 10: 10,649,522–10,649,635, 114 basesExon 9: 10,650,247–10,650,360, 114 basesExon 8: 10,651,581–10,651,694, 114 basesExon 7: 10,652,131–10,652,250, 120 basesExon 6: 10,652,468–10,652,598, 131 basesExon 5: 10,656,398–10,656,458, 61 basesExon 4: 10,658,468–10,658,722, 255 basesExon 3: 10,663,963–10,664,014, 52 basesExon 2: 10,672,701–10,673,006, 306 basesExon 1: 10,673,450–10,673,999, 550 bases2625201510515′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 5.9 kb of the gene's 36.3 kb; 3,657 of those bases code for the protein.

How a genome test reads JAG1

299

positions in JAG1 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 36.3 kb of JAG1, introns included, not only the 5.9 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.). JAG1 gene: jagged canonical Notch ligand 1. Retrieved 17 October 2026, from https://dantelabs.com/genes/jag1

Vancouver

Dante Labs. JAG1 gene: jagged canonical Notch ligand 1 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/jag1

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