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Gene

GJA1

gap junction protein alpha 1

Summary

Cytogenetic location
6q22.31
Coordinates
Chromosome 6: 121,435,646–121,449,727 (GRCh38)
Exons
2 exons across 14.1 kb
Protein
382 amino acids
Also known as
CX43, ODD, ODOD, SDTY3
Previous symbols
ODDD, GJAL
MANE Select transcript
ENST00000282561.4NM_000165.5
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

  • Hereditary Palmoplantar Keratodermas and Pachyonychia Congenita

    • Hereditary palmoplantar keratoderma

      Inherited thickening of the palms and soles, including pachyonychia congenita, mal de Meleda, Nagashima-type and Bothnian keratodermas, keratitis-ichthyosis-deafness syndrome, and the CTSC-related Papillon-Lefèvre and Haim-Munk syndromes.

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

      Diagnosis guides foot care and pain management; for CTSC-related forms early dental treatment protects the teeth, and GJB2-related forms warrant a hearing check.

How GJA1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 6, with a bracket where GJA1 sits. GJA1 and 1 gene near it on chromosome 6, from 120,942,687 to 121,942,686.Chromosome 66q22.31p25.3p25.2p25.1p24.3p24.2p24.1p23p22.3p22.2p22.1p21.33p21.32p21.31p21.2p21.1p12.3p12.2p12.1p11.2p11.1q11.1q11.2q12q13q14.1q14.2q14.3q15q16.1q16.2q16.3q21q22.1q22.2q22.31q22.32q22.33q23.1q23.2q23.3q24.1q24.2q24.3q25.1q25.2q25.3q26q27121 Mb121.2 Mb121.4 Mb121.6 Mb121.8 MbTBC1D32: 121,079,494–121,334,745, reverse strandTBC1D32GJA1: 121,435,646–121,449,727, forward strandGJA1Diagram of GJA1: 2 exons on the forward strand of chromosome 6Exon 2: 38 known disease-causing sitesExon 1: 121,435,646–121,435,832, 187 basesExon 2: 121,446,832–121,449,727, 2,896 bases125′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 3.1 kb of the gene's 14.1 kb; 1,149 of those bases code for the protein.

How a genome test reads GJA1

38

positions in GJA1 where ClinVar classes a change as pathogenic or likely pathogenic

38 of them (100%) fall in regions short reads find hard.

  • Low mappability (8 sites)Regions where 100 bp or 250 bp reads cannot be placed uniquely.
  • Segmental duplications (38 sites)Copies of at least 1 kb sharing at least 90% identity with another part of the genome (paralogues, pseudogenes); reads may align to the wrong copy.

A whole genome covers all 14.1 kb of GJA1, introns included, not only the 3.1 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.). GJA1 gene: gap junction protein alpha 1. Retrieved 17 October 2026, from https://dantelabs.com/genes/gja1

Vancouver

Dante Labs. GJA1 gene: gap junction protein alpha 1 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/gja1

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