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Gene

ATP1A3

ATPase Na+/K+ transporting subunit alpha 3

Summary

Cytogenetic location
19q13.2
Coordinates
Chromosome 19: 41,966,582–41,994,230 (GRCh38)
Exons
23 exons across 27.6 kb
Protein
1,013 amino acids
Inheritance
Autosomal dominant
Previous symbols
DYT12
MANE Select transcript
ENST00000648268.1NM_152296.5
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 reports relevant to this gene

  • Autosomal Dominant Cerebellar Ataxias (SCAs and DRPLA)

    • Autosomal Dominant Cerebellar AtaxiaAutosomal dominant

      A group of dominantly inherited ataxias, including SCA1, SCA2, SCA3 (Machado-Joseph disease), SCA6, SCA7, SCA17, SCA27B and DRPLA, caused by repeat expansions or point variants in genes such as ATXN1, ATXN2, ATXN3, CACNA1A, ATXN7, TBP, ATN1 and FGF14.

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

      Genetic counselling and presymptomatic testing for relatives, physiotherapy and symptom management; some forms, such as SCA27B, may respond to specific medication.

  • Dystonia, Myotonia, Paroxysmal Dyskinesia

    • Dystonia 12Autosomal dominant

      Rapid-onset dystonia-parkinsonism (RDP) is a very rare movement disorder, characterized by the abrupt onset of parkinsonism and dystonia, often triggered by physical or psychological stress.

      • 2 GenCC submitters rate it definitive or strong
    • ATP1A3-related neurological disorderAutosomal dominant

      A spectrum including rapid-onset dystonia-parkinsonism, alternating hemiplegia of childhood and CAPOS syndrome, caused by variants in ATP1A3.

      • ClinGen rates the link definitive
      • 7 GenCC submitters rate it definitive or strong
    • Inherited Dystonia

      Umbrella term covering inherited dystonias, including DYT-TOR1A early-onset generalized dystonia, DYT-THAP1, myoclonus-dystonia (SGCE) and KMT2B-related dystonia.

      • 2 GenCC submitters rate it definitive or strong

  • Hereditary Optic Neuropathy

    • Hereditary Optic Atrophy

      Inherited loss of optic nerve fibres, most often autosomal dominant optic atrophy caused by changes in OPA1, and including rarer types caused by OPA3, DNM1L, SSBP1 and other genes.

      • 3 GenCC submitters rate it definitive or strong

Broader groupings

  • Epilepsy (Full Panel)

    • Epilepsy

      One of 171 genes linked to it

      A brain disorder characterized by episodes of abnormally increased neuronal discharge resulting in transient episodes of sensory or motor neurological dysfunction, or psychic dysfunction. These episodes may or may not be associated with loss of consciousness or convulsions.

      • 2 GenCC submitters rate it definitive or strong

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 ATP1A3 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 19, with a bracket where ATP1A3 sits. ATP1A3 and 32 genes near it on chromosome 19, from 41,480,406 to 42,480,405.Chromosome 1919q13.2p13.3p13.2p13.13p13.12p13.11p12p11q11q12q13.11q13.12q13.13q13.2q13.31q13.32q13.33q13.41q13.42q13.4341.6 Mb41.8 Mb42 Mb42.2 Mb42.4 MbCEACAM21: 41,549,518–41,586,844, forward strandCEACAM21CEACAM4: 41,619,014–41,627,082, reverse strandCEACAM4CEACAM7: 41,666,629–41,706,976, reverse strandCEACAM7CEACAM5: 41,708,585–41,730,519, forward strandCEACAM5: 41,708,657–41,756,737, forward strandCEACAM6: 41,750,977–41,772,211, forward strandCEACAM6CEACAM3: 41,796,587–41,811,557, forward strandCEACAM3LYPD4: 41,837,073–41,844,718, reverse strandLYPD4DMRTC2: 41,844,743–41,852,333, forward strandDMRTC2RPS19: 41,859,848–41,872,931, forward strandRPS19CD79A: 41,877,104–41,881,372, forward strandCD79AARHGEF1: 41,883,063–41,930,150, forward strandARHGEF1ERFL: 41,907,704–41,928,449, reverse strandERFLRABAC1: 41,956,681–41,959,390, reverse strandRABAC1: 41,956,879–41,994,232, reverse strandATP1A3: 41,966,582–41,994,230, reverse strandATP1A3GRIK5: 41,998,315–42,070,240, reverse strandGRIK5ZNF574: 42,068,477–42,083,096, forward strandZNF574POU2F2: 42,086,110–42,196,585, reverse strandPOU2F2DEDD2: 42,198,593–42,220,140, reverse strandDEDD2: 42,215,133–42,232,149, reverse strandZNF526: 42,216,774–42,231,887, forward strandZNF526GSK3A: 42,226,225–42,242,625, reverse strandGSK3A: 42,234,583–42,255,132, reverse strandERF: 42,247,569–42,255,172, reverse strandCIC: 42,268,508–42,295,801, forward strandCICPAFAH1B3: 42,297,023–42,303,546, reverse strandPAFAH1B3PRR19: 42,302,098–42,310,821, forward strandPRR19TMEM145: 42,313,299–42,325,064, forward strandTMEM145MEGF8: 42,325,518–42,378,769, forward strandMEGF8CNFN: 42,387,019–42,390,299, reverse strandCNFNLIPE: 42,401,497–42,427,388, reverse strandLIPECXCL17: 42,427,995–42,443,029, reverse strandCXCL17Diagram of ATP1A3: 23 exons on the reverse strand of chromosome 19Exon 22: 2 known disease-causing sitesExon 21: 6 known disease-causing sitesExon 20: 8 known disease-causing sitesExon 19: 8 known disease-causing sitesExon 18: 10 known disease-causing sitesExon 17: 15 known disease-causing sitesExon 16: 11 known disease-causing sitesExon 15: 2 known disease-causing sitesExon 14: 3 known disease-causing sitesExon 13: 5 known disease-causing sitesExon 12: 2 known disease-causing sitesExon 11: 1 known disease-causing siteExon 10: 1 known disease-causing siteExon 9: 12 known disease-causing sitesExon 8: 12 known disease-causing sitesExon 6: 2 known disease-causing sitesExon 5: 5 known disease-causing sitesExon 4: 3 known disease-causing sitesExon 23: 41,966,582–41,966,965, 384 basesExon 22: 41,967,249–41,967,340, 92 basesExon 21: 41,967,662–41,967,763, 102 basesExon 20: 41,968,785–41,968,915, 131 basesExon 19: 41,969,435–41,969,580, 146 basesExon 18: 41,970,185–41,970,308, 124 basesExon 17: 41,970,388–41,970,542, 155 basesExon 16: 41,975,629–41,975,797, 169 basesExon 15: 41,976,416–41,976,566, 151 basesExon 14: 41,977,936–41,978,072, 137 basesExon 13: 41,978,151–41,978,326, 176 basesExon 12: 41,978,606–41,978,798, 193 basesExon 11: 41,981,502–41,981,636, 135 basesExon 10: 41,981,722–41,981,831, 110 basesExon 9: 41,981,908–41,982,106, 199 basesExon 8: 41,984,918–41,985,186, 269 basesExon 7: 41,985,306–41,985,423, 118 basesExon 6: 41,985,864–41,985,998, 135 basesExon 5: 41,986,116–41,986,229, 114 basesExon 4: 41,987,936–41,988,139, 204 basesExon 3: 41,988,318–41,988,377, 60 basesExon 2: 41,988,476–41,988,562, 87 basesExon 1: 41,994,071–41,994,230, 160 bases23201510515′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 3.6 kb of the gene's 27.6 kb; 3,042 of those bases code for the protein.

How a genome test reads ATP1A3

126

positions in ATP1A3 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 27.6 kb of ATP1A3, introns included, not only the 3.6 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.). ATP1A3 gene: ATPase Na+/K+ transporting subunit alpha 3. Retrieved 17 October 2026, from https://dantelabs.com/genes/atp1a3

Vancouver

Dante Labs. ATP1A3 gene: ATPase Na+/K+ transporting subunit alpha 3 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/atp1a3

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