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Gene

ATP1A1

ATPase Na+/K+ transporting subunit alpha 1

Summary

Cytogenetic location
1p13.1
Coordinates
Chromosome 1: 116,373,244–116,404,774 (GRCh38)
Exons
23 exons across 31.5 kb
Protein
1,023 amino acids
MANE Select transcript
ENST00000295598.10NM_000701.8
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

  • 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.

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.

      • ClinGen rates the link definitive
      • 4 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

How ATP1A1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 1, with a bracket where ATP1A1 sits. ATP1A1 and 5 genes near it on chromosome 1, from 115,889,009 to 116,889,008.Chromosome 11p13.1p36.33p36.32p36.31p36.23p36.22p36.21p36.13p36.12p36.11p35.3p35.2p35.1p34.3p34.2p34.1p33p32.3p32.2p32.1p31.3p31.2p31.1p22.3p22.2p22.1p21.3p21.2p21.1p13.3p13.2p13.1p12p11.2p11.1q11q12q21.1q21.2q21.3q22q23.1q23.2q23.3q24.1q24.2q24.3q25.1q25.2q25.3q31.1q31.2q31.3q32.1q32.2q32.3q41q42.11q42.12q42.13q42.2q42.3q43q44116 Mb116.2 Mb116.4 Mb116.6 Mb116.8 MbSLC22A15: 115,976,310–116,072,747, forward strandSLC22A15MAB21L3: 116,111,068–116,138,149, forward strandMAB21L3ATP1A1: 116,373,244–116,404,774, forward strandATP1A1CD58: 116,499,485–116,571,061, reverse strandCD58IGSF3: 116,574,393–116,667,820, reverse strandIGSF3CD2: 116,754,370–116,769,229, forward strandCD2Diagram of ATP1A1: 23 exons on the forward strand of chromosome 1Exon 6: 1 known disease-causing siteExon 8: 2 known disease-causing sitesExon 9: 1 known disease-causing siteExon 12: 1 known disease-causing siteExon 13: 3 known disease-causing sitesExon 18: 1 known disease-causing siteExon 19: 3 known disease-causing sitesExon 20: 1 known disease-causing siteExon 1: 116,373,244–116,373,523, 280 basesExon 2: 116,384,014–116,384,124, 111 basesExon 3: 116,384,783–116,384,842, 60 basesExon 4: 116,387,288–116,387,491, 204 basesExon 5: 116,388,131–116,388,244, 114 basesExon 6: 116,388,638–116,388,772, 135 basesExon 7: 116,388,902–116,389,019, 118 basesExon 8: 116,389,439–116,389,707, 269 basesExon 9: 116,390,213–116,390,411, 199 basesExon 10: 116,390,782–116,390,891, 110 basesExon 11: 116,392,854–116,392,988, 135 basesExon 12: 116,393,531–116,393,723, 193 basesExon 13: 116,395,110–116,395,285, 176 basesExon 14: 116,396,598–116,396,734, 137 basesExon 15: 116,397,888–116,398,038, 151 basesExon 16: 116,398,621–116,398,789, 169 basesExon 17: 116,398,930–116,399,084, 155 basesExon 18: 116,399,420–116,399,543, 124 basesExon 19: 116,400,861–116,401,006, 146 basesExon 20: 116,401,130–116,401,260, 131 basesExon 21: 116,401,554–116,401,655, 102 basesExon 22: 116,403,884–116,403,975, 92 basesExon 23: 116,404,416–116,404,774, 359 bases15101520235′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 3.7 kb of the gene's 31.5 kb; 3,072 of those bases code for the protein.

How a genome test reads ATP1A1

13

positions in ATP1A1 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 31.5 kb of ATP1A1, introns included, not only the 3.7 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.). ATP1A1 gene: ATPase Na+/K+ transporting subunit alpha 1. Retrieved 17 October 2026, from https://dantelabs.com/genes/atp1a1

Vancouver

Dante Labs. ATP1A1 gene: ATPase Na+/K+ transporting subunit alpha 1 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/atp1a1

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