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Gene

ATP5F1A

ATP synthase F1 subunit alpha

Summary

Cytogenetic location
18q21.1
Coordinates
Chromosome 18: 46,080,248–46,098,296 (GRCh38)
Exons
12 exons across 18 kb
Protein
553 amino acids
Also known as
ATP5A, hATP1, OMR, ORM
Previous symbols
ATP5AL2, ATPM, ATP5A1
MANE Select transcript
ENST00000398752.11NM_004046.6
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

  • Primary Mitochondrial Disease

    • Combined Oxidative Phosphorylation Deficiency

      Disorders, usually caused by nuclear genes involved in mitochondrial protein production, that reduce several respiratory chain complexes at once and often cause severe multisystem disease in childhood.

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

      Knowing can end a diagnostic search and guide surveillance and supportive care.

    • Mitochondrial Respiratory Chain Complex Deficiency

      One of 61 genes linked to it

      Isolated deficiencies of complex I, II, III, IV or V, caused by variants in nuclear or mitochondrial genes, which can affect the brain, muscles, heart, liver and other energy-demanding organs.

      • 1 GenCC submitter rates it definitive or strong
      What knowing changes

      Knowing can end a diagnostic search and guide surveillance of affected organs and avoidance of drugs toxic to mitochondria.

How ATP5F1A is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 18, with a bracket where ATP5F1A sits. ATP5F1A and 9 genes near it on chromosome 18, from 45,589,272 to 46,589,271.Chromosome 1818q21.1p11.32p11.31p11.23p11.22p11.21p11.1q11.1q11.2q12.1q12.2q12.3q21.1q21.2q21.31q21.32q21.33q22.1q22.2q22.3q2345.6 Mb45.8 Mb46 Mb46.2 Mb46.4 MbSLC14A2: 45,212,995–45,683,688, forward strandSLC14A2SLC14A1: 45,687,025–45,752,521, forward strandSLC14A1EPG5: 45,800,477–45,967,346, reverse strandEPG5SIGLEC15: 45,825,675–45,844,218, forward strandSIGLEC15PSTPIP2: 45,983,536–46,072,367, reverse strandPSTPIP2ATP5F1A: 46,080,248–46,098,296, reverse strandATP5F1AHAUS1: 46,104,326–46,129,589, forward strandHAUS1ARK2N: 46,173,497–46,321,788, forward strandARK2NARK2C: 46,326,809–46,463,140, forward strandARK2CLOXHD1: 46,476,971–46,657,220, reverse strandLOXHD1Diagram of ATP5F1A: 12 exons on the reverse strand of chromosome 18Exon 9: 1 known disease-causing siteExon 5: 1 known disease-causing siteExon 12: 46,080,248–46,084,363, 4,116 basesExon 11: 46,084,504–46,084,654, 151 basesExon 10: 46,086,113–46,086,257, 145 basesExon 9: 46,086,387–46,086,494, 108 basesExon 8: 46,087,008–46,087,232, 225 basesExon 7: 46,087,341–46,087,492, 152 basesExon 6: 46,088,109–46,088,257, 149 basesExon 5: 46,089,566–46,089,732, 167 basesExon 4: 46,089,823–46,089,996, 174 basesExon 3: 46,091,682–46,091,851, 170 basesExon 2: 46,095,053–46,095,131, 79 basesExon 1: 46,098,172–46,098,296, 125 bases1210864215′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 5.8 kb of the gene's 18 kb; 1,662 of those bases code for the protein.

How a genome test reads ATP5F1A

3

positions in ATP5F1A 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 18 kb of ATP5F1A, introns included, not only the 5.8 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.). ATP5F1A gene: ATP synthase F1 subunit alpha. Retrieved 17 October 2026, from https://dantelabs.com/genes/atp5f1a

Vancouver

Dante Labs. ATP5F1A gene: ATP synthase F1 subunit alpha [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/atp5f1a

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