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Gene

ATP9A

ATPase phospholipid transporting 9A

Summary

Cytogenetic location
20q13.2
Coordinates
Chromosome 20: 51,596,514–51,768,390 (GRCh38)
Exons
28 exons across 171.9 kb
Protein
1,047 amino acids
Also known as
KIAA0611, ATPIIA
MANE Select transcript
ENST00000338821.6NM_006045.3
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

No Genome Test report reads ATP9A yet. The test sequences your whole genome, so your data includes it all the same.

How ATP9A is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 20, with a bracket where ATP9A sits. ATP9A and 3 genes near it on chromosome 20, from 51,182,452 to 52,182,451.Chromosome 2020q13.2p13p12.3p12.2p12.1p11.23p11.22p11.21p11.1q11.1q11.21q11.22q11.23q12q13.11q13.12q13.13q13.2q13.31q13.32q13.3351.2 Mb51.4 Mb51.6 Mb51.8 Mb52 MbNFATC2: 51,386,957–51,563,072, reverse strandNFATC2ATP9A: 51,596,514–51,768,390, reverse strandATP9ASALL4: 51,782,331–51,802,578, reverse strandSALL4ZFP64: 52,046,638–52,204,308, reverse strandZFP64Diagram of ATP9A: 28 exons on the reverse strand of chromosome 20Exon 25: 1 known disease-causing siteExon 19: 1 known disease-causing siteExon 17: 1 known disease-causing siteExon 28: 51,596,514–51,601,347, 4,834 basesExon 27: 51,604,817–51,605,020, 204 basesExon 26: 51,607,527–51,607,584, 58 basesExon 25: 51,608,518–51,608,626, 109 basesExon 24: 51,610,101–51,610,165, 65 basesExon 23: 51,613,677–51,613,832, 156 basesExon 22: 51,617,490–51,617,554, 65 basesExon 21: 51,618,662–51,618,806, 145 basesExon 20: 51,618,954–51,619,043, 90 basesExon 19: 51,622,074–51,622,172, 99 basesExon 18: 51,625,192–51,625,362, 171 basesExon 17: 51,627,600–51,627,683, 84 basesExon 16: 51,628,980–51,629,072, 93 basesExon 15: 51,639,343–51,639,504, 162 basesExon 14: 51,656,938–51,657,150, 213 basesExon 13: 51,669,997–51,670,109, 113 basesExon 12: 51,671,115–51,671,257, 143 basesExon 11: 51,674,153–51,674,313, 161 basesExon 10: 51,676,132–51,676,208, 77 basesExon 9: 51,689,064–51,689,139, 76 basesExon 8: 51,690,739–51,690,819, 81 basesExon 7: 51,694,008–51,694,102, 95 basesExon 6: 51,696,093–51,696,144, 52 basesExon 5: 51,697,424–51,697,482, 59 basesExon 4: 51,712,966–51,713,074, 109 basesExon 3: 51,725,819–51,725,932, 114 basesExon 2: 51,729,834–51,729,978, 145 basesExon 1: 51,768,302–51,768,390, 89 bases2825201510515′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 7.9 kb of the gene's 171.9 kb; 3,144 of those bases code for the protein.

How a genome test reads ATP9A

4

positions in ATP9A 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 171.9 kb of ATP9A, introns included, not only the 7.9 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.
  • 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.). ATP9A gene: ATPase phospholipid transporting 9A. Retrieved 17 October 2026, from https://dantelabs.com/genes/atp9a

Vancouver

Dante Labs. ATP9A gene: ATPase phospholipid transporting 9A [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/atp9a

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