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Gene

ATP11A

ATPase phospholipid transporting 11A

Summary

Cytogenetic location
13q34
Coordinates
Chromosome 13: 112,690,038–112,887,168 (GRCh38)
Exons
30 exons across 197.1 kb
Protein
1,134 amino acids
Inheritance
Autosomal dominant
Also known as
ATPIH, ATPIS, KIAA1021
MANE Select transcript
ENST00000375645.8NM_015205.3
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

  • Hearing Loss and Deafness

    • Auditory Neuropathy

      Hearing loss in which the inner ear detects sound but the signal is not passed on normally to the hearing nerve, including inherited forms caused by OTOF and other genes.

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

      Identifying the cause can affect the choice between hearing aids and cochlear implants, and OTOF-related forms are the subject of gene-therapy trials.

    • Autosomal Dominant Nonsyndromic Hearing LossAutosomal dominant

      Autosomal dominant form of nonsyndromic deafness.

      • ClinGen rates the link moderate
      • 1 GenCC submitter rates it definitive or strong
    • Nonsyndromic Genetic Hearing Loss

      One of 97 genes linked to it

      Inherited hearing loss without other medical features, including the common recessive forms caused by GJB2, OTOF, SLC26A4, STRC and many other genes, as well as dominant, X-linked and mitochondrial forms.

      • ClinGen rates the link moderate
      • 1 GenCC submitter rates it definitive or strong
      What knowing changes

      Knowing the genetic cause can guide hearing support and cochlear implant decisions, gene-therapy trial eligibility (for example OTOF) and family counselling.

  • Pelizaeus-Merzbacher Disease & Hypomyelinating Leukodystrophies

    • Hypomyelinating leukodystrophy 24 (ATP11A)Autosomal dominant

      A rare inherited form of hypomyelinating leukodystrophy, in which myelin in the brain does not form normally, causing delayed development and movement problems.

      • 1 GenCC submitter rates it definitive or strong

Broader groupings

  • Other Inherited Leukodystrophies

    • Leukodystrophy (other and unspecified types)

      One of 80 genes linked to it

      Inherited conditions that damage or prevent the normal formation of myelin, the white matter of the brain and spinal cord. Different types follow autosomal recessive, autosomal dominant or X-linked inheritance depending on the gene involved.

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

      Knowing the specific genetic cause can end a diagnostic search, guide supportive care and surveillance, show whether a specific treatment exists, and allow testing of relatives.

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 ATP11A is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 13, with a bracket where ATP11A sits. ATP11A and 8 genes near it on chromosome 13, from 112,288,603 to 113,288,602.Chromosome 1313q34p13p12p11.2p11.1q11q12.11q12.12q12.13q12.2q12.3q13.1q13.2q13.3q14.11q14.12q14.13q14.2q14.3q21.1q21.2q21.31q21.32q21.33q22.1q22.2q22.3q31.1q31.2q31.3q32.1q32.2q32.3q33.1q33.2q33.3q34112.4 Mb112.6 Mb112.8 Mb113 Mb113.2 MbSPACA7: 112,376,309–112,434,695, forward strandSPACA7TUBGCP3: 112,485,005–112,588,205, reverse strandTUBGCP3ATP11A: 112,690,038–112,887,168, forward strandATP11AMCF2L: 112,894,330–113,100,412, forward strandMCF2LF7: 113,105,762–113,120,685, forward strandF7F10: 113,122,771–113,149,531, forward strandF10PROZ: 113,158,388–113,173,625, forward strandPROZPCID2: 113,177,117–113,209,458, reverse strandPCID2CUL4A: 113,208,193–113,267,108, forward strandCUL4ADiagram of ATP11A: 30 exons on the forward strand of chromosome 13Exon 12: 1 known disease-causing siteExon 26: 1 known disease-causing siteExon 1: 112,690,038–112,690,455, 418 basesExon 2: 112,785,135–112,785,257, 123 basesExon 3: 112,804,957–112,805,046, 90 basesExon 4: 112,806,213–112,806,293, 81 basesExon 5: 112,810,619–112,810,726, 108 basesExon 6: 112,816,083–112,816,211, 129 basesExon 7: 112,819,304–112,819,407, 104 basesExon 8: 112,819,900–112,819,950, 51 basesExon 9: 112,823,345–112,823,409, 65 basesExon 10: 112,824,344–112,824,425, 82 basesExon 11: 112,825,430–112,825,580, 151 basesExon 12: 112,826,694–112,826,891, 198 basesExon 13: 112,831,375–112,831,548, 174 basesExon 14: 112,832,860–112,833,023, 164 basesExon 15: 112,834,589–112,834,660, 72 basesExon 16: 112,836,178–112,836,251, 74 basesExon 17: 112,842,276–112,842,379, 104 basesExon 18: 112,851,037–112,851,218, 182 basesExon 19: 112,854,279–112,854,530, 252 basesExon 20: 112,855,911–112,856,085, 175 basesExon 21: 112,857,818–112,857,920, 103 basesExon 22: 112,858,145–112,858,290, 146 basesExon 23: 112,859,393–112,859,452, 60 basesExon 24: 112,860,287–112,860,414, 128 basesExon 25: 112,862,440–112,862,575, 136 basesExon 26: 112,871,735–112,871,800, 66 basesExon 27: 112,873,573–112,873,676, 104 basesExon 28: 112,875,776–112,875,941, 166 basesExon 29: 112,878,217–112,878,303, 87 basesExon 30: 112,881,876–112,887,168, 5,293 bases1510152025305′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 9.1 kb of the gene's 197.1 kb; 3,405 of those bases code for the protein.

How a genome test reads ATP11A

3

positions in ATP11A 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 197.1 kb of ATP11A, introns included, not only the 9.1 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.). ATP11A gene: ATPase phospholipid transporting 11A. Retrieved 17 October 2026, from https://dantelabs.com/genes/atp11a

Vancouver

Dante Labs. ATP11A gene: ATPase phospholipid transporting 11A [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/atp11a

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