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Gene

ATP6AP2

ATPase H+ transporting accessory protein 2

Summary

Cytogenetic location
Xp11.4
Coordinates
Chromosome X: 40,580,970–40,606,848 (GRCh38)
Exons
9 exons across 25.9 kb
Protein
350 amino acids
Also known as
PRR, M8-9, RENR, (P)RR, APT6M8-9, ATP6M8-9
Previous symbols
ATP6IP2
MANE Select transcript
ENST00000636580.2NM_005765.3
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

    • Congenital Disorders of Glycosylation

      • Congenital Disorders of Glycosylation (CDG)

        One of 98 genes linked to it

        A large group of inherited conditions in which sugar chains (glycans) are not correctly built or attached to proteins and lipids, often affecting the brain, liver, blood clotting, growth and many other body systems. Most are autosomal recessive, but some are X-linked or autosomal dominant.

        • 2 GenCC submitters rate it definitive or strong

    • 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

    • Intellectual Disability

      • One of 233 genes linked to it

        • ClinGen rates the link definitive
        • 3 GenCC submitters rate it definitive or strong

    How ATP6AP2 is laid out

    • Coding sequence
    • Untranslated region
    • Intron
    • Direction of transcription
    • Known disease-causing sites
    • Stretches short reads find hard
    Chromosome X, with a bracket where ATP6AP2 sits. ATP6AP2 and 6 genes near it on chromosome X, from 40,093,909 to 41,093,908.Chromosome XXp11.4p22.33p22.32p22.31p22.2p22.13p22.12p22.11p21.3p21.2p21.1p11.4p11.3p11.23p11.22p11.21p11.1q11.1q11.2q12q13.1q13.2q13.3q21.1q21.2q21.31q21.32q21.33q22.1q22.2q22.3q23q24q25q26.1q26.2q26.3q27.1q27.2q27.3q2840.2 Mb40.4 Mb40.6 Mb40.8 Mb41 MbBCOR: 40,049,815–40,177,329, reverse strandBCORATP6AP2: 40,580,970–40,606,848, forward strandATP6AP2MPC1L: 40,623,428–40,624,136, forward strandMPC1LCXorf38: 40,626,921–40,647,572, reverse strandCXorf38MED14: 40,648,305–40,735,924, reverse strandMED14: 40,834,445–40,934,085, forward strandUSP9X: 41,085,346–41,236,579, forward strandUSP9XDiagram of ATP6AP2: 9 exons on the forward strand of chromosome XExon 3: 1 known disease-causing siteExon 4: 1 known disease-causing siteExon 7: 1 known disease-causing siteExon 1: 40,580,970–40,581,102, 133 basesExon 2: 40,588,986–40,589,116, 131 basesExon 3: 40,591,234–40,591,365, 132 basesExon 4: 40,597,249–40,597,344, 96 basesExon 5: 40,597,527–40,597,664, 138 basesExon 6: 40,598,681–40,598,734, 54 basesExon 7: 40,599,592–40,599,741, 150 basesExon 8: 40,600,762–40,600,881, 120 basesExon 9: 40,605,561–40,606,848, 1,288 bases1246895′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 2.2 kb of the gene's 25.9 kb; 1,053 of those bases code for the protein.

    How a genome test reads ATP6AP2

    3

    positions in ATP6AP2 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 25.9 kb of ATP6AP2, introns included, not only the 2.2 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.). ATP6AP2 gene: ATPase H+ transporting accessory protein 2. Retrieved 17 October 2026, from https://dantelabs.com/genes/atp6ap2

    Vancouver

    Dante Labs. ATP6AP2 gene: ATPase H+ transporting accessory protein 2 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/atp6ap2

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