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Gene

ATP6AP1

ATPase H+ transporting accessory protein 1

Summary

Cytogenetic location
Xq28
Coordinates
Chromosome X: 154,428,677–154,436,516 (GRCh38)
Exons
10 exons across 7.8 kb
Protein
470 amino acids
Also known as
ORF, XAP-3, VATPS1, 16A, Ac45, XAP3, CF2
Previous symbols
ATP6S1, ATP6IP1
MANE Select transcript
ENST00000369762.7NM_001183.6
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 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.

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

    • Other Inborn Errors of Immunity

      • Inborn error of immunity

        One of 114 genes linked to it

        Inherited disorders of the immune system caused by changes in single genes, affecting how the body fights infection or regulates inflammation.

        • 2 GenCC submitters rate it definitive or strong
      • Immunodeficiency Disease

        One of 170 genes linked to it

        Disease in which there is a deficiency or defect in the mechanisms of immunity, either cellular or humoral.

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

        HSCT for SCID and severe PIDs; immunoglobulin replacement (IVIG/SCIG) for antibody deficiencies; leniolisib (Joenja, FDA 2023) for APDS; gene therapy for ADA-SCID; abatacept for CTLA4/LRBA deficiency; prophylactic antibiotics; G-CSF for CGD

    How ATP6AP1 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 ATP6AP1 sits. ATP6AP1 and 37 genes near it on chromosome X, from 153,932,597 to 154,932,596.Chromosome XXq28p22.33p22.32p22.31p22.2p22.13p22.12p22.11p21.3p21.2p21.1p11.4p11.3p11.23p11.22p11.21p11.1q11.1q11.2q12q13.1q13.2q13.3q21.1q21.2q21.31q21.32q21.33q22.1q22.2q22.3q23q24q25q26.1q26.2q26.3q27.1q27.2q27.3q28154 Mb154.2 Mb154.4 Mb154.6 Mb154.8 MbARHGAP4: 153,907,367–153,934,999, reverse strandNAA10: 153,928,799–153,935,083, reverse strandNAA10RENBP: 153,935,269–153,944,688, reverse strandRENBPHCFC1: 153,946,434–153,972,427, reverse strandHCFC1TMEM187: 153,972,290–153,983,194, forward strandTMEM187IRAK1: 154,010,501–154,020,650, reverse strandIRAK1MECP2: 154,021,573–154,137,103, reverse strandMECP2OPN1LW: 154,144,243–154,159,032, forward strandOPN1LWOPN1MW: 154,182,596–154,196,861, forward strandOPN1MWOPN1MW2: 154,219,756–154,233,286, forward strandOPN1MW2OPN1MW3: 154,257,582–154,271,090, forward strandOPN1MW3TEX28: 154,271,265–154,295,853, reverse strandTEX28TKTL1: 154,295,795–154,330,350, forward strandTKTL1FLNA: 154,348,524–154,374,643, reverse strandFLNAEMD: 154,379,205–154,381,574, forward strandRPL10: 154,389,955–154,409,168, forward strandDNASE1L1: 154,401,236–154,412,119, reverse strandTAFAZZIN: 154,409,456–154,421,726, forward strandTAFAZZINATP6AP1: 154,428,677–154,436,516, forward strandATP6AP1GDI1: 154,436,600–154,443,467, forward strandGDI1FAM50A: 154,444,103–154,450,655, forward strandFAM50APLXNA3: 154,458,275–154,477,779, forward strandLAGE3: 154,477,598–154,479,291, reverse strandUBL4A: 154,483,717–154,486,661, reverse strandUBL4ASLC10A3: 154,487,306–154,490,690, reverse strandFAM3A: 154,505,019–154,516,882, reverse strandFAM3AG6PD: 154,517,825–154,547,584, reverse strandG6PDIKBKG: 154,541,179–154,568,543, forward strandIKBKGCTAG1A: 154,585,133–154,586,816, forward strandCTAG1ACTAG1B: 154,617,609–154,619,282, reverse strandCTAG1BCTAG2: 154,651,972–154,653,579, reverse strandCTAG2GAB3: 154,675,249–154,751,583, reverse strandGAB3DKC1: 154,762,741–154,777,697, forward strandDKC1MPP1: 154,778,684–154,821,039, reverse strandMPP1SMIM9: 154,823,348–154,834,662, reverse strandSMIM9F8: 154,835,788–155,026,940, reverse strandF8H2AB1: 154,884,972–154,885,558, forward strandH2AB1F8A1: 154,886,355–154,888,061, forward strandF8A1Diagram of ATP6AP1: 10 exons on the forward strand of chromosome XExon 2: 2 known disease-causing sitesExon 4: 2 known disease-causing sitesExon 9: 1 known disease-causing siteExon 1: 154,428,677–154,428,853, 177 basesExon 2: 154,429,048–154,429,174, 127 basesExon 3: 154,431,830–154,431,904, 75 basesExon 4: 154,432,266–154,432,459, 194 basesExon 5: 154,432,931–154,432,971, 41 basesExon 6: 154,433,635–154,433,720, 86 basesExon 7: 154,434,208–154,434,446, 239 basesExon 8: 154,435,139–154,435,186, 48 basesExon 9: 154,435,274–154,435,505, 232 basesExon 10: 154,435,682–154,436,516, 835 bases123456789105′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 2.1 kb of the gene's 7.8 kb; 1,413 of those bases code for the protein.

    How a genome test reads ATP6AP1

    8

    positions in ATP6AP1 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 7.8 kb of ATP6AP1, introns included, not only the 2.1 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.). ATP6AP1 gene: ATPase H+ transporting accessory protein 1. Retrieved 17 October 2026, from https://dantelabs.com/genes/atp6ap1

    Vancouver

    Dante Labs. ATP6AP1 gene: ATPase H+ transporting accessory protein 1 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/atp6ap1

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