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Gene

ATP6V1A

ATPase H+ transporting V1 subunit A

Summary

Cytogenetic location
3q13.31
Coordinates
Chromosome 3: 113,747,035–113,812,056 (GRCh38)
Exons
15 exons across 65 kb
Protein
617 amino acids
Also known as
Vma1, VA68
Previous symbols
VPP2, ATP6A1, ATP6V1A1
MANE Select transcript
ENST00000273398.8NM_001690.4
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

  • Cutis Laxa

    • Cutis laxa (CL) is an inherited or acquired connective tissue disorder characterized by wrinkled, redundant and sagging inelastic skin associated with skeletal and developmental anomalies and, in some cases, with severe systemic involvement. Several different forms of inherited CL have been described, differentiated on the basis of the mode of inheritance and differences in the extent of internal organ involvement, associated anomalies and disease severity.

      • 4 GenCC submitters rate it definitive or strong

Broader groupings

  • 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.

      • 3 GenCC submitters rate it definitive or strong

How ATP6V1A is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 3, with a bracket where ATP6V1A sits. ATP6V1A and 14 genes near it on chromosome 3, from 113,279,546 to 114,279,545.Chromosome 33q13.31p26.3p26.2p26.1p25.3p25.2p25.1p24.3p24.2p24.1p23p22.3p22.2p22.1p21.33p21.32p21.31p21.2p21.1p14.3p14.2p14.1p13p12.3p12.2p12.1p11.2p11.1q11.1q11.2q12.1q12.2q12.3q13.11q13.12q13.13q13.2q13.31q13.32q13.33q21.1q21.2q21.3q22.1q22.2q22.3q23q24q25.1q25.2q25.31q25.32q25.33q26.1q26.2q26.31q26.32q26.33q27.1q27.2q27.3q28q29113.4 Mb113.6 Mb113.8 Mb114 Mb114.2 MbBOC: 113,210,846–113,287,463, forward strandBOCCFAP44: 113,286,930–113,441,610, reverse strandCFAP44SPICE1-CFAP44: 113,361,901–113,515,151, reverse strandSPICE1-CFAP44SPICE1: 113,442,718–113,515,606, reverse strandSPICE1SIDT1: 113,532,400–113,629,714, forward strandSIDT1USF3: 113,632,051–113,696,667, reverse strandUSF3NAA50: 113,716,458–113,746,786, reverse strandNAA50ATP6V1A: 113,747,035–113,812,056, forward strandATP6V1AGRAMD1C: 113,828,182–113,947,179, forward strandGRAMD1CZDHHC23: 113,947,706–113,965,401, forward strandZDHHC23CCDC191: 113,964,137–114,056,594, reverse strandCCDC191QTRT2: 114,005,833–114,088,542, forward strandQTRT2DRD3: 114,127,580–114,199,407, reverse strandDRD3ZNF80: 114,234,631–114,237,578, reverse strandZNF80TIGIT: 114,276,913–114,310,288, forward strandTIGITDiagram of ATP6V1A: 15 exons on the forward strand of chromosome 3Exon 4: 2 known disease-causing sitesExon 7: 1 known disease-causing siteExon 8: 3 known disease-causing sitesExon 9: 2 known disease-causing sitesExon 10: 1 known disease-causing siteExon 12: 1 known disease-causing siteExon 14: 1 known disease-causing siteExon 15: 1 known disease-causing siteExon 1: 113,747,035–113,747,113, 79 basesExon 2: 113,778,741–113,778,835, 95 basesExon 3: 113,781,050–113,781,178, 129 basesExon 4: 113,784,224–113,784,438, 215 basesExon 5: 113,784,696–113,784,833, 138 basesExon 6: 113,786,232–113,786,383, 152 basesExon 7: 113,788,713–113,788,875, 163 basesExon 8: 113,789,732–113,789,840, 109 basesExon 9: 113,794,872–113,794,994, 123 basesExon 10: 113,795,090–113,795,204, 115 basesExon 11: 113,795,876–113,795,939, 64 basesExon 12: 113,798,243–113,798,446, 204 basesExon 13: 113,803,583–113,803,677, 95 basesExon 14: 113,805,354–113,805,525, 172 basesExon 15: 113,809,335–113,812,056, 2,722 bases12468101214155′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 4.6 kb of the gene's 65 kb; 1,854 of those bases code for the protein.

How a genome test reads ATP6V1A

12

positions in ATP6V1A 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 65 kb of ATP6V1A, introns included, not only the 4.6 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.). ATP6V1A gene: ATPase H+ transporting V1 subunit A. Retrieved 16 October 2026, from https://dantelabs.com/genes/atp6v1a

Vancouver

Dante Labs. ATP6V1A gene: ATPase H+ transporting V1 subunit A [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/atp6v1a

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