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Atp6v1a Gene Detail
Summary
  • Symbol
    Atp6v1a
  • Name
    ATPase, H+ transporting, lysosomal V1 subunit A
  • Synonyms
    Atp6a1, lysosomal 70kDa, VA68, VPP2
  • Feature Type
    protein coding gene
  • IDs
    MGI:1201780
    NCBI Gene: 11964
  • Alliance
    gene page
  • Transcription Start Sites
    15 TSS
Location &
Maps
more
  • Sequence Map
    Chr16:43905765-43960055 bp, - strand
    From NCBI annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 16, 28.44 cM, cytoband B4
  • Mapping Data
    2 experiments
Strain
Comparison
more
  • SNPs within 2kb
    1315 from dbSNP Build 142
  • Strain Annotations
    18
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_1201780
 protein coding gene Chr16:43905765-43960068 (-)
129S1/SvImJ MGP_129S1SvImJ_G0022834
 protein coding gene Chr16:42812469-42870267 (-)
A/J MGP_AJ_G0022799
 protein coding gene Chr16:40884512-40939962 (-)
AKR/J MGP_AKRJ_G0022771
 protein coding gene Chr16:42200531-42252079 (-)
BALB/cJ MGP_BALBcJ_G0022800
 protein coding gene Chr16:40874267-40928301 (-)
C3H/HeJ MGP_C3HHeJ_G0022564
 protein coding gene Chr16:42391433-42447233 (-)
C57BL/6NJ MGP_C57BL6NJ_G0023247
 protein coding gene Chr16:43803777-43860900 (-)
CAROLI/EiJ MGP_CAROLIEiJ_G0020762
 protein coding gene Chr16:40940044-40994287 (-)
CAST/EiJ MGP_CASTEiJ_G0022090
 protein coding gene Chr16:42590324-42683401 (-)
CBA/J MGP_CBAJ_G0022535
 protein coding gene Chr16:45644484-45707356 (-)
DBA/2J MGP_DBA2J_G0022667
 protein coding gene Chr16:40615949-40684125 (-)
FVB/NJ MGP_FVBNJ_G0022642
 protein coding gene Chr16:40588295-40643311 (-)
LP/J MGP_LPJ_G0022735
 protein coding gene Chr16:42526083-42584229 (-)
NOD/ShiLtJ MGP_NODShiLtJ_G0022661
 protein coding gene Chr16:45042263-45101729 (-)
NZO/HlLtJ MGP_NZOHlLtJ_G0023262
 protein coding gene Chr16:42221929-42279039 (-)
PWK/PhJ MGP_PWKPhJ_G0021830
 protein coding gene Chr16:41014145-41102989 (-)
SPRET/EiJ MGP_SPRETEiJ_G0021661
 protein coding gene Chr16:42119423-42174690 (-)
WSB/EiJ MGP_WSBEiJ_G0022134
 protein coding gene Chr16:42315295-42372713 (-)



Homology
more
  • Human Ortholog
    ATP6V1A, ATPase H+ transporting V1 subunit A
  • Vertebrate Orthologs
    4
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    ATP6V1A, ATPase H+ transporting V1 subunit A
  • Synonyms
    ARCL2D, ATP6A1, ATP6V1A1, DEE93, HO68, IECEE3, VA68, Vma1, VPP2
  • Links
    NCBI Gene ID: 523
    UniProt: P38606

  • Chr Location
    3q13.31; chr3:113746770-113812056 (+)  GRCh38
Human Diseases
more
  • Diseases
    2 with human ATP6V1A associations

Human Disease Mouse Models
      
IDs
IDs
Click on a disease name to see all genes associated with that disease.

Mutations,
Alleles, and
Phenotypes
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  • Phenotype Summary
    2 phenotypes from 1 allele in 1 genetic background
    12 phenotype references
Phenotype Overview

adipose tissue
behavior/neurological
cardiovascular system
cellular
craniofacial
digestive/alimentary system
embryo
endocrine/exocrine glands
growth/size/body
hearing/vestibular/ear
hematopoietic system
homeostasis/metabolism
integument
immune system
limbs/digits/tail
liver/biliary system
mortality/aging
muscle
nervous system
pigmentation
renal/urinary system
reproductive system
respiratory system
skeleton
taste/olfaction
neoplasm
vision/eye

Click cells to view annotations.
Gene Ontology
(GO)
Classifications
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  • All GO Annotations
    60
  • GO References
    16
Molecular Function

carbohydrate derivative binding
cytoskeletal protein binding
DNA binding
enzyme regulator
hydrolase
ligase
lipid binding
oxidoreductase
RNA binding
signaling receptor activity
signaling receptor binding
transcription
transferase
transporter
Biological Process

carbohydrate derivative metabolism
cell differentiation
cell population proliferation
cellular component organization
DNA-templated transcription
establishment of localization
homeostatic process
immune system process
lipid metabolic process
programmed cell death
protein metabolic process
response to stimulus
signaling
system development
Cellular Component

cell projection
cytoplasmic vesicle
cytoskeleton
cytosol
endoplasmic reticulum
endosome
extracellular region
Golgi apparatus
mitochondrion
membraneless organelle
nucleus
organelle envelope
organelle lumen
plasma membrane
protein-containing complex
synapse
vacuole
Click cells to view annotations.
Expression
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Expression Overview

early conceptus
embryo ectoderm
embryo endoderm
embryo mesoderm
embryo mesenchyme
extraembryonic component
alimentary system
auditory system
branchial arches
cardiovascular system
connective tissue
endocrine system
exocrine system
hemolymphoid system
integumental system
limbs
liver and biliary system
musculoskeletal system
nervous system
olfactory system
reproductive system
respiratory system
urinary system
visual system
Click cells to view annotations.


  • Assay Results
    845
  • Tissues
    108
  • cDNA Data
    346
  • Literature Summary
    8
Sequences &
Gene Models
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Representative SequencesLengthStrain/SpeciesFlank
genomic 11964 NCBI Gene Model | MGI Sequence Detail 54291 C57BL/6J ±  kb
transcript NM_001358204 RefSeq | MGI Sequence Detail 4200 C57BL/6  
polypeptide P50516 UniProt | EBI | MGI Sequence Detail 617 Not Applicable  
For the selected sequence
Protein
Information
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  • UniProt
    4 Sequences
  • Protein Ontology
    PR:000004480 V-type proton ATPase catalytic subunit A
    (term hierarchy)
  • PDB
    9BRA, 9BRQ, 9BRR, 9BRS, 9BRT, 9BRU
  • EC
    7.1.2.2
  • InterPro Domains
    IPR020003 ATPase, alpha/beta subunit, nucleotide-binding domain, active site
    IPR004100 ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain
    IPR036121 ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily
    IPR000194 ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain
    IPR024034 ATPase, F1/V1 complex, beta/alpha subunit, C-terminal
    IPR005725 ATPase, V1 complex, subunit A
    IPR031686 ATPsynthase alpha/beta subunit, N-terminal extension
    IPR023366 ATP synthase subunit alpha, N-terminal domain-like superfamily
    IPR027417 P-loop containing nucleoside triphosphate hydrolase
    IPR022878 V-type ATP synthase catalytic alpha chain
  • GlyGen
    P50516 2 sites, 1 N-linked glycan (1 site), 1 O-linked glycan (1 site)
Molecular
Reagents
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  • All nucleic 347
    cDNA 346
    Primer pair 1

    Microarray probesets 6
Other
Accession IDs
less
MGI:2146472
References
more
  • Summaries
    All 58
    Developmental Gene Expression 8
    Gene Ontology 16
    Phenotypes 12
  • Earliest
    J:31176 Laitala-Leinonen T, et al., Resorption-cycle-dependent polarization of mRNAs for different subunits of V-ATPase in bone-resorbing osteoclasts. Mol Biol Cell. 1996 Jan;7(1):129-42
  • Latest
    J:365055 Liu M, et al., GPNMB and ATP6V1A interact to mediate microglia phagocytosis of multiple types of pathological particles. Cell Rep. 2025 Mar 25;44(3):115343
Contributing Projects:
Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
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Funding Information
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Send questions and comments to User Support. 		last database update
09/30/2025
MGI 6.24 		The Jackson Laboratory