Gene Gene information from NCBI Gene database.
Entrez ID 523
Gene name ATPase H+ transporting V1 subunit A
Gene symbol ATP6V1A
Synonyms (NCBI Gene)
ARCL2DATP6A1ATP6V1A1DEE93HO68IECEE3VA68VPP2Vma1
Chromosome 3
Chromosome location 3q13.31
Summary This gene encodes a component of vacuolar ATPase (V-ATPase), a multisubunit enzyme that mediates acidification of eukaryotic intracellular organelles. V-ATPase dependent organelle acidification is necessary for such intracellular processes as protein sort
SNPs SNP information provided by dbSNP.
9
SNP ID Visualize variation Clinical significance Consequence
rs755278709 G>A,T Likely-pathogenic Splice donor variant
rs869312870 A>G Likely-pathogenic Missense variant, coding sequence variant
rs1060505036 C>T Pathogenic Missense variant, coding sequence variant
rs1060505037 G>A Pathogenic Missense variant, coding sequence variant
rs1553709380 C>G Pathogenic Missense variant, coding sequence variant
miRNA miRNA information provided by mirtarbase database.
974
miRTarBase ID miRNA Experiments Reference
MIRT023734 hsa-miR-1-3p Proteomics 18668040
MIRT029234 hsa-miR-26b-5p Microarray 19088304
MIRT044054 hsa-miR-361-5p CLASH 23622248
MIRT714795 hsa-miR-4704-5p HITS-CLIP 19536157
MIRT714794 hsa-miR-6873-5p HITS-CLIP 19536157
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
55
GO ID Ontology Definition Evidence Reference
GO:0000139 Component Golgi membrane NAS 32001091
GO:0000166 Function Nucleotide binding IEA
GO:0000221 Component Vacuolar proton-transporting V-type ATPase, V1 domain IDA 33065002
GO:0005515 Function Protein binding IPI 23035048, 33208464
GO:0005524 Function ATP binding IEA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
607027 851 ENSG00000114573
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
P38606
Protein name V-type proton ATPase catalytic subunit A (V-ATPase subunit A) (EC 7.1.2.2) (V-ATPase 69 kDa subunit) (Vacuolar ATPase isoform VA68) (Vacuolar proton pump subunit alpha)
Protein function Catalytic subunit of the V1 complex of vacuolar(H+)-ATPase (V-ATPase), a multisubunit enzyme composed of a peripheral complex (V1) that hydrolyzes ATP and a membrane integral complex (V0) that translocates protons (PubMed:8463241). V-ATPase is r
PDB 6WLZ , 6WM2 , 6WM3 , 6WM4 , 7U4T , 7UNF
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF02874 ATP-synt_ab_N 21 83 ATP synthase alpha/beta family, beta-barrel domain Domain
PF16886 ATP-synt_ab_Xtn 99 221 ATPsynthase alpha/beta subunit N-term extension Family
PF00006 ATP-synt_ab 230 455 ATP synthase alpha/beta family, nucleotide-binding domain Domain
Tissue specificity TISSUE SPECIFICITY: High expression in the skin. {ECO:0000269|PubMed:28065471}.
Sequence
Sequence length 617
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  Oxidative phosphorylation
Metabolic pathways
Phagosome
mTOR signaling pathway
Synaptic vesicle cycle
Collecting duct acid secretion
Vibrio cholerae infection
Epithelial cell signaling in Helicobacter pylori infection
Human papillomavirus infection
Rheumatoid arthritis
  ROS and RNS production in phagocytes
Insulin receptor recycling
Transferrin endocytosis and recycling
Amino acids regulate mTORC1
Ion channel transport
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
20
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Autosomal recessive cutis laxa type 2D Likely pathogenic; Pathogenic rs2549719217, rs1060505037 RCV003389392
RCV000477689
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Cerebral visual impairment and intellectual disability Likely pathogenic; Pathogenic rs869312870 RCV000210381
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Developmental and epileptic encephalopathy 93 Likely pathogenic; Pathogenic rs1709263798, rs2108033397, rs2108034196, rs2549723939, rs2549723925, rs2549725080, rs2549719217, rs1553709855, rs1553710664, rs1553709380, rs1553710694, rs1559759089, rs1709072898 RCV001330826
RCV002255188
RCV003336498
RCV002305680
RCV002305681
View all (8 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Encephalopathy Likely pathogenic rs2108033397 RCV001526547
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
ATP6V1A-related disorder Uncertain significance; Benign; Likely benign; Conflicting classifications of pathogenicity ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
AUTOSOMAL RECESSIVE CUTIS LAXA TYPE 2, CLASSIC TYPE GWAS catalog, Orphanet
GWAS catalog, Orphanet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
CONGENITAL ACCESSORY SKIN TAG Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
CUTIS LAXA Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Alzheimer Disease Alzheimer disease Pubtator 33476559 Associate
★☆☆☆☆
Found in Text Mining only
Alzheimer Disease Alzheimer disease Pubtator 33981384 Inhibit
★☆☆☆☆
Found in Text Mining only
Atrial Septal Defects Atrial Septal Defect HPO_DG
★☆☆☆☆
Found in Text Mining only
Atrophy Atrophy Pubtator 35675510 Associate
★☆☆☆☆
Found in Text Mining only
Attention deficit hyperactivity disorder Attention Deficit Hyperactivity Disorder HPO_DG
★☆☆☆☆
Found in Text Mining only
Autistic Disorder Autism HPO_DG
★☆☆☆☆
Found in Text Mining only
Autosomal recessive cutis laxa type 2, classic type Cutis Laxa Orphanet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Bilateral Cryptorchidism Cryptorchidism HPO_DG
★☆☆☆☆
Found in Text Mining only
Blepharophimosis Blepharophimosis HPO_DG
★☆☆☆☆
Found in Text Mining only
Blepharoptosis Ptosis HPO_DG
★☆☆☆☆
Found in Text Mining only