Aliases for ATP6V0D2 Gene

Aliases for ATP6V0D2 Gene

  • ATPase H+ Transporting V0 Subunit D2 2 3 5
  • ATPase, H+ Transporting, Lysosomal 38kDa, V0 Subunit D2 2 2 3
  • V-Type Proton ATPase Subunit D 2 3 4
  • Vacuolar Proton Pump Subunit D 2 3 4
  • V-ATPase Subunit D 2 3 4
  • VMA6 2 3
  • ATPase, H+ Transporting, Lysosomal 38kDa, V0 Subunit D Isoform 2 2
  • ATPase, H+ Transporting, Lysosomal 38kD, V0 Subunit D Isoform 2 2
  • ATP6V0D2 5
  • FLJ38708 2
  • ATP6D2 3

External Ids for ATP6V0D2 Gene

Previous HGNC Symbols for ATP6V0D2 Gene

  • ATP6D2

Previous GeneCards Identifiers for ATP6V0D2 Gene

  • GC00U991214
  • GC08P086843
  • GC08P087067
  • GC08P087180
  • GC08P082320
  • GC08P086999

Summaries for ATP6V0D2 Gene

GeneCards Summary for ATP6V0D2 Gene

ATP6V0D2 (ATPase H+ Transporting V0 Subunit D2) is a Protein Coding gene. Diseases associated with ATP6V0D2 include Autosomal Recessive Distal Renal Tubular Acidosis and Distal Renal Tubular Acidosis. Among its related pathways are Insulin receptor recycling and Lysosome. Gene Ontology (GO) annotations related to this gene include proton transmembrane transporter activity. An important paralog of this gene is ATP6V0D1.

UniProtKB/Swiss-Prot Summary for ATP6V0D2 Gene

  • Subunit of the integral membrane V0 complex of vacuolar ATPase. Vacuolar ATPase is responsible for acidifying a variety of intracellular compartments in eukaryotic cells, thus providing most of the energy required for transport processes in the vacuolar system. May play a role in coupling of proton transport and ATP hydrolysis (By similarity).

Tocris Summary for ATP6V0D2 Gene

  • H+-ATPase (also known as vacuolar ATPase, V-ATPase) is a enzyme transporter that functions to acidify intracellular compartments in eukaryotic cells. It is ubiquitously expressed and is present in endomembrane organelles such as vacuoles, lysosomes and endosomes.

No data available for Entrez Gene Summary , CIViC Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for ATP6V0D2 Gene

Genomics for ATP6V0D2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for ATP6V0D2 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH08J086098 Promoter 0.8 EPDnew Ensembl 250.1 +112.3 112278 2 ZNF10 REST ATP6V0D2 WWP1 WWP1-AS1 ENSG00000253699 PSKH2 RF00017-6597 ENSG00000253675 SLC7A13
GH08J085987 Enhancer 0.5 Ensembl 250.7 -0.2 -222 0.6 CTCF ZBTB7B RAD21 SMC3 ZNF143 POLR2A TRIM22 ATP6V0D2 LOC107986954 LOC101929627
GH08J085986 Enhancer 0.3 Ensembl 250.7 -1.0 -991 0.5 FOS ATP6V0D2 LOC107986954 LOC101929627
GH08J085973 Enhancer 1 Ensembl ENCODE dbSUPER 0.4 -12.4 -12422 3.8 ZNF654 REST CEBPB CTCF ZNF217 EP300 RAD21 SMC3 JUND PKNOX1 CA2 CA3-AS1 CA1 piR-42694-162 LOC107986954 ATP6V0D2 LOC101929627
GH08J085958 Enhancer 1.3 Ensembl ENCODE dbSUPER 0.3 -27.6 -27564 2.9 MYC NCOR1 IKZF1 ZNF592 NFIC NONO REST HES1 MBD2 ZNF513 CA3-AS1 CA2 E2F5 piR-42694-162 HSALNG0066724 ATP6V0D2 LOC101929627
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around ATP6V0D2 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for ATP6V0D2

Top Transcription factor binding sites by QIAGEN in the ATP6V0D2 gene promoter:
  • C/EBPalpha
  • CP2
  • FOXD1
  • FOXD3
  • NF-E2
  • NF-E2 p45
  • RP58
  • Sox5
  • Sox9
  • SRY

Genomic Locations for ATP6V0D2 Gene

Latest Assembly
chr8:85,987,323-86,154,225
(GRCh38/hg38)
Size:
166,903 bases
Orientation:
Plus strand

Previous Assembly
chr8:87,111,139-87,166,454
(GRCh37/hg19 by Entrez Gene)
Size:
55,316 bases
Orientation:
Plus strand

chr8:86,999,552-87,166,457
(GRCh37/hg19 by Ensembl)
Size:
166,906 bases
Orientation:
Plus strand

Genomic View for ATP6V0D2 Gene

Genes around ATP6V0D2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ATP6V0D2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ATP6V0D2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ATP6V0D2 Gene

Proteins for ATP6V0D2 Gene

  • Protein details for ATP6V0D2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8N8Y2-VA0D2_HUMAN
    Recommended name:
    V-type proton ATPase subunit d 2
    Protein Accession:
    Q8N8Y2

    Protein attributes for ATP6V0D2 Gene

    Size:
    350 amino acids
    Molecular mass:
    40426 Da
    Quaternary structure:
    • V-ATPase is a heteromultimeric enzyme composed of a peripheral catalytic V1 complex (components A to H) attached to an integral membrane V0 proton pore complex (components: a, c, c', c'' and d).

neXtProt entry for ATP6V0D2 Gene

Post-translational modifications for ATP6V0D2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for ATP6V0D2 Gene

Antibodies for research

No data available for DME Specific Peptides for ATP6V0D2 Gene

Domains & Families for ATP6V0D2 Gene

Gene Families for ATP6V0D2 Gene

HGNC:
IUPHAR :
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for ATP6V0D2 Gene

InterPro:
Blocks:
  • H+-transporting two-sector ATPase, C (AC39) subunit

Suggested Antigen Peptide Sequences for ATP6V0D2 Gene

GenScript: Design optimal peptide antigens:
  • Vacuolar proton pump subunit d 2 (VA0D2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8N8Y2

UniProtKB/Swiss-Prot:

VA0D2_HUMAN :
  • Belongs to the V-ATPase V0D/AC39 subunit family.
Family:
  • Belongs to the V-ATPase V0D/AC39 subunit family.
genes like me logo Genes that share domains with ATP6V0D2: view

Function for ATP6V0D2 Gene

Molecular function for ATP6V0D2 Gene

UniProtKB/Swiss-Prot Function:
Subunit of the integral membrane V0 complex of vacuolar ATPase. Vacuolar ATPase is responsible for acidifying a variety of intracellular compartments in eukaryotic cells, thus providing most of the energy required for transport processes in the vacuolar system. May play a role in coupling of proton transport and ATP hydrolysis (By similarity).

Phenotypes From GWAS Catalog for ATP6V0D2 Gene

Gene Ontology (GO) - Molecular Function for ATP6V0D2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 18752060
GO:0015078 proton transmembrane transporter activity IEA --
GO:0046961 proton-transporting ATPase activity, rotational mechanism IBA 21873635
genes like me logo Genes that share ontologies with ATP6V0D2: view
genes like me logo Genes that share phenotypes with ATP6V0D2: view

Animal Models for ATP6V0D2 Gene

MGI Knock Outs for ATP6V0D2:

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ATP6V0D2

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for ATP6V0D2 Gene

Localization for ATP6V0D2 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for ATP6V0D2 gene
Compartment Confidence
plasma membrane 5
extracellular 4
endosome 4
lysosome 4
nucleus 3
cytosol 3
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for ATP6V0D2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005765 lysosomal membrane IBA 21873635
GO:0005768 endosome IEA --
GO:0005769 early endosome IBA 21873635
GO:0010008 endosome membrane TAS --
GO:0016020 membrane IDA 18752060
genes like me logo Genes that share ontologies with ATP6V0D2: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for ATP6V0D2 Gene

Pathways & Interactions for ATP6V0D2 Gene

genes like me logo Genes that share pathways with ATP6V0D2: view

Gene Ontology (GO) - Biological Process for ATP6V0D2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006811 ion transport IEA --
GO:0007034 vacuolar transport IBA 21873635
GO:0007035 vacuolar acidification IBA 21873635
GO:0008286 insulin receptor signaling pathway TAS --
GO:0016241 regulation of macroautophagy NAS 22982048
genes like me logo Genes that share ontologies with ATP6V0D2: view

No data available for SIGNOR curated interactions for ATP6V0D2 Gene

Drugs & Compounds for ATP6V0D2 Gene

(6) Drugs for ATP6V0D2 Gene - From: DrugBank, HMDB, and Tocris

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
tiludronate Approved, Investigational, Vet_approved Pharma Target, inhibitor 2
Water Approved Pharma 0
Phosphate Experimental Pharma 0
Bafilomycin A1 Experimental Pharma V-ATPase inhibitor,selective and reversible, H+-ATPase (vacuolar) inhibitor 0
Concanamycin A Experimental Pharma V-type (vacuolar) H+-ATPase inhibitor, H+-ATPase (vacuolar) inhibitor 0

(1) Additional Compounds for ATP6V0D2 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
ADP
  • 5'-Adenylphosphoric acid
  • Adenosine 5'-diphosphate
  • ADENOSINE-5'-diphosphATE
  • H3ADP
  • 5'-Adenylphosphate
58-64-0

(2) Tocris Compounds for ATP6V0D2 Gene

Compound Action Cas Number
Bafilomycin A1 H+-ATPase (vacuolar) inhibitor 88899-55-2
Concanamycin A H+-ATPase (vacuolar) inhibitor 80890-47-7
genes like me logo Genes that share compounds with ATP6V0D2: view

Transcripts for ATP6V0D2 Gene

mRNA/cDNA for ATP6V0D2 Gene

1 REFSEQ mRNAs :
3 NCBI additional mRNA sequence :
3 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ATP6V0D2

Alternative Splicing Database (ASD) splice patterns (SP) for ATP6V0D2 Gene

No ASD Table

Relevant External Links for ATP6V0D2 Gene

GeneLoc Exon Structure for
ATP6V0D2

Expression for ATP6V0D2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for ATP6V0D2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for ATP6V0D2 Gene

This gene is overexpressed in Kidney - Cortex (x44.7).

Protein differential expression in normal tissues from HIPED for ATP6V0D2 Gene

This gene is overexpressed in Frontal cortex (24.6) and Bone (21.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for ATP6V0D2 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for ATP6V0D2

SOURCE GeneReport for Unigene cluster for ATP6V0D2 Gene:

Hs.436360

mRNA Expression by UniProt/SwissProt for ATP6V0D2 Gene:

Q8N8Y2-VA0D2_HUMAN
Tissue specificity: Kidney, osteoclast and lung.

Evidence on tissue expression from TISSUES for ATP6V0D2 Gene

  • Kidney(4.5)
  • Intestine(4.3)
  • Bone(2.3)
genes like me logo Genes that share expression patterns with ATP6V0D2: view

Primer products for research

No data available for Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for ATP6V0D2 Gene

Orthologs for ATP6V0D2 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for ATP6V0D2 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia ATP6V0D2 29 30
  • 99.81 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia ATP6V0D2 29 30
  • 89.62 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Atp6v0d2 29 16 30
  • 87.62 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Atp6v0d2 29
  • 86.76 (n)
Cow
(Bos Taurus)
Mammalia ATP6V0D2 29 30
  • 85.81 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia ATP6V0D2 30
  • 85 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia ATP6V0D2 30
  • 84 (a)
OneToOne
Chicken
(Gallus gallus)
Aves ATP6V0D2 29 30
  • 71.77 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia ATP6V0D2 30
  • 72 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia atp6v0d2 29
  • 69.53 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta VhaAC39-1 30
  • 62 (a)
ManyToMany
VhaAC39-2 30
  • 41 (a)
ManyToMany
Worm
(Caenorhabditis elegans)
Secernentea vha-16 30
  • 61 (a)
OneToMany
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes VMA6 30
  • 43 (a)
OneToMany
Corn
(Zea mays)
Liliopsida Zm.5094 29
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.9989 30
  • 60 (a)
OneToMany
Species where no ortholog for ATP6V0D2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Zebrafish (Danio rerio)

Evolution for ATP6V0D2 Gene

ENSEMBL:
Gene Tree for ATP6V0D2 (if available)
TreeFam:
Gene Tree for ATP6V0D2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for ATP6V0D2: view image
Alliance of Genome Resources:
Additional Orthologs for ATP6V0D2

Paralogs for ATP6V0D2 Gene

Paralogs for ATP6V0D2 Gene

(1) SIMAP similar genes for ATP6V0D2 Gene using alignment to 3 proteins:

  • VA0D2_HUMAN
  • E5RHJ7_HUMAN
  • E5RIR3_HUMAN
genes like me logo Genes that share paralogs with ATP6V0D2: view

Variants for ATP6V0D2 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for ATP6V0D2 Gene

SNP ID Clinical significance and condition Chr 08 pos Variation AA Info Type
rs142355302 Likely Benign: not provided 86,152,842(+) C/A
NM_152565.1(ATP6V0D2):c.918C>A (p.Asn306Lys)
MISSENSE
rs150698519 Benign: not provided 86,151,541(+) G/T
NM_152565.1(ATP6V0D2):c.891+1G>T
SPLICE_DONOR
rs745714325 Likely Benign: not provided 86,151,513(+) A/C
NM_152565.1(ATP6V0D2):c.864A>C (p.Thr288=)
SYNONYMOUS
rs10094744 -- p.Gly272Arg
rs4263741 -- p.Glu295Lys

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for ATP6V0D2 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for ATP6V0D2 Gene

Variant ID Type Subtype PubMed ID
dgv7262n100 CNV gain 25217958
dgv7263n100 CNV gain 25217958
esv2508953 CNV deletion 19546169
esv2585991 CNV deletion 19546169
esv2737262 CNV deletion 23290073
esv2761443 CNV gain 21179565
esv3543786 CNV deletion 23714750
esv3572885 CNV loss 25503493
esv3891432 CNV gain 25118596
nsv1028959 CNV gain 25217958
nsv1124357 CNV deletion 24896259
nsv1128170 CNV deletion 24896259
nsv428204 CNV gain 18775914
nsv611673 CNV loss 21841781
nsv611674 CNV gain 21841781

Variation tolerance for ATP6V0D2 Gene

Residual Variation Intolerance Score: 80.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.93; 59.55% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ATP6V0D2 Gene

Human Gene Mutation Database (HGMD)
ATP6V0D2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
ATP6V0D2
Leiden Open Variation Database (LOVD)
ATP6V0D2

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ATP6V0D2 Gene

Disorders for ATP6V0D2 Gene

MalaCards: The human disease database

(3) MalaCards diseases for ATP6V0D2 Gene - From: COP and GCD

- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for ATP6V0D2

genes like me logo Genes that share disorders with ATP6V0D2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for ATP6V0D2 Gene

Publications for ATP6V0D2 Gene

  1. Molecular cloning and characterization of novel tissue-specific isoforms of the human vacuolar H(+)-ATPase C, G and d subunits, and their evaluation in autosomal recessive distal renal tubular acidosis. (PMID: 12384298) Smith AN … Karet FE (Gene 2002) 2 3 4
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  3. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3
  4. Lactate inhibits ATP6V0d2 expression in tumor-associated macrophages to promote HIF-2α-mediated tumor progression. (PMID: 30431439) Liu N … Yang XP (The Journal of clinical investigation 2019) 3
  5. Vγ9Vδ2 T cells inhibit immature dendritic cell transdifferentiation into osteoclasts through downregulation of RANK, c‑Fos and ATP6V0D2. (PMID: 30066839) Zhu X … Chen J (International journal of molecular medicine 2018) 3

Products for ATP6V0D2 Gene

Sources for ATP6V0D2 Gene