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ATP6V0D2 Gene(Protein Coding)

ATPase H+ Transporting V0 Subunit D2

GCID:
GC08P085987
GIFtS:
46
Genes Participants
UDN Logo

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 3
  • Vacuolar Proton Pump Subunit D 2 3 4
  • V-ATPase Subunit D 2 3 4
  • ATPase, H+ Transporting, Lysosomal 38kDa, V0 Subunit D Isoform 2 2
  • ATPase, H+ Transporting, Lysosomal 38kD, V0 Subunit D Isoform 2 2
  • V-Type Proton ATPase Subunit D 2 3
  • ATP6D2 3
  • VMA6 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 Craniometaphyseal Dysplasia, Autosomal Dominant and Neurotic Disorder. Among its related pathways are Innate Immune System and Rheumatoid arthritis. Gene Ontology (GO) annotations related to this gene include hydrogen ion transmembrane transporter activity. An important paralog of this gene is ATP6V0D1.

UniProtKB/Swiss-Prot 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.

Additional gene information for ATP6V0D2 Gene

No data available for Entrez Gene Summary , CIViC summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ATP6V0D2 Gene

Genomics for ATP6V0D2 Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for ATP6V0D2 Gene

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
GH08I086098 Promoter/Enhancer 0.9 EPDnew Ensembl 550.1 +111.5 111525 0.5 FOSL1 ZNF10 REST ATP6V0D2 WWP1 LOC105375624 PSKH2 ENSG00000253675
GH08I085989 Enhancer 0.5 dbSUPER 0.8 +3.8 3767 2.5 GATA3 POLR2A ATF7 ATF2 FOXA1 ATP6V0D2 RPL36AP31
GH08I085999 Enhancer 0.9 ENCODE dbSUPER 0.4 +14.7 14685 4.9 MXI1 PKNOX1 JUN MAX CEBPG RAD21 RFX5 CTBP1 GATA3 RCOR1 PSKH2 CA2 CA3-AS1 CA1 ATP6V0D2 RPL36AP31
GH08I085973 Enhancer 0.9 ENCODE dbSUPER 0.4 -13.8 -13766 0.1 CTCF TEAD4 NEUROD1 RAD21 CHAMP1 ARID2 HNF4G SMC3 ZNF444 MIXL1 CA2 CA3-AS1 ATP6V0D2 LOC105375622
GH08I085958 Enhancer 1.2 ENCODE dbSUPER 0.3 -27.8 -27799 2.4 HDGF PKNOX1 ATF1 ARNT NCOA2 ZNF280A TCF12 ZNF766 GATA2 E2F8 CA2 CA3-AS1 ATP6V0D2 LOC105375622
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around ATP6V0D2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the ATP6V0D2 gene promoter:

Genomic Locations for ATP6V0D2 Gene

Genomic Locations for ATP6V0D2 Gene
chr8:85,987,323-86,154,228
(GRCh38/hg38)
Size:
166,906 bases
Orientation:
Plus strand
chr8:86,999,552-87,166,457
(GRCh37/hg19)

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 Structure • Gene Density

RefSeq DNA sequence for ATP6V0D2 Gene

Proteins for ATP6V0D2 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • 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

Protein Expression for ATP6V0D2 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for ATP6V0D2 Gene

No Post-translational modifications

Other Protein References for ATP6V0D2 Gene

ENSEMBL proteins:
REFSEQ proteins:

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:
ProtoNet:

Suggested Antigen Peptide Sequences for ATP6V0D2 Gene

GenScript: Design optimal peptide antigens:

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

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

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:0008553 hydrogen-exporting ATPase activity, phosphorylative mechanism IBA --
GO:0015078 hydrogen ion transmembrane transporter activity IEA --
GO:0046961 proton-transporting ATPase activity, rotational mechanism IBA --
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:

CRISPR Products

Inhibitory RNA Products

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 5
lysosome 4
endosome 4
cytosol 3
nucleus 2
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for ATP6V0D2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005765 lysosomal membrane IBA --
GO:0005768 endosome IEA --
GO:0005769 early endosome IEA,IBA --
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:0006810 transport IEA --
GO:0006811 ion transport IEA --
GO:0007034 vacuolar transport IBA --
GO:0007035 vacuolar acidification IBA --
GO:0008286 insulin receptor signaling pathway TAS --
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

Products:

  1. Drug

(5) Drugs for ATP6V0D2 Gene - From: HMDB and Tocris

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

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

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
ADP
  • Adenosindiphosphorsaeure
  • Adenosine 5'-pyrophosphate
  • Adenosine diphosphate
  • Adenosine pyrophosphate
  • Adenosine-5'-diphosphate
 Full agonist, Agonist 58-64-0
Phosphate
  • NFB Orthophosphate
  • O-Phosphoric acid
  • Ortho-phosphate
  • Orthophosphate (PO43-)
  • Orthophosphate(3-)
 14265-44-2

(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

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for ATP6V0D2 Gene

(1) REFSEQ mRNAs :
(3) Additional mRNA sequences :
(27) Selected AceView cDNA sequences:
(3) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for ATP6V0D2 Gene

ATPase, H+ transporting, lysosomal 38kDa, V0 subunit d2:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

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

No ASD Table

Relevant External Links for ATP6V0D2 Gene

GeneLoc Exon Structure for
ATP6V0D2
ECgene alternative splicing isoforms for
ATP6V0D2

Expression for ATP6V0D2 Gene

Products:

  1. Primer

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

mRNA expression in normal human tissues for ATP6V0D2 Gene
mRNA expression by BioGPS for ATP6V0D2 GenemRNA expression by GTEx 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, PaxDb, MaxQB, and MOPED for ATP6V0D2 Gene



NURSA nuclear receptor signaling pathways regulating expression of ATP6V0D2 Gene:

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(4.4)
  • Intestine(4.1)
  • Bone(2.1)
genes like me logo Genes that share expression patterns with ATP6V0D2: view

Primer Products

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 33 34
  • 99.81 (n)
dog
(Canis familiaris)
 Mammalia ATP6V0D2 33 34
  • 89.62 (n)
mouse
(Mus musculus)
 Mammalia Atp6v0d2 33 16 34
  • 87.62 (n)
rat
(Rattus norvegicus)
 Mammalia Atp6v0d2 33
  • 86.76 (n)
cow
(Bos Taurus)
 Mammalia ATP6V0D2 33 34
  • 85.81 (n)
platypus
(Ornithorhynchus anatinus)
 Mammalia ATP6V0D2 34
  • 85 (a)
 OneToOne
oppossum
(Monodelphis domestica)
 Mammalia ATP6V0D2 34
  • 84 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves ATP6V0D2 33 34
  • 71.77 (n)
lizard
(Anolis carolinensis)
 Reptilia ATP6V0D2 34
  • 72 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia atp6v0d2 33
  • 69.53 (n)
fruit fly
(Drosophila melanogaster)
 Insecta VhaAC39-1 34
  • 62 (a)
 ManyToMany
VhaAC39-2 34
  • 41 (a)
 ManyToMany
worm
(Caenorhabditis elegans)
 Secernentea vha-16 34
  • 61 (a)
 OneToMany
baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes VMA6 34
  • 43 (a)
 OneToMany
corn
(Zea mays)
 Liliopsida Zm.5094 33
sea squirt
(Ciona savignyi)
 Ascidiacea CSA.9989 34
  • 60 (a)
 OneToMany
Species where no ortholog for ATP6V0D2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 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)

Paralogs for ATP6V0D2 Gene

Paralogs for ATP6V0D2 Gene

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

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

Variants for ATP6V0D2 Gene

Sequence variations from dbSNP and Humsavar for ATP6V0D2 Gene

SNP ID Clin Chr 08 pos Variation AA Info Type
rs1000037737 -- 86,148,347(+) C/A intron_variant
rs1000039794 -- 86,141,944(+) C/T intron_variant
rs1000061633 -- 86,106,834(+) T/G intron_variant
rs1000069317 -- 86,128,243(+) G/A intron_variant
rs1000126912 -- 86,099,986(+) C/T intron_variant

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

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

Disorders for ATP6V0D2 Gene

MalaCards: The human disease database

(2) MalaCards diseases for ATP6V0D2 Gene - From: HGMD and DISEASES

Disorder Aliases PubMed IDs
craniometaphyseal dysplasia, autosomal dominant
  • cmdd
neurotic disorder
  • depressive neurosis
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for ATP6V0D2

ATLAS of Genetics and Cytogenetics in Oncology and Haematology
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 58
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  3. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  4. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin EL … Gygi SP (Cell 2015) 3 58
  5. Expression, purification and characterization of human vacuolar-type H(+)-ATPase subunit d1 and d2 in Escherichia coli. (PMID: 24631925) Lim H … Kim YJ (Protein expression and purification 2014) 3 58

Products for ATP6V0D2 Gene

Sources for ATP6V0D2 Gene

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