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Aliases for ATP6V1D Gene

Aliases for ATP6V1D Gene

  • ATPase H+ Transporting V1 Subunit D 2 3 5
  • ATPase, H+ Transporting, Lysosomal (Vacuolar Proton Pump) 2 3
  • ATPase, H+ Transporting, Lysosomal 34kDa, V1 Subunit D 2 3
  • V-ATPase 28 KDa Accessory Protein 3 4
  • Vacuolar Proton Pump Subunit D 3 4
  • V-ATPase Subunit D 3 4
  • ATP6M 3 4
  • VATD 3 4
  • H(+)-Transporting Two-Sector ATPase, Subunit M 3
  • ATPase, H+ Transporting Lysosomal, Member M 3
  • Vacuolar Proton Pump Delta Polypeptide 3
  • Vacuolar Proton-ATPase Subunit D 3
  • Vacuolar ATP Synthase Subunit D 3
  • V-Type Proton ATPase Subunit D 3
  • Vacuolar Proton Pump D Subunit 3
  • Vacuolar H-ATPase Subunit D 3
  • V-ATPase D Subunit 3
  • VMA8 3

External Ids for ATP6V1D Gene

Previous HGNC Symbols for ATP6V1D Gene

  • ATP6M

Previous GeneCards Identifiers for ATP6V1D Gene

  • GC14M065309
  • GC14M061598
  • GC14M065792
  • GC14M065794
  • GC14M066874
  • GC14M067804
  • GC14M047974
  • GC14M067761

Summaries for ATP6V1D Gene

Entrez Gene Summary for ATP6V1D Gene

  • 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 sorting, zymogen activation, receptor-mediated endocytosis, and synaptic vesicle proton gradient generation. V-ATPase is composed of a cytosolic V1 domain and a transmembrane V0 domain. The V1 domain consists of three A and three B subunits, two G subunits plus the C, D, E, F, and H subunits. The V1 domain contains the ATP catalytic site. The V0 domain consists of five different subunits: a, c, c', c", and d. Additional isoforms of many of the V1 and V0 subunit proteins are encoded by multiple genes or alternatively spliced transcript variants. This gene encodes the V1 domain D subunit protein. [provided by RefSeq, Jul 2008]

GeneCards Summary for ATP6V1D Gene

ATP6V1D (ATPase H+ Transporting V1 Subunit D) is a Protein Coding gene. Among its related pathways are Ion channel transport and Immune System. GO annotations related to this gene include ATPase activity, coupled to transmembrane movement of substances.

UniProtKB/Swiss-Prot for ATP6V1D Gene

  • Subunit of the peripheral V1 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 (By similarity). May play a role in cilium biogenesis through regulation of the transport and the localization of proteins to the cilium.

Tocris Summary for ATP6V1D 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.

Gene Wiki entry for ATP6V1D Gene

No data available for PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ATP6V1D Gene

Genomics for ATP6V1D Gene

Regulatory Elements for ATP6V1D Gene

Enhancers for ATP6V1D Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH14F067312 0.4 ENCODE 37.2 +48.2 48187 0.2 ESRRA PKNOX1 TEAD3 GATA3 CTBP1 ZNF207 RCOR1 FOS FOSL2 MAFK ATP6V1D EIF2S1 LOC105370541 GC14M067260 GC14M067261
GH14F067356 0.2 ENCODE 25.8 +1.0 1047 5.4 HDGF PKNOX1 ARNT CREB3L1 WRNIP1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 ATP6V1D PLEK2 ENSG00000258561 GPHN EIF2S1 ENSG00000199755
GH14F067343 1.1 ENCODE 25.4 +16.1 16095 1.5 ATP6V1D GPHN ENSG00000199755 EIF2S1
GH14F067267 0.9 Ensembl ENCODE 25.2 +90.7 90745 4.2 CTCF MAX ZNF384 RFX5 ZNF316 PRDM10 ZNF600 MAFK RFX1 ZNF362 ATP6V1D PLEK2 MPP5 EIF2S1 GPHN GC14M067260 GC14M067261 LOC105370541
GH14F067296 0.3 FANTOM5 25.1 +63.5 63475 0.3 RAD21 FOS CREM THAP11 CEBPB SREBF1 NFIL3 CEBPA PRDM1 SOX13 ATP6V1D GC14M067260 GC14M067261 LOC105370541
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around ATP6V1D on UCSC Golden Path with GeneCards custom track

Promoters for ATP6V1D Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000419638 765 3801 HDGF PKNOX1 ARNT CREB3L1 WRNIP1 ARID4B SIN3A FEZF1 DMAP1 ZNF2

Genomic Location for ATP6V1D Gene

Chromosome:
14
Start:
67,294,371 bp from pter
End:
67,360,265 bp from pter
Size:
65,895 bases
Orientation:
Minus strand

Genomic View for ATP6V1D Gene

Genes around ATP6V1D on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ATP6V1D Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ATP6V1D Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ATP6V1D Gene

Proteins for ATP6V1D Gene

  • Protein details for ATP6V1D Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y5K8-VATD_HUMAN
    Recommended name:
    V-type proton ATPase subunit D
    Protein Accession:
    Q9Y5K8
    Secondary Accessions:
    • B2RE33
    • Q9Y688

    Protein attributes for ATP6V1D Gene

    Size:
    247 amino acids
    Molecular mass:
    28263 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). Interacts with SNX10; may play a role in ciliogenesis.

neXtProt entry for ATP6V1D Gene

Post-translational modifications for ATP6V1D Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for ATP6V1D Gene

Domains & Families for ATP6V1D Gene

Gene Families for ATP6V1D Gene

HGNC:
IUPHAR :

Protein Domains for ATP6V1D Gene

Graphical View of Domain Structure for InterPro Entry

Q9Y5K8

UniProtKB/Swiss-Prot:

VATD_HUMAN :
  • Belongs to the V-ATPase D subunit family.
Family:
  • Belongs to the V-ATPase D subunit family.
genes like me logo Genes that share domains with ATP6V1D: view

Function for ATP6V1D Gene

Molecular function for ATP6V1D Gene

UniProtKB/Swiss-Prot Function:
Subunit of the peripheral V1 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 (By similarity). May play a role in cilium biogenesis through regulation of the transport and the localization of proteins to the cilium.

Gene Ontology (GO) - Molecular Function for ATP6V1D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 18752060
GO:0042626 ATPase activity, coupled to transmembrane movement of substances IEA --
genes like me logo Genes that share ontologies with ATP6V1D: view
genes like me logo Genes that share phenotypes with ATP6V1D: view

Animal Models for ATP6V1D Gene

MGI Knock Outs for ATP6V1D:

Animal Model Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for ATP6V1D Gene

Localization for ATP6V1D Gene

Subcellular locations from UniProtKB/Swiss-Prot for ATP6V1D Gene

Membrane; Peripheral membrane protein; Cytoplasmic side. Note=Localizes to centrosome and the base of the cilium.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for ATP6V1D Gene COMPARTMENTS Subcellular localization image for ATP6V1D gene
Compartment Confidence
cytosol 5
extracellular 5
lysosome 5
vacuole 5
nucleus 3
plasma membrane 2

Gene Ontology (GO) - Cellular Components for ATP6V1D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005765 lysosomal membrane IDA 17897319
GO:0005813 colocalizes_with centrosome IDA 21844891
GO:0005829 cytosol TAS --
GO:0005929 colocalizes_with cilium IDA 21844891
GO:0016020 membrane IEA,IDA 18752060
genes like me logo Genes that share ontologies with ATP6V1D: view

Pathways & Interactions for ATP6V1D Gene

genes like me logo Genes that share pathways with ATP6V1D: view

Gene Ontology (GO) - Biological Process for ATP6V1D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport IEA --
GO:0006811 ion transport IEA --
GO:0008286 insulin receptor signaling pathway TAS --
GO:0015992 proton transport IEA --
GO:0016241 regulation of macroautophagy NAS 22982048
genes like me logo Genes that share ontologies with ATP6V1D: view

No data available for SIGNOR curated interactions for ATP6V1D Gene

Drugs & Compounds for ATP6V1D Gene

(5) Drugs for ATP6V1D Gene - From: HMDB and Tocris

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Water Approved Pharma 0
Adenosine triphosphate Approved Nutra 0
Disulfiram Approved Pharma Reversibly stimulates SERCA Ca2+-ATPase; displays a range of other activities 35
Bafilomycin A1 Experimental Pharma V-ATPase inhibitor,selective and reversible, H+-ATPase (vacuolar) inhibitor 0
Concanamycin A Pharma V-type (vacuolar) H+-ATPase inhibitor, H+-ATPase (vacuolar) inhibitor 0

(2) Additional Compounds for ATP6V1D 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

(3) Tocris Compounds for ATP6V1D Gene

Compound Action Cas Number
Bafilomycin A1 H+-ATPase (vacuolar) inhibitor 88899-55-2
Concanamycin A H+-ATPase (vacuolar) inhibitor 80890-47-7
Disulfiram Reversibly stimulates SERCA Ca2+-ATPase; displays a range of other activities 97-77-8
genes like me logo Genes that share compounds with ATP6V1D: view

Transcripts for ATP6V1D Gene

Unigene Clusters for ATP6V1D Gene

ATPase, H+ transporting, lysosomal 34kDa, V1 subunit D:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for ATP6V1D Gene

ExUns: 1 ^ 2a · 2b · 2c · 2d · 2e · 2f ^ 3 ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7a · 7b ^ 8a · 8b ^ 9 ^ 10 ^ 11a · 11b ^ 12 ^ 13 ^ 14a · 14b
SP1: - - - - -
SP2: - -
SP3: - - - -
SP4: - - -
SP5: -
SP6: -
SP7: - -
SP8: -
SP9:

Relevant External Links for ATP6V1D Gene

GeneLoc Exon Structure for
ATP6V1D
ECgene alternative splicing isoforms for
ATP6V1D

Expression for ATP6V1D Gene

mRNA expression in normal human tissues for ATP6V1D Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for ATP6V1D Gene

This gene is overexpressed in Brain (23.7) and Frontal cortex (7.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for ATP6V1D Gene



Protein tissue co-expression partners for ATP6V1D Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of ATP6V1D Gene:

ATP6V1D

SOURCE GeneReport for Unigene cluster for ATP6V1D Gene:

Hs.272630
genes like me logo Genes that share expression patterns with ATP6V1D: view

Primer Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for ATP6V1D Gene

Orthologs for ATP6V1D Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for ATP6V1D Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia ATP6V1D 34 35
  • 100 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia ATP6V1D 35
  • 96 (a)
OneToOne
dog
(Canis familiaris)
Mammalia ATP6V1D 34 35
  • 94.47 (n)
cow
(Bos Taurus)
Mammalia ATP6V1D 34 35
  • 94.33 (n)
mouse
(Mus musculus)
Mammalia Atp6v1d 34 16 35
  • 91.09 (n)
rat
(Rattus norvegicus)
Mammalia Atp6v1d 34
  • 90.15 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 35
  • 88 (a)
OneToMany
-- 35
  • 74 (a)
OneToMany
-- 35
  • 69 (a)
OneToMany
chicken
(Gallus gallus)
Aves ATP6V1D 34 35
  • 80.7 (n)
lizard
(Anolis carolinensis)
Reptilia ATP6V1D 35
  • 83 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia atp6v1d 34
  • 76.38 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.22727 34
zebrafish
(Danio rerio)
Actinopterygii atp6v1d 34 35
  • 74.76 (n)
zgc55524 34
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.731 34
fruit fly
(Drosophila melanogaster)
Insecta Vha36 36
  • 72 (a)
EG:BACR25B3.4 36
  • 69 (a)
Vha36-3 35
  • 68 (a)
OneToMany
Vha36-1 34 35
  • 64.49 (n)
CG13167 36
  • 37 (a)
Vha36-2 35
  • 24 (a)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010298 34
  • 67.55 (n)
worm
(Caenorhabditis elegans)
Secernentea F55H2.2 36
  • 67 (a)
vha-14 34 35
  • 63.33 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0A01991g 34
  • 59.31 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes VMA8 34 35 37
  • 58.57 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AAR130C 34
  • 54.85 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT3G58730 34
  • 59.68 (n)
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.3362 34
rice
(Oryza sativa)
Liliopsida Os04g0643100 34
  • 53.25 (n)
barley
(Hordeum vulgare)
Liliopsida Hv.8141 34
sea squirt
(Ciona savignyi)
Ascidiacea CSA.7229 35
  • 69 (a)
OneToOne
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes vma8 34
  • 56.21 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU08035 34
  • 55.28 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.7657 34
Species where no ortholog for ATP6V1D was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • 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)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for ATP6V1D Gene

ENSEMBL:
Gene Tree for ATP6V1D (if available)
TreeFam:
Gene Tree for ATP6V1D (if available)

Paralogs for ATP6V1D Gene

genes like me logo Genes that share paralogs with ATP6V1D: view

No data available for Paralogs for ATP6V1D Gene

Variants for ATP6V1D Gene

Sequence variations from dbSNP and Humsavar for ATP6V1D Gene

SNP ID Clin Chr 14 pos Sequence Context AA Info Type
rs10129185 -- 67,350,197(+) TCCTA(A/C)GGGAA intron-variant
rs10135163 -- 67,351,695(+) TTCTT(C/T)TTTTT intron-variant
rs10135498 -- 67,352,024(+) taaca(C/T)ctgta intron-variant
rs10135565 -- 67,344,915(+) aAACA(A/G)GAGTG intron-variant
rs10135656 -- 67,344,904(+) acaaa(A/C)aaaaa intron-variant

Structural Variations from Database of Genomic Variants (DGV) for ATP6V1D Gene

Variant ID Type Subtype PubMed ID
esv2751285 CNV gain 17911159
nsv456331 CNV gain 19166990
nsv470651 CNV gain 18288195
nsv479730 CNV novel sequence insertion 20440878
nsv564961 CNV gain 21841781
nsv832821 CNV gain 17160897

Variation tolerance for ATP6V1D Gene

Residual Variation Intolerance Score: 39.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.32; 7.05% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for ATP6V1D Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
ATP6V1D

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ATP6V1D Gene

Disorders for ATP6V1D Gene

Relevant External Links for ATP6V1D

Genetic Association Database (GAD)
ATP6V1D
Human Genome Epidemiology (HuGE) Navigator
ATP6V1D
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
ATP6V1D

No disorders were found for ATP6V1D Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for ATP6V1D Gene

Publications for ATP6V1D Gene

  1. A SNX10/V-ATPase pathway regulates ciliogenesis in vitro and in vivo. (PMID: 21844891) Chen Y. … Pei D. (Cell Res. 2012) 3 4 64
  2. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey S.D. … Anand S. (Diabetes Care 2010) 3 46 64
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  5. Yeast two-hybrid screening identifies binding partners of human Tom34 that have ATPase activity and form a complex with Tom34 in the cytosol. (PMID: 11913976) Yang C.-S. … Weiner H. (Arch. Biochem. Biophys. 2002) 3 22 64

Products for ATP6V1D Gene

Sources for ATP6V1D Gene

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