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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 Rheumatoid arthritis and Insulin receptor recycling. Gene Ontology (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

Additional gene information for ATP6V1D Gene

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

Genomics for ATP6V1D Gene

GeneHancer (GH) Regulatory Elements for ATP6V1D Gene

Promoters and enhancers for ATP6V1D 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
GH14J067356 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 675.8 +1.0 1046 5.4 HDGF PKNOX1 CLOCK ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 ZBTB7B ATP6V1D EIF2S1 ZFYVE26 PLEK2 ENSG00000258561 GPHN ENSG00000199755
GH14J067238 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 23.8 +119.4 119447 5 PKNOX1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 ZBTB7B YY1 ZNF207 FOS MPP5 ATP6V1D EIF2S1 ENSG00000258561 ENSG00000258988
GH14J067268 Promoter/Enhancer 1.4 EPDnew Ensembl ENCODE 25.2 +90.4 90411 3.6 PKNOX1 MAX SIN3A ZNF384 RFX5 ZNF335 ZNF316 POLR2A PRDM10 ZNF600 MPP5 ATP6V1D PLEK2 EIF2S1 GPHN GC14M067261 GC14M067260 GC14P067341
GH14J067409 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 15.4 -52.1 -52096 5.6 PKNOX1 ATF1 SIN3A GLIS2 ELK1 ATF7 FOS DEK SMARCB1 ZNF518A PLEK2 ATP6V1D ZFYVE26 PLEKHH1 MIR5694
GH14J067312 Enhancer 0.8 ENCODE 37.2 +48.2 48186 0.2 PKNOX1 CLOCK FOXA2 NFIB NEUROD1 SIN3A BMI1 ZNF207 FOS RCOR1 ATP6V1D EIF2S1 FAM71D GC14P067341 GC14M067260 GC14M067261 MPP5
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around ATP6V1D on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the ATP6V1D gene promoter:
  • AP-1
  • PPAR-gamma2
  • PPAR-gamma1
  • C/EBPalpha
  • IRF-1
  • SRF (504 AA)
  • SRF
  • FOXD1
  • c-Ets-1
  • AREB6

Genomic Locations for ATP6V1D Gene

Genomic Locations for ATP6V1D Gene
chr14:67,294,371-67,360,265
(GRCh38/hg38)
Size:
65,895 bases
Orientation:
Minus strand
chr14:67,761,088-67,826,982
(GRCh37/hg19)
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 :
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

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.

Phenotypes From GWAS Catalog for ATP6V1D Gene

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:
  • Atp6v1d Atp6v1d<tm1b(EUCOMM)Hmgu>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ATP6V1D

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
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 ATP6V1D gene
Compartment Confidence
plasma membrane 5
extracellular 5
cytosol 5
lysosome 5
nucleus 3

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for ATP6V1D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005765 lysosomal membrane HDA 17897319
GO:0005813 colocalizes_with centrosome IDA 21844891
GO:0005829 cytosol TAS --
GO:0005886 plasma membrane TAS --
GO:0005929 colocalizes_with cilium IDA 21844891
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:0006811 ion transport IEA --
GO:0008286 insulin receptor signaling pathway TAS --
GO:0016241 regulation of macroautophagy NAS 22982048
GO:0030030 cell projection organization IEA --
GO:0033572 transferrin transport TAS --
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

(7) Drugs for ATP6V1D Gene - From: DrugBank, HMDB, and Tocris

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Dalfopristin Approved Pharma Target, inhibitor 2
Water Approved Pharma 0
Virginiamycin M1 Experimental Pharma Target 0
Bafilomycin A1 Experimental Pharma V-ATPase inhibitor,selective and reversible, H+-ATPase (vacuolar) inhibitor 0
Coenzyme A Investigational Nutra Target 0

(2) Additional Compounds for ATP6V1D 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
Full agonist, Agonist, Partial agonist, Antagonist, Gating inhibitor 58-64-0
Phosphate
  • [po(OH)3]
  • Acide phosphorique
  • Acidum phosphoricum
  • H3PO4
  • Orthophosphoric acid
14265-44-2

(2) 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
genes like me logo Genes that share compounds with ATP6V1D: view

Transcripts for ATP6V1D Gene

mRNA/cDNA for ATP6V1D Gene

Unigene Clusters for ATP6V1D Gene

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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ATP6V1D

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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, 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

Evidence on tissue expression from TISSUES for ATP6V1D Gene

  • Nervous system(4.9)
  • Heart(4.4)
genes like me logo Genes that share expression patterns with ATP6V1D: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer 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 33
  • 100 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia ATP6V1D 34
  • 96 (a)
OneToOne
dog
(Canis familiaris)
Mammalia ATP6V1D 34 33
  • 94.47 (n)
OneToOne
cow
(Bos Taurus)
Mammalia ATP6V1D 34 33
  • 94.33 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Atp6v1d 16 34 33
  • 91.09 (n)
rat
(Rattus norvegicus)
Mammalia Atp6v1d 33
  • 90.15 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 34
  • 88 (a)
OneToMany
-- 34
  • 74 (a)
OneToMany
-- 34
  • 69 (a)
OneToMany
chicken
(Gallus gallus)
Aves ATP6V1D 34 33
  • 80.7 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia ATP6V1D 34
  • 83 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia atp6v1d 33
  • 76.38 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.22727 33
zebrafish
(Danio rerio)
Actinopterygii atp6v1d 34 33
  • 74.76 (n)
OneToOne
zgc55524 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.731 33
fruit fly
(Drosophila melanogaster)
Insecta Vha36 35
  • 72 (a)
EG:BACR25B3.4 35
  • 69 (a)
Vha36-3 34
  • 68 (a)
OneToMany
Vha36-1 34 33
  • 64.49 (n)
OneToMany
CG13167 35
  • 37 (a)
Vha36-2 34
  • 24 (a)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010298 33
  • 67.55 (n)
worm
(Caenorhabditis elegans)
Secernentea F55H2.2 35
  • 67 (a)
vha-14 34 33
  • 63.33 (n)
OneToOne
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0A01991g 33
  • 59.31 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes VMA8 36 34 33
  • 58.57 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AAR130C 33
  • 54.85 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT3G58730 33
  • 59.68 (n)
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.3362 33
rice
(Oryza sativa)
Liliopsida Os04g0643100 33
  • 53.25 (n)
barley
(Hordeum vulgare)
Liliopsida Hv.8141 33
sea squirt
(Ciona savignyi)
Ascidiacea CSA.7229 34
  • 69 (a)
OneToOne
Cin.7657 33
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes vma8 33
  • 56.21 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU08035 33
  • 55.28 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.7657 33
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)
Aminode:
Evolutionary constrained regions (ECRs) for ATP6V1D: view image

Paralogs for ATP6V1D Gene

(1) SIMAP similar genes for ATP6V1D Gene using alignment to 12 proteins:

  • VATD_HUMAN
  • G3V2S6_HUMAN
  • G3V2V6_HUMAN
  • G3V341_HUMAN
  • G3V3T8_HUMAN
  • G3V559_HUMAN
  • G3V5S7_HUMAN
  • H0YJ55_HUMAN
  • H0YJH8_HUMAN
  • H0YJS0_HUMAN
  • Q6PJ05_HUMAN
  • Q8N5Z9_HUMAN
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 Variation AA Info Type
rs1000145660 -- 67,337,458(-) A/G downstream_transcript_variant
rs1000200965 -- 67,354,008(-) C/T intron_variant
rs1000238844 -- 67,358,168(-) C/T intron_variant
rs1000519060 -- 67,359,244(-) G/A intron_variant
rs1000571710 -- 67,359,522(-) G/C 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)

Additional Variant Information 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

Additional Disease Information for ATP6V1D

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

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 research 2012) 3 4 58
  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 SD … DREAM investigators (Diabetes care 2010) 3 44 58
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  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 CS … Weiner H (Archives of biochemistry and biophysics 2002) 3 22 58

Products for ATP6V1D Gene

Sources for ATP6V1D Gene

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