ATP6V0D1 ATPase H+ transporting V0 subunit d1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: ATP6V0D1provided by HGNC
Official Full Name: ATPase H+ transporting V0 subunit d1provided by HGNC
Primary source: HGNC:HGNC:13724
See related: Ensembl:ENSG00000159720 MIM:607028; AllianceGenome:HGNC:13724
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: P39; VATX; VMA6; ATP6D; ATP6DV; VPATPD
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 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 encoded protein is known as the D subunit and is found ubiquitously. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in brain (RPKM 53.8), thyroid (RPKM 41.0) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 16q22.1

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	16	NC_000016.10 (67438019..67481157, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	16	NC_060940.1 (73232795..73275929, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	16	NC_000016.9 (67471922..67515060, complement)

Chromosome 16 - NC_000016.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

ATP6V0D1 promotes alkaliptosis by blocking STAT3-mediated lysosomal pH homeostasis.
Title: ATP6V0D1 promotes alkaliptosis by blocking STAT3-mediated lysosomal pH homeostasis.
The secondary structures of d1 and d2 subunits were highly similar, but the relative stability against thermal stress was higher for d1 than d2.
Title: Expression, purification and characterization of human vacuolar-type H(+)-ATPase subunit d1 and d2 in Escherichia coli.
Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
Observational study of gene-disease association. (HuGE Navigator)
Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
two adjacent enhancers inside the first intron of the neighboring (1.4 kb downstream) ATPase gene (ATP6V0D1) modulate the human AgRP promoter with profound spatiotemporal variation
Title: Control elements in the neighboring ATPase gene influence spatiotemporal expression of the human agouti-related protein.
Using shotgun mass spectrometry, we found this protein differentially expressed in the dorsolateral prefrontal cortex from patients with schizophrenia
Title: Prefrontal cortex shotgun proteome analysis reveals altered calcium homeostasis and immune system imbalance in schizophrenia.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp120	env	Tandem affinity purification and mass spectrometry analysis identify V-type proton ATPase subunit d1 (ATP6V0D1; VPATPD), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Gag-Pol	gag-pol	Tandem affinity purification and mass spectrometry analysis identify V-type proton ATPase subunit d1 (ATP6V0D1; VPATPD), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Nef	nef	Tandem affinity purification and mass spectrometry analysis identify V-type proton ATPase subunit d1 (ATP6V0D1; VPATPD), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Pr55(Gag)	gag	Tandem affinity purification and mass spectrometry analysis identify V-type proton ATPase subunit d1 (ATP6V0D1; VPATPD), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

NoName (e-PCR)
- UniSTS:9484

PMC314306P7 (e-PCR)
- UniSTS:272939

PMC314306P8 (e-PCR)
- UniSTS:272940

PMC310777P2 (e-PCR)
- UniSTS:272686

D8S2279 (e-PCR)
- UniSTS:473907

RH65050 (e-PCR)
- UniSTS:85353

D1S1423 (e-PCR)
- UniSTS:149619

D1S1425 (e-PCR)
- UniSTS:149621

D11S3114 (e-PCR)
- UniSTS:152207

RH11782 (e-PCR)
- UniSTS:7409

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein-containing complex binding	IEA Inferred from Electronic Annotation more info
enables proton-transporting ATPase activity, rotational mechanism	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in cellular response to increased oxygen levels	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cilium assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in intracellular iron ion homeostasis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in proton transmembrane transport	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of macroautophagy	NAS Non-traceable Author Statement more info	PubMed
involved_in synaptic vesicle lumen acidification	IEA Inferred from Electronic Annotation more info
involved_in vacuolar acidification	IBA Inferred from Biological aspect of Ancestor more info
involved_in vacuolar transport	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in apical plasma membrane	IEA Inferred from Electronic Annotation more info
located_in axon terminus	IEA Inferred from Electronic Annotation more info
colocalizes_with centrosome	IDA Inferred from Direct Assay more info	PubMed
located_in clathrin-coated vesicle membrane	IEA Inferred from Electronic Annotation more info
is_active_in early endosome	IBA Inferred from Biological aspect of Ancestor more info
located_in endosome membrane	TAS Traceable Author Statement more info
located_in extracellular exosome	HDA more info	PubMed
located_in lysosomal membrane	HDA more info	PubMed
located_in lysosomal membrane	TAS Traceable Author Statement more info
located_in membrane	IDA Inferred from Direct Assay more info	PubMed
located_in phagocytic vesicle membrane	TAS Traceable Author Statement more info
part_of plasma membrane proton-transporting V-type ATPase complex	IBA Inferred from Biological aspect of Ancestor more info
located_in synaptic vesicle membrane	IEA Inferred from Electronic Annotation more info
part_of vacuolar proton-transporting V-type ATPase complex	IBA Inferred from Biological aspect of Ancestor more info
part_of vacuolar proton-transporting V-type ATPase complex	IDA Inferred from Direct Assay more info	PubMed
part_of vacuolar proton-transporting V-type ATPase complex	NAS Non-traceable Author Statement more info	PubMed
part_of vacuolar proton-transporting V-type ATPase, V0 domain	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: V-type proton ATPase subunit d 1

Names: 32 kDa accessory protein; ATPase, H+ transporting, lysosomal (vacuolar proton pump), member D; ATPase, H+ transporting, lysosomal 38kDa, V0 subunit d1; H(+)-transporting two-sector ATPase, subunit D; V-ATPase 40 KDa accessory protein; V-ATPase AC39 subunit; V-ATPase subunit d 1; V-ATPase, subunit D; vacuolar proton pump subunit d 1

NP_004682.2

EC 7.1.2.2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.