ATP6V0D2
protein-codingATPase H+ transporting V0 subunit d2, the group of V-type ATPase subunits
Gene summary
Predicted to contribute to proton-transporting ATPase activity, rotational mechanism. Predicted to be involved in vacuolar acidification and vacuolar transport. Located in apical plasma membrane. Part of vacuolar proton-transporting V-type ATPase complex. [provided by Alliance of Genome Resources, Jun 2026]
- ATP6D2
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~166.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0020066
Submitter: Ambry Genetics
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to ATP6V0D2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_152565.1. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 69 | 1 | 1 | 71 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 69 | 2 | 2 | 73 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_689778.1 | 8 | MANE Select | |
| Ensembl | ENSP00000285393.3 | 8 | MANE Select | |
| Ensembl | ENSP00000429731.1 | 1 | Standard | |
| Ensembl | ENSP00000428382.1 | 1 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Synaptic vesicle cycle - Homo sapiens (human)
- Phagosome - Homo sapiens (human)
- Lysosome - Homo sapiens (human)
- Epithelial cell signaling in Helicobacter pylori infection - Homo sapiens (human)
- Oxidative phosphorylation - Homo sapiens (human)
Biological Process
- vacuolar transport
- vacuolar acidification
- insulin receptor signaling pathway
- ATP hydrolysis coupled proton transport
- regulation of macroautophagy
Molecular Function
- protein binding
- proton-exporting ATPase activity, phosphorylative mechanism
- proton-transporting ATPase activity, rotational mechanism
Cellular Component
- lysosomal membrane
- early endosome
- endosome membrane
- membrane
- apical plasma membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000285393
- Coding exons
- 8
- Length
- 166906
- Individuals with no LoFs
- 125400
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 344
- Defined
- 125744
- p
- 0.00137
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.769 | 222 | 192 | 1.16 | 0.0000104 | 2308 |
| Missense (PolyPhen) | 72 | 65.559 | 1.0982 | 814 | ||
| Synonymous | -0.700 | 82 | 74.3 | 1.10 | 0.00000426 | 645 |
| Loss of Function | 0.250 | 17 | 18.1 | 0.937 | 0.00000101 | 219 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00018 | 0.00018 | rare |
| Latino/Admixed American | 0.00047 | 0.00046 | rare |
| Ashkenazi Jewish | 0.0027 | 0.0026 | notable |
| East Asian | 0.014 | 0.014 | notable |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00024 | 0.00024 | rare |
| South Asian | 0.00049 | 0.00046 | rare |
| Other | 0.00084 | 0.00081 | rare |
dbNSFP Gene Annotations
Source:
- Function
- 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). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.136
Intolerance Scores
- LoFtool
- 0.816
- RVIS EVS
- 0.13
- RVIS percentile EVS
- 63.36
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.307
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |