ATP6V0D1
ATPase H+ transporting V0 subunit d1, the group of V-type ATPase subunits
Basic information
Region (hg38): 16:67438013-67481181
Previous symbols: [ "ATP6D" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP6V0D1 gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 7 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 7 | 0 | 0 |
Variants in ATP6V0D1
This is a list of pathogenic ClinVar variants found in the ATP6V0D1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 16-67438551-C-T | not specified | Uncertain significance (Jan 17, 2024) | ||
| 16-67438568-C-T | not specified | Uncertain significance (Aug 02, 2022) | ||
| 16-67438587-C-T | not specified | Uncertain significance (Dec 28, 2023) | ||
| 16-67438649-A-G | not specified | Uncertain significance (Apr 09, 2024) | ||
| 16-67438798-G-A | not specified | Uncertain significance (May 31, 2023) | ||
| 16-67439017-C-T | not specified | Uncertain significance (Mar 28, 2023) | ||
| 16-67439134-C-T | not specified | Uncertain significance (Jun 12, 2023) | ||
| 16-67439332-T-C | not specified | Uncertain significance (Apr 06, 2024) | ||
| 16-67444591-C-T | not specified | Uncertain significance (Oct 12, 2021) | ||
| 16-67453649-G-A | not specified | Uncertain significance (May 30, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ATP6V0D1 | protein_coding | protein_coding | ENST00000290949 | 8 | 43224 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.988 | 0.0124 | 125737 | 0 | 8 | 125745 | 0.0000318 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.93 | 102 | 226 | 0.451 | 0.0000148 | 2325 |
| Missense in Polyphen | 34 | 82.736 | 0.41095 | 884 | ||
| Synonymous | 0.0823 | 96 | 97.0 | 0.989 | 0.00000678 | 670 |
| Loss of Function | 3.67 | 1 | 17.7 | 0.0566 | 9.40e-7 | 196 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000120 | 0.000119 |
| Ashkenazi Jewish | 0.0000992 | 0.0000992 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000352 | 0.0000352 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
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). May play a role in cilium biogenesis through regulation of the transport and the localization of proteins to the cilium (By similarity). In aerobic conditions, involved in intracellular iron homeostasis, thus triggering the activity of Fe(2+) prolyl hydroxylase (PHD) enzymes, and leading to HIF1A hydroxylation and subsequent proteasomal degradation (PubMed:28296633). {ECO:0000250, ECO:0000269|PubMed:28296633}.;
- Pathway
- 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);Tuberculosis - Homo sapiens (human);Collecting duct acid secretion - Homo sapiens (human);Vibrio cholerae infection - Homo sapiens (human);Viral carcinogenesis - Homo sapiens (human);Rheumatoid arthritis - Homo sapiens (human);XBP1(S) activates chaperone genes;Signal Transduction;Transferrin endocytosis and recycling;Ion channel transport;adenosine ribonucleotides <i>de novo</i> biosynthesis;Insulin receptor recycling;Signaling by Insulin receptor;ROS, RNS production in phagocytes;Innate Immune System;Immune System;Transport of small molecules;superpathway of purine nucleotide salvage;Iron uptake and transport;Signaling by Receptor Tyrosine Kinases;purine nucleotides <i>de novo</i> biosynthesis
(Consensus)
Recessive Scores
- pRec
- 0.260
Intolerance Scores
- loftool
- 0.193
- rvis_EVS
- -0.36
- rvis_percentile_EVS
- 28.63
Haploinsufficiency Scores
- pHI
- 0.180
- hipred
- Y
- hipred_score
- 0.745
- ghis
- 0.619
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.957
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Atp6v0d1
- Phenotype
- endocrine/exocrine gland phenotype; renal/urinary system phenotype; skeleton phenotype; hematopoietic system phenotype; reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); limbs/digits/tail phenotype;
Zebrafish Information Network
- Gene name
- atp6v0d1
- Affected structure
- neuromast hair cell
- Phenotype tag
- abnormal
- Phenotype quality
- absent
Gene ontology
- Biological process
- cellular iron ion homeostasis;vacuolar transport;vacuolar acidification;brain development;insulin receptor signaling pathway;ATP hydrolysis coupled proton transport;regulation of macroautophagy;transferrin transport;ion transmembrane transport;cellular response to increased oxygen levels;IRE1-mediated unfolded protein response;cilium assembly;proton transmembrane transport
- Cellular component
- lysosomal membrane;early endosome;centrosome;synaptic vesicle;endosome membrane;membrane;apical plasma membrane;vacuolar proton-transporting V-type ATPase complex;phagocytic vesicle membrane;proton-transporting V-type ATPase, V0 domain;plasma membrane proton-transporting V-type ATPase complex;axon terminus;extracellular exosome
- Molecular function
- protein binding;proton-exporting ATPase activity, phosphorylative mechanism;protein-containing complex binding;proton-transporting ATPase activity, rotational mechanism