ATP6V0A1
ATPase H+ transporting V0 subunit a1, the group of V-type ATPase subunits|MicroRNA protein coding host genes
Basic information
Region (hg38): 17:42458844-42522582
Previous symbols: [ "VPP1", "ATP6N1", "ATP6N1A" ]
Links
Phenotypes
GenCC
Source:
- complex neurodevelopmental disorder (Limited), mode of inheritance: AD
- developmental and epileptic encephalopathy 104 (Strong), mode of inheritance: AD
- neurodevelopmental disorder with epilepsy and brain atrophy (Moderate), mode of inheritance: AR
- developmental and epileptic encephalopathy 104 (Strong), mode of inheritance: AD
- neurodevelopmental disorder with epilepsy and brain atrophy (Strong), mode of inheritance: AR
- developmental and epileptic encephalopathy 104 (Definitive), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Developmental and epileptic encephalopathy 104; Neurodevelopmental disorder with epilepsy and brain atrophy | AD/AR | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Craniofacial; Neurologic | 33833240; 34909687 |
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn_genetic_diseases (47 variants)
- not_provided (41 variants)
- Developmental_and_epileptic_encephalopathy_104 (21 variants)
- Neurodevelopmental_disorder_with_epilepsy_and_brain_atrophy (12 variants)
- Global_developmental_delay (2 variants)
- ATP6V0A1-related_condition (2 variants)
- not_specified (2 variants)
- Seizure (2 variants)
- Pyloric_stenosis (1 variants)
- Microcephaly (1 variants)
- Intellectual_disability (1 variants)
- Severe_global_developmental_delay (1 variants)
- Focal-onset_seizure (1 variants)
- Esophageal_atresia (1 variants)
- Cerebellar_ataxia (1 variants)
- Prostate_cancer (1 variants)
- Autism (1 variants)
- Hypotonia (1 variants)
- Lower_limb_spasticity (1 variants)
- Large_for_gestational_age (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP6V0A1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001130021.3. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 92 | 103 | ||||
| nonsense | 1 | |||||
| start loss | 0 | |||||
| frameshift | 2 | |||||
| splice donor/acceptor (+/-2bp) | 4 | |||||
| Total | 7 | 6 | 96 | 2 | 0 |
Highest pathogenic variant AF is 0.0000041106646
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ATP6V0A1 | protein_coding | protein_coding | ENST00000264649 | 20 | 63768 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.998 | 0.00203 | 125733 | 0 | 14 | 125747 | 0.0000557 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.74 | 246 | 476 | 0.517 | 0.0000268 | 5562 |
| Missense in Polyphen | 83 | 223.43 | 0.37148 | 2580 | ||
| Synonymous | 1.04 | 157 | 174 | 0.900 | 0.00000991 | 1569 |
| Loss of Function | 5.56 | 7 | 49.0 | 0.143 | 0.00000300 | 520 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000150 | 0.000150 |
| Ashkenazi Jewish | 0.0000992 | 0.0000992 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000538 | 0.0000527 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000328 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Required for assembly and activity of the vacuolar ATPase. Potential role in differential targeting and regulation of the enzyme for a specific organelle (By similarity). {ECO:0000250}.;
- 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);Rheumatoid arthritis - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Neutrophil degranulation;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;Purine metabolism;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
- 0.503
Intolerance Scores
- loftool
- 0.0440
- rvis_EVS
- -0.69
- rvis_percentile_EVS
- 15.2
Haploinsufficiency Scores
- pHI
- 0.446
- hipred
- Y
- hipred_score
- 0.683
- ghis
- 0.612
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.410
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Atp6v0a1
- Phenotype
- cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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); adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan);
Zebrafish Information Network
- Gene name
- atp6v0a1a
- Affected structure
- neural crest cell
- Phenotype tag
- abnormal
- Phenotype quality
- increased amount
Gene ontology
- Biological process
- vacuolar acidification;insulin receptor signaling pathway;ATP hydrolysis coupled proton transport;regulation of macroautophagy;transferrin transport;ion transmembrane transport;neutrophil degranulation;toxin transport
- Cellular component
- vacuolar proton-transporting V-type ATPase, V0 domain;lysosomal membrane;Golgi apparatus;cytosol;plasma membrane;endosome membrane;integral component of membrane;vacuolar proton-transporting V-type ATPase complex;nuclear speck;secretory granule membrane;phagocytic vesicle membrane;melanosome;intracellular membrane-bounded organelle;extracellular exosome;ficolin-1-rich granule membrane
- Molecular function
- protein binding;proton-transporting ATPase activity, rotational mechanism;ATPase binding