ATP6V1G2
Basic information
Region (hg38): 6:31544444-31548427
Previous symbols: [ "ATP6G", "ATP6G2" ]
Links
Phenotypes
GenCC
Source:
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 ATP6V1G2 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 | 6 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 6 | 0 | 0 |
Variants in ATP6V1G2
This is a list of pathogenic ClinVar variants found in the ATP6V1G2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 6-31545428-T-C | not specified | Uncertain significance (Jan 08, 2024) | ||
| 6-31545466-A-G | not specified | Uncertain significance (Jul 13, 2022) | ||
| 6-31545492-G-C | not specified | Uncertain significance (Nov 01, 2022) | ||
| 6-31545509-T-A | not specified | Uncertain significance (Feb 05, 2024) | ||
| 6-31546134-T-C | not specified | Uncertain significance (May 03, 2023) | ||
| 6-31546200-C-T | not specified | Uncertain significance (Nov 08, 2022) | ||
| 6-31547563-T-A | Rheumatoid arthritis | risk factor (Feb 01, 2003) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ATP6V1G2 | protein_coding | protein_coding | ENST00000303892 | 3 | 3966 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00286 | 0.819 | 125737 | 0 | 10 | 125747 | 0.0000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.841 | 52 | 72.1 | 0.721 | 0.00000419 | 764 |
| Missense in Polyphen | 8 | 18.01 | 0.44421 | 222 | ||
| Synonymous | 0.751 | 21 | 25.9 | 0.812 | 0.00000131 | 226 |
| Loss of Function | 1.11 | 5 | 8.47 | 0.590 | 5.36e-7 | 70 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000796 | 0.0000791 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Catalytic subunit of the peripheral V1 complex of vacuolar ATPase (V-ATPase). V-ATPase is responsible for acidifying a variety of intracellular compartments in eukaryotic cells.;
- Pathway
- mTOR signaling pathway - Homo sapiens (human);Synaptic vesicle cycle - Homo sapiens (human);Phagosome - Homo sapiens (human);Epithelial cell signaling in Helicobacter pylori infection - Homo sapiens (human);Oxidative phosphorylation - Homo sapiens (human);Collecting duct acid secretion - Homo sapiens (human);Vibrio cholerae infection - Homo sapiens (human);Rheumatoid arthritis - Homo sapiens (human);Signal Transduction;Transferrin endocytosis and recycling;Ion channel transport;Insulin receptor recycling;Signaling by Insulin receptor;ROS, RNS production in phagocytes;Innate Immune System;Immune System;Transport of small molecules;Iron uptake and transport;Signaling by Receptor Tyrosine Kinases
(Consensus)
Intolerance Scores
- loftool
- 0.486
- rvis_EVS
- -0.01
- rvis_percentile_EVS
- 52.85
Haploinsufficiency Scores
- pHI
- 0.132
- hipred
- N
- hipred_score
- 0.332
- ghis
- 0.463
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.825
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Atp6v1g2
- Phenotype
Gene ontology
- Biological process
- insulin receptor signaling pathway;regulation of macroautophagy;transferrin transport;ion transmembrane transport;proton transmembrane transport
- Cellular component
- cytosol;vacuolar proton-transporting V-type ATPase complex;melanosome
- Molecular function
- proton-exporting ATPase activity, phosphorylative mechanism;ATPase activity, coupled to transmembrane movement of substances