ATP6V1C2
Basic information
Region (hg38): 2:10721100-10785110
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (53 variants)
- not_provided (5 variants)
- Distal_renal_tubular_acidosis (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP6V1C2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001039362.2. 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 | 53 | 55 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 1 | 53 | 1 | 1 |
Highest pathogenic variant AF is 0.000483856
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
ATP6V1C2 | protein_coding | protein_coding | ENST00000272238 | 13 | 63462 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
2.85e-8 | 0.917 | 125682 | 0 | 66 | 125748 | 0.000262 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.827 | 205 | 241 | 0.850 | 0.0000131 | 2793 |
Missense in Polyphen | 50 | 69.48 | 0.71963 | 832 | ||
Synonymous | 0.167 | 97 | 99.1 | 0.979 | 0.00000616 | 816 |
Loss of Function | 1.80 | 16 | 25.9 | 0.618 | 0.00000140 | 296 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000882 | 0.000882 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000165 | 0.000163 |
Finnish | 0.000462 | 0.000462 |
European (Non-Finnish) | 0.000176 | 0.000176 |
Middle Eastern | 0.000165 | 0.000163 |
South Asian | 0.000165 | 0.000163 |
Other | 0.000326 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Subunit of the peripheral V1 complex of vacuolar ATPase. Subunit C is necessary for the assembly of the catalytic sector of the enzyme and is likely to have a specific function in its catalytic activity. 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)
Recessive Scores
- pRec
- 0.118
Intolerance Scores
- loftool
- 0.921
- rvis_EVS
- -0.02
- rvis_percentile_EVS
- 52.09
Haploinsufficiency Scores
- pHI
- 0.134
- hipred
- N
- hipred_score
- 0.341
- ghis
- 0.516
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.289
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | High |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Atp6v1c2
- Phenotype
Gene ontology
- Biological process
- insulin receptor signaling pathway;ATP hydrolysis coupled proton transport;regulation of macroautophagy;positive regulation of Wnt signaling pathway;transferrin transport;ion transmembrane transport
- Cellular component
- vacuolar proton-transporting V-type ATPase, V1 domain;lysosomal membrane;cytosol;extracellular exosome
- Molecular function
- proton-exporting ATPase activity, phosphorylative mechanism;proton-transporting ATPase activity, rotational mechanism;protein dimerization activity