ATP6V1C1
ATPase H+ transporting V1 subunit C1, the group of V-type ATPase subunits
Basic information
Region (hg38): 8:103021063-103073051
Previous symbols: [ "ATP6D", "ATP6C" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- DOORS syndrome (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP6V1C1 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 | 18 | 19 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 1 | 0 | 18 | 0 | 0 |
Variants in ATP6V1C1
This is a list of pathogenic ClinVar variants found in the ATP6V1C1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 8-103040884-G-T | not specified | Uncertain significance (Oct 01, 2024) | ||
| 8-103040924-A-G | not specified | Uncertain significance (Mar 04, 2024) | ||
| 8-103040925-A-G | not specified | Uncertain significance (Sep 29, 2022) | ||
| 8-103048897-G-A | not specified | Uncertain significance (Dec 14, 2024) | ||
| 8-103048945-G-T | not specified | Uncertain significance (Feb 02, 2024) | ||
| 8-103051067-A-G | not specified | Uncertain significance (Jun 22, 2023) | ||
| 8-103051073-A-G | not specified | Uncertain significance (Feb 05, 2024) | ||
| 8-103051086-A-T | not specified | Uncertain significance (Nov 06, 2023) | ||
| 8-103051103-A-G | not specified | Uncertain significance (Mar 21, 2022) | ||
| 8-103052734-G-T | not specified | Uncertain significance (Mar 23, 2023) | ||
| 8-103053957-G-A | not specified | Uncertain significance (Oct 07, 2024) | ||
| 8-103055868-G-A | not specified | Likely benign (Jan 23, 2025) | ||
| 8-103055911-G-A | not specified | Uncertain significance (Dec 06, 2024) | ||
| 8-103063146-G-A | not specified | Uncertain significance (Nov 07, 2022) | ||
| 8-103064750-G-A | DOORS syndrome | Pathogenic (Mar 31, 2024) | ||
| 8-103064769-T-C | not specified | Uncertain significance (Sep 14, 2022) | ||
| 8-103066349-A-G | not specified | Uncertain significance (Jan 16, 2024) | ||
| 8-103066364-A-G | not specified | Uncertain significance (Aug 21, 2024) | ||
| 8-103066434-C-T | not specified | Uncertain significance (Apr 12, 2023) | ||
| 8-103068728-A-G | not specified | Uncertain significance (Feb 28, 2023) | ||
| 8-103068741-C-G | not specified | Uncertain significance (Oct 05, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ATP6V1C1 | protein_coding | protein_coding | ENST00000395862 | 12 | 51989 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000154 | 0.993 | 125702 | 0 | 26 | 125728 | 0.000103 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.71 | 126 | 193 | 0.653 | 0.00000937 | 2516 |
| Missense in Polyphen | 26 | 56.003 | 0.46426 | 736 | ||
| Synonymous | -0.474 | 77 | 71.9 | 1.07 | 0.00000372 | 675 |
| Loss of Function | 2.40 | 10 | 22.2 | 0.451 | 9.98e-7 | 294 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000213 | 0.000213 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000171 | 0.000163 |
| Finnish | 0.0000468 | 0.0000462 |
| European (Non-Finnish) | 0.0000896 | 0.0000879 |
| Middle Eastern | 0.000171 | 0.000163 |
| South Asian | 0.000238 | 0.000229 |
| Other | 0.00 | 0.00 |
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);miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase;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
- 0.149
Intolerance Scores
- loftool
- 0.521
- rvis_EVS
- -0.52
- rvis_percentile_EVS
- 21.2
Haploinsufficiency Scores
- pHI
- 0.315
- hipred
- Y
- hipred_score
- 0.663
- ghis
- 0.668
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.850
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Atp6v1c1
- Phenotype
- nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic 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);
Gene ontology
- Biological process
- insulin receptor signaling pathway;ATP hydrolysis coupled proton transport;regulation of macroautophagy;transferrin transport;ion transmembrane transport;proton transmembrane transport
- Cellular component
- vacuolar proton-transporting V-type ATPase, V1 domain;lysosomal membrane;cytosol;plasma membrane;proton-transporting two-sector ATPase complex;cytoplasmic vesicle;apical part of cell;extracellular exosome
- Molecular function
- transporter activity;protein binding;proton-exporting ATPase activity, phosphorylative mechanism;proton-transporting ATPase activity, rotational mechanism