ATP6V1H
Basic information
Region (hg38): 8:53715543-53843558
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 ATP6V1H 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 | 21 | 21 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 1 | 1 | ||||
non coding | 0 | |||||
Total | 0 | 0 | 21 | 0 | 0 |
Variants in ATP6V1H
This is a list of pathogenic ClinVar variants found in the ATP6V1H region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
8-53715971-C-T | not specified | Uncertain significance (Jun 06, 2023) | ||
8-53715981-C-A | not specified | Uncertain significance (Apr 20, 2023) | ||
8-53715981-C-T | not specified | Uncertain significance (Jan 04, 2024) | ||
8-53743581-T-C | not specified | Uncertain significance (Mar 11, 2022) | ||
8-53743617-T-C | not specified | Uncertain significance (Feb 16, 2023) | ||
8-53743628-T-C | not specified | Uncertain significance (Aug 12, 2021) | ||
8-53743674-C-T | not specified | Uncertain significance (Jun 06, 2023) | ||
8-53756556-G-A | not specified | Uncertain significance (Apr 23, 2024) | ||
8-53756610-C-A | not specified | Uncertain significance (Sep 22, 2022) | ||
8-53769634-T-A | Uncertain significance (-) | |||
8-53769743-A-G | not specified | Likely benign (Jul 26, 2023) | ||
8-53772113-T-C | not specified | Uncertain significance (Feb 13, 2024) | ||
8-53795648-C-T | not specified | Uncertain significance (Mar 20, 2023) | ||
8-53795733-G-A | not specified | Uncertain significance (May 23, 2023) | ||
8-53801841-T-C | not specified | Uncertain significance (Dec 28, 2022) | ||
8-53811203-G-C | not specified | Uncertain significance (Feb 15, 2023) | ||
8-53814729-T-C | not specified | Uncertain significance (Jan 30, 2024) | ||
8-53814739-C-T | not specified | Uncertain significance (Apr 18, 2023) | ||
8-53817496-T-C | not specified | Uncertain significance (Mar 02, 2023) | ||
8-53817500-C-G | not specified | Uncertain significance (Aug 04, 2021) | ||
8-53829452-T-C | not specified | Uncertain significance (May 29, 2024) | ||
8-53833024-G-A | not specified | Uncertain significance (Feb 10, 2022) | ||
8-53841605-T-C | not specified | Uncertain significance (May 26, 2024) | ||
8-53841612-G-C | not specified | Uncertain significance (Sep 23, 2023) | ||
8-53841648-G-C | not specified | Uncertain significance (Feb 27, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
ATP6V1H | protein_coding | protein_coding | ENST00000359530 | 13 | 128002 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.000145 | 1.00 | 125728 | 0 | 20 | 125748 | 0.0000795 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.28 | 212 | 272 | 0.781 | 0.0000151 | 3204 |
Missense in Polyphen | 70 | 111.58 | 0.62738 | 1365 | ||
Synonymous | 0.860 | 83 | 93.6 | 0.887 | 0.00000524 | 856 |
Loss of Function | 3.14 | 12 | 30.8 | 0.389 | 0.00000159 | 356 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000597 | 0.0000597 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000109 | 0.000109 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.000115 | 0.000114 |
Middle Eastern | 0.000109 | 0.000109 |
South Asian | 0.000101 | 0.0000980 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Subunit of the peripheral V1 complex of vacuolar ATPase. Subunit H activates the ATPase activity of the enzyme and couples ATPase activity to proton flow. 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 (By similarity). Involved in the endocytosis mediated by clathrin-coated pits, required for the formation of endosomes. {ECO:0000250}.;
- Pathway
- mTOR signaling pathway - Homo sapiens (human);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);Vibrio cholerae infection - Homo sapiens (human);Rheumatoid arthritis - Homo sapiens (human);Disease;Signal Transduction;Transferrin endocytosis and recycling;Ion channel transport;adenosine ribonucleotides <i>de novo</i> biosynthesis;Host Interactions of HIV factors;HIV Infection;Insulin receptor recycling;Signaling by Insulin receptor;ROS, RNS production in phagocytes;Infectious disease;Innate Immune System;Immune System;Transport of small molecules;superpathway of purine nucleotide salvage;Nef Mediated CD4 Down-regulation;Nef-mediates down modulation of cell surface receptors by recruiting them to clathrin adapters;The role of Nef in HIV-1 replication and disease pathogenesis;Iron uptake and transport;Signaling by Receptor Tyrosine Kinases;purine nucleotides <i>de novo</i> biosynthesis;Nef Mediated CD8 Down-regulation
(Consensus)
Recessive Scores
- pRec
- 0.182
Intolerance Scores
- loftool
- 0.0719
- rvis_EVS
- -0.73
- rvis_percentile_EVS
- 14.02
Haploinsufficiency Scores
- pHI
- 0.137
- hipred
- Y
- hipred_score
- 0.593
- ghis
- 0.611
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.926
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Atp6v1h
- Phenotype
- cellular phenotype; homeostasis/metabolism phenotype; skeleton phenotype; immune 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); hematopoietic system phenotype;
Zebrafish Information Network
- Gene name
- atp6v1h
- Affected structure
- melanocyte
- Phenotype tag
- abnormal
- Phenotype quality
- translucent
Gene ontology
- Biological process
- endocytosis;vacuolar acidification;insulin receptor signaling pathway;ATP hydrolysis coupled proton transport;regulation of macroautophagy;transferrin transport;ion transmembrane transport;regulation of defense response to virus by virus;regulation of catalytic activity
- Cellular component
- vacuolar proton-transporting V-type ATPase, V1 domain;lysosomal membrane;cytosol;plasma membrane;extracellular exosome
- Molecular function
- protein binding;ATPase activity;enzyme regulator activity;proton-transporting ATPase activity, rotational mechanism