ATP6V1D
ATPase H+ transporting V1 subunit D, the group of V-type ATPase subunits
Basic information
Region (hg38): 14:67294371-67360265
Previous symbols: [ "ATP6M" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
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 ATP6V1D 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 | 11 | 11 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 11 | 0 | 0 |
Variants in ATP6V1D
This is a list of pathogenic ClinVar variants found in the ATP6V1D region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 14-67301408-C-T | not specified | Uncertain significance (Jan 23, 2024) | ||
| 14-67301432-A-C | PALS1-related disorder | Likely benign (Jan 09, 2024) | ||
| 14-67302051-G-A | not specified | Uncertain significance (Aug 12, 2021) | ||
| 14-67302061-G-C | not specified | Uncertain significance (Aug 15, 2023) | ||
| 14-67302101-G-C | not specified | Uncertain significance (Mar 16, 2022) | ||
| 14-67302402-A-T | Benign (Mar 29, 2018) | |||
| 14-67302419-G-A | not specified | Uncertain significance (Dec 19, 2022) | ||
| 14-67302440-G-A | not specified | Uncertain significance (Jun 05, 2024) | ||
| 14-67302458-G-A | not specified | Uncertain significance (Feb 28, 2023) | ||
| 14-67302464-G-A | not specified | Uncertain significance (Feb 28, 2023) | ||
| 14-67302581-C-T | Benign (Oct 19, 2017) | |||
| 14-67312606-A-T | not specified | Uncertain significance (Jun 27, 2022) | ||
| 14-67312618-T-C | not specified | Uncertain significance (Jun 13, 2024) | ||
| 14-67312619-A-G | See cases | Likely benign (Jan 05, 2021) | ||
| 14-67312676-C-G | PALS1-related disorder | Uncertain significance (Jul 18, 2023) | ||
| 14-67312689-C-T | not specified | Uncertain significance (Nov 07, 2022) | ||
| 14-67312698-G-A | not specified | Uncertain significance (Apr 06, 2024) | ||
| 14-67316891-C-A | not specified | Uncertain significance (Jul 20, 2021) | ||
| 14-67316895-A-G | Intellectual disability;Anxiety;Cerebral palsy;Abnormal facial shape;Arachnoid cyst | Pathogenic (-) | ||
| 14-67320309-C-G | not specified | Uncertain significance (Apr 08, 2024) | ||
| 14-67320354-G-C | not specified | Uncertain significance (Jul 13, 2022) | ||
| 14-67320376-C-T | not specified | Uncertain significance (May 27, 2022) | ||
| 14-67321066-G-A | not specified | Uncertain significance (May 26, 2023) | ||
| 14-67321074-C-T | Uncertain significance (Apr 29, 2021) | |||
| 14-67321092-G-A | not specified | Uncertain significance (Nov 09, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ATP6V1D | protein_coding | protein_coding | ENST00000216442 | 9 | 65895 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0000451 | 0.965 | 125718 | 0 | 30 | 125748 | 0.000119 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.13 | 97 | 134 | 0.725 | 0.00000694 | 1599 |
| Missense in Polyphen | 24 | 42.585 | 0.56358 | 550 | ||
| Synonymous | 0.478 | 42 | 46.1 | 0.910 | 0.00000232 | 469 |
| Loss of Function | 1.91 | 10 | 19.0 | 0.527 | 0.00000116 | 200 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000272 | 0.000272 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000218 | 0.000217 |
| Finnish | 0.0000925 | 0.0000924 |
| European (Non-Finnish) | 0.000132 | 0.000132 |
| Middle Eastern | 0.000218 | 0.000217 |
| South Asian | 0.0000982 | 0.0000980 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Subunit of the peripheral V1 complex of vacuolar ATPase. 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). May play a role in cilium biogenesis through regulation of the transport and the localization of proteins to the cilium. {ECO:0000250, ECO:0000269|PubMed:21844891}.;
- 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);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;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
- 0.163
Intolerance Scores
- loftool
- 0.467
- rvis_EVS
- -0.03
- rvis_percentile_EVS
- 51.4
Haploinsufficiency Scores
- pHI
- 0.307
- hipred
- Y
- hipred_score
- 0.663
- ghis
- 0.582
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.341
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Atp6v1d
- Phenotype
- 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype; limbs/digits/tail phenotype;
Gene ontology
- Biological process
- insulin receptor signaling pathway;regulation of macroautophagy;transferrin transport;ion transmembrane transport;neutrophil degranulation;cilium assembly;protein localization to cilium;proton transmembrane transport
- Cellular component
- lysosomal membrane;centrosome;cytosol;plasma membrane;cilium;membrane;proton-transporting V-type ATPase complex;specific granule membrane;extracellular exosome
- Molecular function
- protein binding;proton-transporting ATPase activity, rotational mechanism