ATP10A
Basic information
Region (hg38): 15:25677272-25865184
Previous symbols: [ "ATP10C" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (62 variants)
- Inborn genetic diseases (60 variants)
- ATP10A-related condition (4 variants)
- not specified (3 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP10A 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 | 17 | 13 | 30 | |||
missense | 64 | 14 | 10 | 88 | ||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 1 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region ? | 4 | 4 | ||||
non coding ? | 4 | |||||
Total | 0 | 0 | 65 | 32 | 26 |
Variants in ATP10A
This is a list of pathogenic ClinVar variants found in the ATP10A region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
15-25679366-C-T | not specified | Uncertain significance (Oct 05, 2023) | ||
15-25679435-C-G | Likely benign (Dec 31, 2019) | |||
15-25679435-C-T | Likely benign (May 21, 2018) | |||
15-25679558-G-A | not specified | Uncertain significance (Dec 05, 2022) | ||
15-25679566-G-C | Likely benign (Dec 31, 2019) | |||
15-25679591-G-A | Uncertain significance (Oct 11, 2019) | |||
15-25679621-C-A | not specified | Uncertain significance (Jul 12, 2022) | ||
15-25679625-G-T | not specified | Uncertain significance (Dec 22, 2023) | ||
15-25679637-C-G | not specified | Uncertain significance (Jul 27, 2022) | ||
15-25679650-C-T | ATP10A-related disorder | Likely benign (Feb 04, 2020) | ||
15-25679673-C-A | not specified | Likely benign (Apr 13, 2022) | ||
15-25679718-T-C | not specified | Uncertain significance (Sep 26, 2022) | ||
15-25679738-C-T | not specified | Uncertain significance (Sep 01, 2021) | ||
15-25679740-G-T | not specified | Uncertain significance (Dec 15, 2022) | ||
15-25679748-C-T | not specified | Uncertain significance (Oct 26, 2021) | ||
15-25679762-G-A | not specified | Uncertain significance (Oct 19, 2021) | ||
15-25679849-G-A | not specified | Uncertain significance (Feb 05, 2024) | ||
15-25679918-C-T | not specified | Uncertain significance (Dec 13, 2021) | ||
15-25679931-G-C | not specified | Uncertain significance (Feb 09, 2022) | ||
15-25679947-C-G | ATP10A-related disorder | Benign (Oct 16, 2019) | ||
15-25680111-C-T | Likely benign (Apr 30, 2018) | |||
15-25680137-C-T | Benign/Likely benign (Apr 01, 2023) | |||
15-25680186-G-A | Likely benign (Aug 01, 2023) | |||
15-25680192-C-T | Benign (Dec 31, 2019) | |||
15-25680215-G-C | not specified | Uncertain significance (Jul 12, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
ATP10A | protein_coding | protein_coding | ENST00000356865 | 21 | 187898 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.00183 | 0.998 | 125694 | 0 | 54 | 125748 | 0.000215 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.760 | 824 | 888 | 0.928 | 0.0000551 | 9631 |
Missense in Polyphen | 170 | 227.42 | 0.74753 | 2447 | ||
Synonymous | 0.00321 | 402 | 402 | 1.00 | 0.0000285 | 3089 |
Loss of Function | 5.12 | 17 | 59.7 | 0.285 | 0.00000316 | 649 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000480 | 0.000474 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000277 | 0.000272 |
Finnish | 0.0000924 | 0.0000924 |
European (Non-Finnish) | 0.000179 | 0.000176 |
Middle Eastern | 0.000277 | 0.000272 |
South Asian | 0.000429 | 0.000425 |
Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Catalytic component of a P4-ATPase flippase complex which catalyzes the hydrolysis of ATP coupled to the transport of aminophospholipids from the outer to the inner leaflet of various membranes and ensures the maintenance of asymmetric distribution of phospholipids. Phospholipid translocation seems also to be implicated in vesicle formation and in uptake of lipid signaling molecules (Probable). {ECO:0000305}.;
- Pathway
- Prader-Willi and Angelman Syndrome;Ion channel transport;Transport of small molecules;Phosphatidylinositol phosphate metabolism;Glycerophospholipid metabolism;Vitamin A (retinol) metabolism;Ion transport by P-type ATPases;Arachidonic acid metabolism
(Consensus)
Recessive Scores
- pRec
- 0.158
Intolerance Scores
- loftool
- 0.142
- rvis_EVS
- 1.29
- rvis_percentile_EVS
- 93.86
Haploinsufficiency Scores
- pHI
- 0.118
- hipred
- Y
- hipred_score
- 0.614
- ghis
- 0.518
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.266
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | High | High | High |
Primary Immunodeficiency | High | High | High |
Cancer | High | High | High |
Mouse Genome Informatics
- Gene name
- Atp10a
- Phenotype
Gene ontology
- Biological process
- regulation of cell shape;ion transmembrane transport;phospholipid translocation
- Cellular component
- endoplasmic reticulum;endoplasmic reticulum membrane;plasma membrane;integral component of membrane
- Molecular function
- magnesium ion binding;phospholipid-translocating ATPase activity;protein binding;ATP binding