ATP10A
Basic information
Region (hg38): 15:25677273-25865184
Previous symbols: [ "ATP10C" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (223 variants)
- not_provided (65 variants)
- ATP10A-related_disorder (34 variants)
- Autism_spectrum_disorder (1 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. These statistics are base on transcript: NM_000024490.4. 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 | 31 | 12 | 43 | |||
missense | 218 | 27 | 10 | 255 | ||
nonsense | 1 | |||||
start loss | 0 | |||||
frameshift | 1 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 220 | 58 | 22 |
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