ATP10A

ATPase phospholipid transporting 10A (putative), the group of ATPase phospholipid transporting|MicroRNA protein coding host genes

Basic information

Region (hg38): 15:25677273-25865184

Previous symbols: [ "ATP10C" ]

Links

ENSG00000206190NCBI:57194OMIM:605855HGNC:13542Uniprot:O60312AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ATP10A gene.

  • 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.

EffectPLPVUSLBBSum
synonymous
31
clinvar
12
clinvar
43
missense
218
clinvar
27
clinvar
10
clinvar
255
nonsense
1
clinvar
1
start loss
0
frameshift
1
clinvar
1
splice donor/acceptor (+/-2bp)
0
Total 0 0 220 58 22
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ATP10Aprotein_codingprotein_codingENST00000356865 21187898
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.001830.9981256940541257480.000215
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.7608248880.9280.00005519631
Missense in Polyphen170227.420.747532447
Synonymous0.003214024021.000.00002853089
Loss of Function5.121759.70.2850.00000316649

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0004800.000474
Ashkenazi Jewish0.000.00
East Asian0.0002770.000272
Finnish0.00009240.0000924
European (Non-Finnish)0.0001790.000176
Middle Eastern0.0002770.000272
South Asian0.0004290.000425
Other0.0001630.000163

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianHighHighHigh
Primary ImmunodeficiencyHighHighHigh
CancerHighHighHigh

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